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August 22nd, 2010, 04:00 PM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,950
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H3n2
copy of thread 75820 from August 2008
---------edit1----------
see also this paper:
http://www.pubmedcentral.nih.gov/art...medid=16333111
2001/2002 was a H1N1-season, not much H3N2 around.
The H3N2 in 2002 (A/Taiwan/872/2002) was more similar to the
flu in 1999 (A/Waikato/1/09-08-2000) than to that from 2000 or 2001.
Then in ~May 2002 a new HA appeared with 12 changes
(T31C?,C121A,G156T,T273G,C511A,A512C,A516T(C),G648 A,
G1011A,C1044T,T1149C,C1642T)
{changes[G439A,T114C,C323A,T400C,]were probably made earlier}
and reassorted into existing H3N2.
Most of the mutations are non-synonymous, even many changes
different from A<-->G,C<-->T, which is normal.
It may even have come from swine - there are some closely
related swine-sequences from Hong Kong 2002.
I'm not aware of other epidemics, which started this way,
with a sudden new non-avian HA, maybe 1918-panflu did.
This formed what was called the Fujian-strain, after virus
A/Fujian/411/11-08-2002(H3N2). The full genome of that virus or
any other from that strain from 2002 is not yet available,
even after 6 years ! Such sequences are often withheld for
political reasons or because someone wants to publish a paper
exclusively.
Recently some earlier viruses from that strain were published,
the earliest available is :
A/Hong Kong/CUHK24044/01-06-2002(H3N2). [HA,NA,M available]
Some few of these viruses already appeared in Europe and USA
in season 2002/3 , e.g. A/NY/485/20-01-2003,
A/NY/214/23-04-2003 where we have the full genomes available.
In spring 2003 it was already suspected that this strain
would become dominant but it was not included in the
next season's US-vaccine because of technical problems
to grow it.
Then the HA of that virus reassorted again and acquired 7 new
segments from temporary H3N2. The first public such genome is:
A/Wellington/3/19-05-2003. This virus was dominant in
Australia,NZ 2003 , USA 2003/4 and AUS,NZ 2004.
But then it disappeared suddenly and in mid 2004 the old
strain A/NY/485 became dominant again until now.
a picture of HA1-differences rooted at A/Beijing/353/89
http://magictour.free.fr/panflu/32HUG1.GIF
and here viewed from 1979:
http://magictour.free.fr/panflu/32HUG3.GIF
see here the full genomes since 1972:
http://magictour.free.fr/panflu/h3g2.gif
diversity of H3N2s:
http://magictour.free.fr/panflu/h3anche2.gif
http://magictour.free.fr/panflu/h3dif2.gif
picture with 1067 H3N2 genomes 1999-2007:
http://magictour.free.fr/panflu/geno32k.GIF
mutual differences in the 8 segments of selected H3N2-viruses  in 0/00)
http://magictour.free.fr/panflu/fujian.l6
see also this thread:
http://www.setbb.com/fluwiki2/viewto...forum=fluwiki2
------------edit 2--------------
see here how Panama (o) was replaced by Fujian (.) in Asia,Oceania in 2002:
Code:
ooooooooooooooooooooo.oo..ooooo.o.oo.oo....oo....o...o..o.........................
the first (.) is on June 1st, so within 5-6 months all Pananma was replaced in Asia.
Apparantly not only did Fujian spread very well, but it also killed Pananma.
We regularly see this elimination in pandemics.
How would one flu strain kill another one ? It can't be that the viruses
meet each other so it must be human immunity. People infected by
Fujian (apparantly there were a lot, despite some immunity from Panama)
induced some immunity which didn't let Panama enter later.
Maybe Fujian induced more immunity against Panama than vice versa ?
Also astonishing that this process is so fast with only a fraction of the population infected
but a large proportion of the superspreaders must have been involved
-----------------------------------------------------
2000/1 was the H1N1-season in USA.
2001/2 as well as 2001 and 2002 in NZ was H3N2 with
a 56-reassortment of old viruses from 1998/9
Then the first Fujian variant appeared in June 2002
with an old virus from ~1999, different to the one
from 2001-2
Then in ~May 2003 it reassorted with 7 of the 2001-2 segments
keeping only its HA
-------------------------------------
the closest virus to the first 2002-Fujian virus is a swine virus !
Several papers demonstrated that swine are frequently infected
from human epidemics, maybe the 2002-Fujian-semi-pandemic
started in Swine !
Maybe seasonal flu starts each year from swine in China ?!?
---------edit 2013/05/01-------------
now we have a new virus from Taiwan,March 2002 which already
had the Fujian mutations in HA. It has a different NA
A/Taiwan/92/2002/03/17 (H3N2)
and a paper:
http://www.plosone.org/article/info%...l.pone.0061957
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May 29th, 2011, 04:26 AM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,950
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Re: H3n2
in mid 2002 (China?) in H3N2 suddenly ~10 mutations happened in HA,
no apparant reassortment, the other segments were not much changed.
This virus was then very successful and replaced all other human H3N2
until now.
In 2003 it reasorted, got the 7 segments except HA from an older H3N2
and caused a severe season in USA, starting in November.
Then this reassorted thing disappeared and was replaced by a descendent
of the 2002-virus again.
In 2006/7 only one special strain survived (was detected, that is)
which is the ancestor of all(?) human H3N2 since then
my reconstruction of that 2002 "Fujian" virus
Code:
>A/Index_Fujian/2002(H3N2)
ATGGAAAGAATAAAAGAACTACGGAACCTGATGTCGCAGTCTCGCACTCGCGAGATACTGACAAAAACCACAGTGGACCATATGGCCATAATTAAGAAGTACACATCGGGGAGACAGGAAAAGAACCCGTCACTTAGGATGAAATGGATGATGGCAATGAAATACCCAATCACTGCTGACAAAAGGATAACAGAAATGGTTCCGGAGAGAAATGAACAAGGACAAACTCTATGGAGTAAAATGAGTGATGCTGGATCAGATCGAGTGATGGTATCACCTTTGGCTGTGACATGGTGGAATAGAAATGGACCCGTGACAAGTACGGTCCATTACCCAAAAGTATACAAGACTTATTTTGACAAAGTCGAAAGGTTAAAACATGGAACCTTTGGCCCTGTTCATTTTAGAAATCAAGTCAAGATACGCCGAAGAGTAGACATAAACCCTGGTCATGCAGACCTCAGTGCCAAGGAGGCACAAGATGTAATTATGGAAGTTGTTTTTCCCAATGAAGTGGGAGCCAGGATACTAACATCAGAATCGCAATTAACAATAACTAAAGAGAAAAAAGAAGAACTCCGAGATTGCAAAATTTCTCCCTTGATGGTTGCATACATGTTAGAGAGAGAACTTGTCCGAAAAACAAGATTTCTCCCAGTTGCTGGCGGAACAAGCAGTATATACATTGAAGTTTTACATTTGACTCAAGGAACGTGTTGGGAACAAATGTACACTCCAGGTGGAGAAGTGAGGAATGACGATGTTGACCAAAGCCTAATTATTGCAGCCAGGAACATAGTAAGAAGAGCCGCAGTATCAGCAGATCCACTAGCATCTTTATTGGAGATGTGCCACAGCACACAAATTGGCGGGACAAGGATGGTGGACATTCTTAGACAGAACCCGACTGAAGAACAAGCTGTGGATATATGCAAGGCTGCAATGGGATTGAGAATCAGCTCATCCTTCAGCTTTGGTGGGTTTACATTTAAAAGAACAAGCGGGTCATCAGTCAAAAAAGAGGAAGAAGTGCTTACAGGCAATCTCCAAACATTGAAGATAAGAGTACATGAGGGGTATGAGGAGTTCACAATGGTGGGGAAAAGAGCAACAGCTATACTCAGAAAAGCAACCAGAAGATTGGTTCAGCTCATAGTGAGTGGAAGAGACGAACAGTCAATAGCCGAAGCAATAATTGTGGCCATGGTGTTTTCACAAGAGGATTGCATGATAAAAGCAGTTAGAGGTGACCTGAATTTCGTCAACAGAGCAAATCAGCGGTTGAACCCCATGCATCAGCTTTTAAGGCATTTTCAGAAAGATGCGAAAGTGCTTTTTCAGAATTGGGGAATTGAACACATCGACAGTGTGATGGGAATGGTTGGAGTATTACCAGATATGACTCCAAGCACAGAGATGTCAATGAGAGGAATAAGAGTCAGCAAAATGGGTGTGGATGAATACTCCAGTACAGAGAGGGTGGTGGTTAGCATTGATCGGTTTTTGAGAGTTCGAGACCAACGCGGGAATGTATTATTATCTCCTGAGGAGGTCAGTGAAACACAGGGAACTGAGAGACTGACAATAACTTATTCATCGTCGATGATGTGGGAGATTAACGGTCCTGAGTCGGTTTTGGTCAATACCTATCAATGGATCATCAGAAATTGGGAAGCTGTCAAAATTCAATGGTCTCAGAATCCTGCAATGTTGTACAACAAAATGGAATTTGAACCATTTCAATCTTTAGTCCCCAAGGCCATTAGAAGCCAATACAGTGGGTTTGTCAGAACTCTATTCCAACAAATGAGAGACGTACTTGGGACATTTGACACCACCCAGATAATAAAGCTTCTCCCTTTTGCAGCCGCTCCACCAAAGCAAAGCAGAATGCAGTTCTCTTCACTGACTGTAAATGTGAGGGGATCAGGGATGAGAATACTTGTAAGGGGCAATTCTCCTGTATTCAACTACAACAAGACCACTAAAAGACTAACAATTCTCGGAAAAGATGCCGGCACTTTAATTGAAGACCCAGATGAAAGCACATCCGGAGTGGAGTCCGCCGTATTGAGAGGGTTTCTCATTATAGGTAAGGAAGACAGAAGATACGGGCCAGCATTAAGCATCAATGAACTGAGTAACCTTGCAAAAGGGGAAAAGGCTAATGTGCTAATCGGGCAAGGAGACGTGGTGTTGGTAATGAAACGAAAACGGGACTCTAGCATACTTACTGACAGCCAGACAGCGACCAAAAGAATTCGGATGGCCATCAATTAA
ATGGATGTCAATCCGACTCTACTGTTCCTAAAGGTTCCAGCGCAAAATGCCATAAGCACCACATTCCCTTATACTGGAGATCCTCCATACAGCCATGGAACAGGAACAGGGTACACCATGGACACAGTCAACAGAACACACCAATATTCAGAGAAGGGGAAGTGGACGACAAATACAGAAACTGGGGCACCCCAACTCAACCCAATTGATGGACCACTACCTGAGGATAATGAGCCAAGTGGATATGCACAAACAGACTGTGTCCTGGAGGCTATGGCCTTCCTTGAAGAATCCCACCCAGGTATCTTTGAGAACTCATGCCTTGAAACAATGGAAGTCGTTCAACAAACAAGGGTGGACAAACTAACCCAAGGTCGCCAGACTTATGATTGGACATTAAACAGAAATCAACCGGCAGCAACTGCATTAGCCAACACCATAGAAGTTTTTAGATCGAATGGACTAACAGCTAATGAATCAGGAAGGCTAATAGATTTCCTCAAGGATGTGATGGAATCAATGGATAAAGAGGAAATGGAGATAACAACACACTTTCAAAGAAAAAGGAGAGTAAGAGACAACATGACCAAGAAAATGGTCACACAAAGAACAATAGGGAAGAAAAAACAAAGAGTGAATAAGAGAGGCTATCTAATAAGAGCTTTGACATTGAACACGATGACCAAAGATGCAGAGAGAGGTAAATTAAAAAGAAGGGCTATTGCAACACCCGGGATGCAAATTAGAGGGTTCGTGTACTTCGTTGAAACTTTAGCTAGAAGCATTTGCGAAAAGCTTGAACAGTCTGGACTTCCGGTTGGGGGTAATGAAAAGAAGGCCAAACTGGCAAATGTTGTGAGAAAAATGATGACTAATTCACAAGACACAGAGCTTTCTTTCACAATCACTGGGGACAACACTAAGTGGAATGAAAATCAAAACCCTCGAATGTTTTTGGCGATGATTACATATATCACAAAAAATCAACCTGAGTGGTTCAGAAACATCCTGAGCATCGCACCAATAATGTTCTCAAACAAAATGGCAAGACTGGGAAAAGGATACATGTTCGAGAGTAAGAGAATGAAGCTCCGAACACAAATACCCGCAGAAATGCTAGCAAGCATTGACCTGAAGTATTTCAATGAATCAACAAGGAAGAAAATTGAGAAAATAAGGCCTCTTCTAATAGATGGCACAGCATCATTGAGCCCTGGGATGATGATGGGCATGTTCAACATGCTAAGTACGGTTTTAGGAGTCTCGATACTGAATCTTGGGCAAAAGAAATACACCAAGACAACATACTGGTGGGATGGGCTCCAATCCTCCGACGATTTTGCCCTCATAGTGAATGCACCAAATCATGAGGGAATACAAGCAGGAGTGGATAGATTCTACAGGACCTGCAAGTTAGTGGGAATCAACATGAGCAAAAAGAAGTCCTATATAAATAAAACAGGGACATTTGAATTCACAAGCTTTTTTTATCGATATGGATTTGTGGCTAATTTTAGCATGGAGCTGCCCAGTTTTGGAGTGTCTGGAATAAACGAGTCAGCTGATATGAGCATTGGAGTAACAGTGATAAAGAACAACATGATAAACAATGACCTTGGACCAGCAACAGCCCAGATGGCTCTCCAATTGTTCATCAAAGACTACAGATATACATATAGGTGCCATAGAGGAGACACACAAATTCAGACGAGAAGATCATTCGAGCTAAAGAAGCTGTGGGATCAAACCCAATCAAGGGCAGGACTATTGGTATCAGATGGGGGACCAAACTTATACAATATCCGGAATCTTCACATCCCTGAAGTCTGCTTAAAGTGGGAGCTAATGGATGAGAATTATCGGGGAAGACTTTGTAATCCCCTGAATCCCTTTGTCAGCCATAAAGAAATTGAGTCTGTAAACAATGCTGTAGTGATGCCAGCCCATGGTCCGGCCAAAAGTATGGAATATGATGCCGTTGCAACTACACACTCCTGGATTCCCAAGAGGAACCGCTCTATTCTCAACACAAGCCAAAGGGGAATTCTTGAGGATGAACAGATGTACCAGAAGTGCTGCAACTTGTTCGAGAAATTTTTCCCTAGTAGTTCATATAGGAGACCGATTGGAATTTCTAGCATGGTGGAGGCCATGGTGTCTAGGGCCCGGATTGATGCCAGAATTGACTTCGAGTCTGGACGGATTAAGAAGGAAGAGTTCTCTGAGATCATGAAGATCTGTTCCACCATTGAAGAACTCAGACGGCAAAAATAA
ATGGAAGATTTTGTGCGACAATGCTTCAACCCGATGATTGTCGAACTTGCAGAAAAAGCAATGAAAGAGTATGGGGAGGATCTGAAAATTGAAACAAACAAATTTGCAGCAATATGCACTCACTTGGAGGTATGTTTCATGTATTCAGATTTTCATTTCATCAATGAACAAGGCGAATCAATAGTGGTAGAACTTGATGATCCAAATGCACTGTTAAAGCACAGATTTGAAATAATCGAGGGGAGAGACAGAACAATGGCCTGGACAGTAGTAAACAGTATCTGCAACACTACTGGAGCTGAAAAACCGAAGTTTCTACCAGATTTGTATGATTACAAGGAGAACAGATTCATCGAAATTGGAGTGACAAGGAGAGAAGTCCACATATATTACCTTGAAAAGGCCAATAAGATTAAATCTGAGAACACACACATTCACATTTTCTCATTCACTGGGGAGGAAATGGCCACAAAGGCAGACTACACTCTCGACGAGGAAAGCAGGGCTAGGATTAAGACCAGGCTATTTACCATAAGACAAGAAATGGCCAACAGAGGCCTCTGGGATTCCTTTCGTCAGTCCGAAAGAGGCGAAGAAACAATTGAAGAAAAATTTGAAATCTCAGGAACTATGCGTAGGCTTGCCGACCAAAGTCTCCCACCGAACTTCTCCTGCCTTGAGAATTTTAGAGCCTATGTGGATGGATTCGAACCGAACGGCTGCATTGAGGGCAAGCTTTCTCAAATGTCCAAAGAAGTGAATGCCAAAATTGAACCTTTTCTGAAGACAACACCAAGACCAATCAAACTTCCGAATGGACCTCCTTGTTATCAGCGGTCCAAATTCCTCCTGATGGATGCTTTAAAATTGAGCATTGAAGACCCAAGTCACGAAGGAGAAGGGATCCCATTATATGATGCGATCAAGTGCATAAAAACATTCTTTGGATGGAAAGAACCTTATATAGTCAAACCACACGAAAAGGGAATAAATTCAAATTACCTGCTGTCATGGAAGCAAGTATTGTCAGAATTGCAGGACATTGAAAATGAGGAGAAGATTCCAAGGACTAAAAACATGAAGAAAACGAGTCAACTAAAGTGGGCTCTTGGTGAAAACATGGCACCAGAGAAAGTAGACTTTGAAAACTGCAGAGACATAAGCGATTTGAAGCAATATGATAGTGACGAACCTGAATTAAGGTCACTTTCAAGCTGGATACAGAATGAGTTCAACAAGGCCTGCGAGCTAACTGATTCAATCTGGATAGAGCTCGATGAAATTGGAGAGGACGTAGCCCCAATTGAGTACATTGCAAGCATGAGGAGGAATTATTTCACAGCAGAGGTGTCCCATTGTAGAGCCACTGAGTACATAATGAAGGGGGTATACATTAATACTGCCCTGCTCAATGCATCCTGTGCAGCAATGGACGATTTTCAACTAATTCCCATGATAAGCAAGTGCAGAACTAAAGAGGGAAGGCGAAAAACCAATTTATATGGATTCATCATAAAGGGAAGATCTCATTTAAGGAATGACACAGATGTGGTAAACTTTGTGAGCATGGAGTTTTCTCTCACTGACCCGAGACTTGAGCCACATAAATGGGAGAAATACTGTGTCCTTGAGATAGGAGATATGTTACTAAGAAGTGCCATAGGCCAAATTTCAAGGCCTATGTTCTTGTATGTGAGGACAAACGGAACATCAAAGGTCAAAATGAAATGGGGAATGGAGATGAGACGTTGCCTCCTTCAGTCACTCCAGCAGATCGAGAGCATGATTGAAGCCGAGTCCTCGGTTAAAGAGAAAGACATGACCAAAGAGTTTTTTGAGAATAAATCAGAAGCATGGCCCATTGGGGAGTCCCCCAAGGGAGTGGAAGAAGGTTCCATTGGGAAAGTCTGTAGGACTCTATTGGCTAAGTCAGTGTTCAATAGCCTGTATGCATCACCACAATTGGAAGGATTTTCAGCGGAGTCAAGAAAACTGCTCCTTGTTGTTCAGGCTCTTAGGGACAACCTCGAACCTGGGACCTTTGATCTTGGGGGGCTATATGAAGCAATTGAGGAGTGCCTGATTAATGATCCCTGGGTTTTGCTCAATGCGTCTTGGTTCAACTCCTTCCTGACACATGCATTAAAATAG
ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCCGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTGGAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAGAATGGAACAAGCTCTGCTTGCAAAAGGAGATCTAATAAAAGTTTCTTTAGTAGATTGAATTGGTTGACCCAATTAAAATACAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAAAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAGTGACCAAATCAGCCTATATGCTCAAGCATCAGGAAGAATCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGAATATCGGATCTAGACCCAGGGTAAGGGATGTCTCCAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTCGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAATTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTTCAAAATGTAAACAGGATCACATATGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATCGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGACGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGCACAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCAACCAAATCAATGGGAAACTGAATAGGTTAATCGGGAAAACAAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTCGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAGAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGGTCAATCAGAAATGGAACTTATGACCATGATGTATACAGAGATGAAGCATTAAACAACCGGTTCCAGATCAAAGGTGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATTTGA
ATGGCGTCCCAAGGCACCAAACGGTCTTATGAACAGATGGAAACTGATGGGGATCGCCAGAATGCAACTGAGATTAGGGCATCCGTCGGGAAGATGATTGATGGAATTGGGAGATTCTACATCCAAATGTGCACTGAACTTAAACTCAGTGATTATGAAGGGCGGTTGATCCAGAACAGCTTGACAATAGAGAAAATGGTGCTCTCTGCTTTTGATGAAAGAAGGAATAAATATCTGGAAGAACACCCCAGCGCGGGGAAAGATCCTAAGAAAACTGGGGGGCCCATATACAGGAGAGTAGATGGAAAATGGATGAGGGAACTCGTCCTTTATGACAAAGAAGAAATAAGGCGAATCTGGCGCCAAGCCAACAATGGTGAGGATGCGACAGCTGGTCTAACTCACATAATGATCTGGCATTCCAATTTGAATGATGCAACATACCAGAGGACAAGAGCTCTTGTTCGAACCGGAATGGATCCCAGAATGTGCTCTCTGATGCAGGGCTCGACTCTCCCTAGAAGGTCCGGAGCTGCAGGTGCTGCAGTCAAAGGAATCGGGACAATGGTGATGGAGCTGATCAGAATGGTCAAACGGGGGATCAACGATCGAAATTTCTGGAGAGGTGAGAATGGGCGGAAAACAAGAAGTGCTTATGAGAGAATGTGCAACATTCTTAAAGGAAAATTTCAAACAGCTGCACAAAGAGCAATGGTGGATCAAGTGAGAGAAAGTCGGAACCCAGGAAATGCTGAGATCGAAGATCTCATATTTTTGGCAAGATCTGCATTGATATTGAGAGGGTCAGTTGCTCACAAATCTTGCCTACCTGCCTGTGTGTATGGACCTGCAGTATCCAGTGGGTACGACTTCGAAAAAGAGGGATATTCCTTGGTGGGAATAGACCCTTTCAAACTACTTCAAAATAGCCAAGTATACAGCCTAATCAGACCTAACGAGAATCCAGCACACAAGAGTCAGCTGGTGTGGATGGCATGCCATTCTGCTGCATTTGAAGATTTAAGATTGTTAAGCTTCATCAGAGGGACAAAAGTATCTCCGCGAGGGAAACTTTCAACTAGAGGAGTACAAATTGCTTCAAATGAGAACATGGATAATATGGGATCGAGCACTCTTGAACTGAGAAGCGGGTACTGGGCCATAAGGACCAGGAGTGGAGGAAACACTAATCAACAGAGGGCCTCCGCAGGCCAAACCAGTGTGCAACCTACGTTTTCTGTACAAAGAAACCTCCCATTTGAAAAGTCAACCATCATGGCAGCATTCACTGGAAATACGGAGGGAAGAACTTCAGACATGAGGGCAGAAATCATAAGAATGATGGAAGGTGCAAAACCAGAAGAAGTGTCGTTCCGGGGGAGGGGAGTTTTCGAGCTCTCAGACGAGAAGGCAACGAACCCGATCGTGCCCTCTTTTGATATGAGTAATGAAGGATCTTATTTCTTCGGAGACAATGCAGAAGAGTACGACAATTAA
ATGAATCCAAATCAAAAGATAATAACGATTGGCTCTGTTTCTCTCACCATTTCCACAATATGCTTCTTCATGCAAATTGCCATCCTGATAACTACTGTAACATTGCATTTCAAGCAATATGAATTCAACTCCCCCCCAAACAACCAAGTGATGCTGTGTGAACCAACAATAATAGAAAGAAACATAACAGAGATAGTGTATCTGACCAACACCACCATAGAGAAGGAAATATGCCCCAAACTAGCAGAATACAGAAATTGGTCAAAGCCGCAATGTAACATTACAGGATTTGCACCTTTTTCTAAGGACAATTCGATTCGGCTTTCCGCTGGTGGGGACATCTGGGTGACAAGAGAACCTTATGTGTCATGCGATCCTGACAAGTGTTATCAATTTGCCCTTGGACAGGGAACAACACTAAACAACGTGCATTCAAATGACACAGTACATGATAGGACCCCTTATCGGACCCTATTGATGAATGAGTTGGGTGTTCCATTTCATCTGGGGACCAAGCAAGTGTGCATAGCATGGTCCAGCTCAAGTTGTCACGATGGAAAAGCATGGCTGCATGTTTGTGTAACGGGGGATGATGAAAATGCAACTGCTAGCTTCATTTACAATGGGAGGCTTGTAGATAGTATTGTTTCATGGTCCAAAAAAATCCTCAGGACCCAGGAGTCAGAATGCGTTTGTATCAATGGAACTTGTACAGTAGTAATGACTGATGGGAGTGCTTCAGGAAAAGCTGATACTAAAATACTATTCATTGAGGAGGGGAAAATCGTTCATACTAGCACATTGTCAGGAAGTGCTCAGCATGTCGAGGAGTGCTCCTGTTATCCTCGATATCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGCTCCAATAGGCCCATCGTAGATATAAACATAAAGGATTATAGCATTGTTTCCAGTTATGTGTGCTCAGGACTTGTTGGAGACACACCCAGAAAAAACGACAGCTCCAGCAGTAGCCATTGCTTGGATCCAAACAATGAGGAAGGTGGTCATGGAGTGAAAGGCTGGGCCTTTGATGATGGAAATGACGTGTGGATGGGAAGAACGATCAGCGAGAAGTTACGCTCAGGATATGAAACCTTCAAAGTCATTGAAGGCTGGTCCAACCCTAACTCCAAATTGCAGATAAATAGGCAAGTCATAGTTGACAGAGGTAATAGGTCCGGTTATTCTGGTATTTTCTCTGTTGAAGGCAAAAGCTGCATCAATCGGTGCTTTTATGTGGAGTTGATAAGGGGAAGAAAACAGGAAACTGAAGTCTTGTGGACCTCAAACAGTATTGTTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGATGGGGCGGACATCAATCTCATGCCTATATAA
ATGAGCCTTCTAACCGAGGTCGAAACGTATGTTCTCTCTATCGTTCCATCAGGCCCCCTCAAAGCCGAGATCGCGCAGAGACTTGAAGATGTCTTTGCTGGGAAAAACACAGATCTTGAGGCTCTCATGGAATGGCTAAAGACAAGACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCCTCAATGGGAATGGAGATCCAAATAACATGGACAAAGCAGTTAAACTGTATAGGAAACTTAAGAGGGAGATAACGTTCCATGGGGCCAAAGAAATAGCTCTCAGTTATTCTGCTGGTGCACTTGCCAGTTGCATGGGCCTCATATACAATAGGATGGGGGCTGTAACCACTGAAGTGGCATTTGGCCTGGTATGTGCAACATGTGAGCAGATTGCTGACTCCCAGCACAGGTCTCATAGGCAAATGGTGGCAACAACCAATCCATTAATAAGACATGAGAACAGAATGGTTTTGGCCAGCACTACAGCTAAGGCTATGGAGCAAATGGCTGGATCAAGTGAGCAGGCAGCGGAGGCCATGGAGATTGCTAGTCAGGCCAGGCAAATGGTGCAGGCAATGAGAGCCATTGGGACTCATCCTAGCTCCAGTACTGGTCTAAGAGATGATCTTCTTGAAAATTTGCAGACCTATCAGAAACGAATGGGGGTGCAGATGCAACGATTCAAGTGACCCGCTTGTTGTTGCCGCGAGTATCATTGGGATCTTGCACTTGATATTGTGGATTCTTGATCGTCTTTTTTTCAAATGCGTCTATCGACTCTTCAAACACGGCCTTAAAAGAGGCCCTTCTACGGAAGGAGTACCTGAGTCTATGAGGGAAGAATATCGAAAGGAACAGCAGAATGCTGTGGATGCTGACGACAGTCATTTTGTCAGCATAGAGTTGGAGTAA
ATGGATTCCAACACTGTGTCAAGTTTCCAGGTAGATTGCTTTCTTTGGCATATCCGGAAACAAGTTGTAGACCAAGAACTGAGTGATGCCCCATTCCTTGATCGGCTTCGCCGAGATCAGAGGTCCCTAAGGGGAAGAGGCAATACTCTCGGTCTAGACATCAAAGCAGCCACCCATGTTGGAAAGCAAATTGTAGAAAAGATTCTGAAAGAAGAATCTGATGAGGCACTTAAAATGACCATGGTCTCCACACCTGCTTCGCGATACATAACTGACATGACTATTGAGGAATTGTCAAGAAACTGGTTCATGCTAATGCCCAAGCAGAAAGTGGAAGGACCTCTTTGCATCAGAATGGACCAGGCAATCATGGAGAAAAACATCATGTTGAAAGCGAATTTCAGTGTGATTTTTGACCGACTAGAGACCATAGTATTACTAAGGGCTTTCACCGAAGAGGGAGCAATTGTTGGCGAAATCTCACCATTGCCTTCTTTTCCAGGACATACTATTGAGGATGTCAAAAATGCAATTGGGGTCCTCATCGGAGGACTTGAATGGAATGATAACACAGTTCGAGTCTCTAAAAATCTACAGAGATTCGCTTGGAGAAGCAGTAATGAGAATGGGGGACCTCCACTTACTCCAAAACAGAAACGGAAAATGGCGAGAACAGCTAGGTCAAAAGTTTGAAGAGATAAGATGGCTGATTGAAGAAGTGAGACACAGACTAAAAACAACTGAAAATAGCTTTGAACAAATAACATTCATGCAAGCATTACAACTGCTGTTTGAAGTGGAACAGGAGATAAGAACTTTCTCATTTCAGCTTATTTAA
and of the 2007-ancestor virus:
Code:
>Index/USA-2007(H3N2)
ATGGAAAGAATAAAAGAACTACGGAATCTGATGTCGCAGTCTCGCACTCGCGAGATACTGACAAAAACCACAGTGGACCATATGGCCATAATTAAGAAGTACACATCGGGGAGACAGGAAAAGAACCCGTCACTTAGGATGAAATGGATGATGGCAATGAAATACCCAATCACTGCTGACAAAAGGATAACAGAAATGGTTCCGGAGAGAAATGAACAAGGACAAACTCTATGGAGTAAAATGAGTGATGCTGGATCAGATAGAGTGATGGTATCACCTTTGGCTGTAACATGGTGGAATAGAAATGGACCCGTGACAAGTACGGTCCATTACCCAAAAGTGTACAAGACTTATTTCGACAAAGTCGAAAGGTTAAAACATGGAACCTTTGGCCCTGTTCATTTTAGAAATCAAGTCAAGATACGCAGAAGAGTAGACATAAACCCTGGTCATGCAGACCTCAGTGCCAAAGAGGCACAAGATGTAATTATGGAAGTTGTTTTTCCCAATGAAGTGGGAGCCAGGATACTAACATCAGAATCACAATTAACAATAACTAAAGAGAAAAAAGAAGAACTCCGAGATTGCAAAATTTCTCCCTTGATGGTTGCATACATGTTAGAGAGAGAACTTGTACGAAAAACAAGATTTCTCCCAGTTGCTGGCGGAACAAGCAGTATATACATTGAAGTTTTACATTTGACTCAAGGAACGTGTTGGGAACAAATGTACACTCCAGGTGGAGGAGTGAGGAATGACGATGTTGACCAAAGCCTAATTATTGCGGCCAGGAACATAGTAAGAAGAGCCGCAGTATCAGCAGATCCACTAGCATCTTTATTGGAGATGTGCCACAGCACACAAATTGGCGGGACAAGGATGGTGGACATTCTTAGACAGAACCCGACTGAAGAACAAGCTGTGGATATATGCAAGGCTGCAATGGGATTGAGAATCAGCTCATCCTTCAGCTTTGGTGGGTTTACATTTAAAAGAACAAGCGGGTCATCAGTCAAAAAAGAAGAAGAGGTGCTTACAGGCAATCTCCAAACATTGAAAATAAGAGTACATGAGGGGTATGAGGAGTTCACAATGGTGGGGAAAAGAGCAACAGCTATACTAAGAAAAGCAACCAGAAGATTGGTTCAGCTCATAGTGAGTGGAAGAGACGAACAGTCAATAGCCGAAGCAATAATCGTGGCCATGGTGTTTTCACAAGAGGATTGCATGATAAAAGCAGTTAGAGGTGACCTGAATTTCGTCAACAGAGCAAATCAGCGGTTGAACCCCATGCATCAGCTTTTAAGGCATTTTCAGAAAGATGCGAAAGTGCTTTTTCAAAATTGGGGAGTTGAACACATCGACAGTGTGATGGGAATGATTGGAGTATTACCAGATATGACTCCAAGCACAGAGATGTCAATGAGAGGAATAAGAGTCAGCAAAATGGGTGTGGATGAATACTCCAGTACAGAGAGGGTGGTGGTTAGCATTGATCGGTTTTTGAGAGTTCGAGACCAACGTGGGAATGTATTATTATCTCCTGAGGAGGTCAGTGAAACACAGGGAACTGAGAGACTGACAATAACTTATTCATCGTCGATGATGTGGGAGATTAACGGTCCTGAGTCGGTTTTGGTCAATACCTATCAATGGATCATCAGAAATTGGGAAGCTGTCAAAATTCAATGGTCTCAGAATCCTGCAATGTTGTACAACAAAATGGAATTTGAACCATTTCAATCTTTAGTCCCCAAGGCCATTAGAAGCCAATACAGTGGGTTTGTCAGAACTCTATTCCAACAAATGAGAGACGTACTTGGGACATTTGACACCACCCAGATAATAAAGCTTCTCCCTTTTGCAGCTGCTCCACCAAAGCAAAGCAGAATGCAGTTCTCTTCACTGACTGTGAATGTGAGGGGATCAGGGATGAGAATACTTGTAAGGGGCAATTCTCCTGTATTCAACTACAACAAGACCACTAAAAGACTAACAATTCTCGGAAAAGATGCCGGCACTTTAATTGAAGACCCAGATGAAAGCACATCCGGAGTGGAGTCCGCCGTCTTGAGAGGGTTTCTCATTATAGGTAAGGAAGACAGAAGATACGGACCAGCATTAAGCATCAATGAACTGAGTAACCTTGCAAAAGGGGAAAAGGCTAATGTGCTAATCGGGCAAGGAGACGTGGTGTTGGTAATGAAACGAAAACGGGACTCTAGCATACTTACTGACAGCCAGACAGCGACCAAAAGAATTCGGATGGCCATCAATTAA
ATGGATGTCAATCCGACTCTACTGTTCCTAAAGGTTCCAGCGCAAAATGCCATAAGCACAACATTCCCTTATACTGGAGATCCTCCATACAGCCATGGAACAGGAACAGGGTACACCATGGACACAGTCAACAGAACACACCAATATTCAGAGAAGGGGAAGTGGACGACAAATACAGAAACTGGGGCACCCCAACTCAACCCAATTGATGGACCACTACCTGAGGATAATGAACCAAGTGGATATGCACAAACAGACTGTGTCCTGGAGGCTATGGCCTTCCTTGAAGAATCCCACCCAGGTATCTTTGAGAACTCATGCCTTGAAACAATGGAAGCCGTTCAACAGACAAGGGTGGACAAACTAACCCAAGGTCGCCAGACTTATGATTGGACATTAAACAGAAATCAACCGGCAGCAACTGCATTAGCCAACACCATAGAAGTTTTTAGATCGAACGGATTAACAGCTAATGAATCAGGAAGGCTAATAGATTTCCTCAAGGATGTGATGGAATCAATGGATAAAGAGGAAATGGAGATAACAACACACTTTCAAAGAAAAAGGAGAGTAAGGGACAACATGACCAAGAAAATGGTCACACAAAGAACAATAGGGAAGAAAAAACAAAGAGTGAATAAGAGAGGCTACCTAATAAGAGCTTTGACATTGAACACGATGACCAAAGATGCAGAGAGAGGCAAATTAAAAAGAAGGGCTATTGCAACACCCGGGATGCAAATTAGAGGGTTCGTGTACTTCGTTGAAACTTTAGCTAGAAGCATTTGCGAAAAGCTTGAACAGTCTGGACTTCCGGTTGGGGGTAATGAAAAGAAGGCCAAACTGGCAAATGTTGTGAGAAAAATGATGACTAATTCACAAGACACAGAGCTTTCTTTCACAATCACTGGGGACAACACTAAGTGGAATGAAAATCAAAACCCTCGAATGTTTTTGGCGATGATTACATACATCACAAAAAATCAACCTGAGTGGTTCAGAAACATCCTGAGCATCGCACCAATAATGTTCTCAAACAAAATGGCAAGACTGGGAAAAGGATACATGTTCGAGAGTAAGAGAATGAAGCTCCGGACACAAATACCTGCAGAAATGCTAGCAAGCATTGACCTGAAGTATTTCAATGAATCAACAAGGAAGAAAATTGAGAAAATAAGGCCTCTTCTAATAGATGGCACAGCATCATTGAGCCCTGGAATGATGATGGGCATGTTCAACATGCTAAGTACGGTTTTAGGAGTCTCGATACTGAATCTTGGACAAAAGAAATACACCAAGACAACATACTGGTGGGATGGGCTCCAATCCTCCGACGATTTTGCCCTCATAGTGAATGCACCAAATCATGAGGGAATACAAGCAGGAGTGGATAGATTCTACAGGACCTGCAAGTTAGTGGGAATCAACATGAGCAAAAAGAAGTCCTATATAAATAAAACAGGGACATTTGAATTCACTAGCTTTTTTTATCGATATGGATTTGTGGCTAATTTTAGCATGGAGCTGCCCAGTTTTGGAGTGTCTGGAATAAACGAGTCAGCTGATATGAGCATTGGAGTAACAGTGATAAAGAACAACATGATAAACAATGACCTTGGACCAGCAACAGCCCAAATGGCTCTCCAATTGTTCATCAAAGATTACAGATACACATATAGGTGCCATAGAGGAGACACACAAATCCAGACGAGAAGATCATTCGAGCTAAAGAAGCTGTGGGATCAAACCCAATCAAGGGCAGGACTATTGGTATCAGATGGGGGACCAAACTTATACAATATCCGGAATCTTCACATCCCTGAAGTCTGCTTAAAGTGGGAGCTGATGGATGAGAATTATCGGGGAAGACTTTGTAATCCCCTGAATCCCTTTGTCAGCCATAAAGAAATTGAGTCTGTAAACAATGCTGTAGTAATGCCAGCCCATGGTCCGGCCAAAAGTATGGAATATGATGCCGTTGCAACTACACACTCCTGGATTCCCAAGAGGAACCGCTCTATTCTAAACACAAGCCAAAGGGGAATTCTTGAGGATGAACAGATGTACCAGAAGTGCTGCAACTTGTTCGAGAAATTTTTCCCTAGTAGTTCATATAGGAGACCGATTGGAATTTCTAGCATGGTGGAGGCCATGGTGTCTAGGGCCCGGATTGATGCCAGAATTGACTTCGAGTCTGGACGGATTAAGAAGGAAGAGTTCTCTGAGATCATGAAGATCTGTTCCACCATTGAAGAACTCAGACGGCAAAAATAA
ATGGAAGATTTTGTGCGACAATGCTTCAACCCGATGATTGTCGAACTTGCAGAAAAAGCAATGAAAGAGTATGGGGAGGATCTGAAAATTGAAACAAACAAATTTGCAGCAATATGCACTCACTTGGAGGTGTGTTTCATGTATTCAGATTTTCATTTCATCAATGAACAAGGCGAATCAATAGTGGTAGAACTTGACGATCCAAATGCACTGTTAAAGCACAGATTTGAAATAATCGAGGGGAGAGACAGAACAATGGCCTGGACAGTAGTAAACAGTATCTGCAACACTACTGGAGCTGGAAAACCGAAGTTTCTACCAGATTTGTATGATTACAAGGAGAACAGATTCATCGAAATTGGGGTGACAAGGAGAGAAGTCCACATATATTACCTTGAAAAGGCCAATAAGATTAAATCTGAGAACACACACATTCACATTTTCTCATTCACTGGGGAGGAAATGGCCACAAAGGCAGACTACACTCTCGACGAGGAAAGCAGGGCTAGGATTAAGACCAGGCTGTTTACCATAAGACAAGAAATGGCCAACAGAGGCCTCTGGGATTCCTTTCGTCAGTCCGAAAGAGGCGAAGAAACAATTGAAGAAAAATTTGAAATCACAGGAACTATGCGTAGGCTTGCCGACCAAAGTCTCCCACCGAACTTCTCCTGCCTTGAGAATTTTAGAGCCTATGTGGATGGATTCGAACCGAACGGCTGCATTGAGGGCAAGCTTTCTCAAATGTCCAAAGAAGTGAATGCCCAAATTGAACCTTTTCTGAAGACAACACCAAGACCAATCAAACTTCCGAATGGACCTCCTTGTTATCAGCGGTCCAAATTCCTCCTGATGGATGCTTTAAAATTGAGCATTGAAGACCCAAGTCACGAAGGAGAAGGGATCCCATTATATGATGCGATCAAGTGCATAAAAACATTCTTTGGATGGAAAGAACCTTATATAGTCAAACCACACGAAAAGGGAATAAATTCAAATTACCTGCTGTCATGGAAGCAAGTACTGTCAGAATTGCAGGACATTGAAAATGAGGAGAAGATTCCAAGGACTAAAAACATGAAGAAAACGAGTCAACTGAAGTGGGCTCTTGGTGAAAACATGGCACCAGAGAAGGTAGACTTTGAAAACTGCAGAGACATAAGCGATTTGAAGCAATATGATAGTGACGAACCTGAATTAAGGTCACTTTCAAGCTGGATACAGAATGAGTTCAACAAGGCCTGTGAGCTAACTGATTCAGTCTGGATAGAGCTCGATGAAATTGGAGAGGACGTAGCCCCAATTGAGCACATTGCAAGCATGAGAAGGAATTATTTCACAGCAGAGGTGTCCCATTGTAGAGCCACTGAATACATAATGAAGGGGGTATACATTAACACTGCCCTGCTCAATGCATCCTGTGCAGCAATGGACGATTTTCAACTAATTCCCATGATAAGCAAGTGCAGAACTAAAGAGGGAAGGCGAAAAACCAATTTATATGGATTCATCATAAAGGGAAGATCTCATTTAAGGAATGACACAGACGTGGTAAATTTTGTGAGCATGGAGTTTTCTCTCACTGACCCGAGACTTGAGCCACATAAATGGGAGAAATACTGTGTCCTTGAGATAGGAGATATGTTACTAAGAAGTGCCATAGGCCAAATTTCAAGGCCTATGTTCTTGTATGTGAGGACAAACGGAACATCAAAGGTCAAAATGAAATGGGGAATGGAGATGAGACGTTGCCTCCTTCAGTCACTCCAGCAGATCGAGAGCATGATTGAAGCCGAGTCCTCGGTTAAAGAGAAAGACATGACCAAAGAGTTTTTTGAGAATAAATCAGAAGCATGGCCCATTGGGGAGTCCCCCAAGGGAGTGGAAGAAGGTTCCATTGGGAAAGTCTGTAGGACTCTATTGGCTAAGTCAGTATTCAATAGCCTGTATGCATCACCACAATTGGAAGGATTTTCAGCGGAGTCAAGAAAACTGCTCCTTGTTGTTCAGGCTCTTAGGGACAACCTCGAACCTGGGACCTTTGATCTTGGGGGGCTATATGAAGCAATTGAGGAGTGCCTGATTAATGATCCCTGGGTTTTGCTCAATGCGTCTTGGTTCAACTCCTTCCTGACACATGCATTAAAATAG
ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGCTCTGCTTGCATAAGGAGATCTAATAACAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAAATTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAAAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAATGACCAAATCTTCCTGTATGCTCAAGCATCAGGAAGAATCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGAATATCGGATCTAGACCCAGAGTAAGGAATATCCCCAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAATTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATCGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAATAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATAGGTTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTCGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACCAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGAGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGCGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATTTGA
ATGGCGTCCCAAGGCACCAAACGGTCTTATGAACAGATGGAAACTGATGGGGATCGCCAGAATGCAACTGAGATTAGGGCATCCGTCGGGAAGATGATTGATGGAATTGGGAGATTCTACATCCAAATGTGCACTGAACTTAAACTCAGTGATCATGAAGGGCGGTTGATCCAGAACAGCTTGACAATAGAGAAAATGGTGCTCTCTGCTTTTGATGAAAGAAGGAATAAATACCTGGAAGAACACCCCAGCGCGGGGAAAGATCCCAAGAAAACTGGGGGGCCCATATACAGGAGAGTAGATGGAAAATGGATGAGGGAACTCGTCCTTTATGACAAAGAAGAAATAAGGCGAATCTGGCGCCAAGCCAACAATGGTGAGGATGCTACATCTGGTCTAACTCACATAATGATTTGGCATTCCAATTTGAATGATGCAACATACCAGAGGACAAGAGCTCTTGTTCGAACTGGAATGGATCCCAGAATGTGCTCTCTGATGCAGGGCTCGACTCTCCCTAGAAGGTCCGGAGCTGCAGGTGCTGCAGTCAAAGGAATCGGGACAATGGTGATGGAACTGATCAGAATGGTCAAACGGGGGATCAACGATCGAAATTTTTGGAGAGGTGAGAATGGGCGGAAAACAAGAAGTGCTTATGAGAGAATGTGCAACATTCTTAAAGGAAAATTTCAAACAGCTGCACAAAGAGCAATGGTGGATCAAGTGAGAGAAAGTCGGAACCCAGGAAACGCTGAGATCGAAGATCTCATATTTTTAGCAAGATCTGCATTGATATTGAGAGGATCAGTTGCTCACAAATCTTGCCTACCTGCCTGTGCGTATGGACCTGCAGTATCCAGTGGGTACGACTTCGAAAAAGAGGGATATTCCTTGGTGGGAATAGACCCTTTCAAACTACTTCAAAATAGCCAAATATACAGCTTAATCAGACCTAACGAGAATCCAGCACACAAGAGTCAGCTGGTGTGGATGGCATGCCATTCTGCTGCATTTGAAGATTTAAGATTGTTAAGCTTCATCAGAGGGACAAAAGTATCTCCTCGGGGGAAACTGTCAACTAGAGGAGTACAAATTGCTTCAAATGAGAACATGGATAATATGGGATCGAGCACTCTTGAACTGAGAAGCGGGTACTGGGCCATAAGGACCAGGAGTGGAGGAAACACTAATCAACAGAGGGCCTCCGCAGGCCAAACCAGTGTGCAACCTACGTTTTCTGTACAAAGAAACCTCCCATTTGAAAAGTCAACCATCATGGCAGCATTCACTGGAAATACGGAGGGAAGAACTTCAGACATGAGGGCAGAAATCATAAGAATGATGGAAGGTGCAAAACCAGAAGAAGTGTCATTCCGGGGGAGGGGAGTTTTCGAGCTCTCAGACGAGAAGGCAACGAACCCGATCGTGCCCTCTTTTGATATGAGTAATGAAGGATCTTATTTCTTCGGAGACAATGCAGAAGAGTACGACAATTAA
ATGAATCCAAATCAAAAGATAATAACGATTGGCTCTGTTTCTCTCACCATTTCCACAATATGCTTCTTCATGCAAATTGCCATCTTGATAACTACTGTAACATTGCATTTCAAGCAATATGAATTCAACTCCCCCCCAAACAACCAAGTGATGCTGTGTGAACCAACAATAATAGAAAGAAACATAACAGAGATAGTGTATCTGACCAACACCACCATAGAGAAGGAAATATGCCCCAAACTAGCAGAATACAGAAATTGGTCAAAGCCGCAATGTGACATTACAGGATTTGCACCTTTTTCTAAGGACAATTCGATTAGGCTTTCCGCTGGTGGGGACATCTGGGTGACAAGAGAACCTTATGTGTCATGCGATCCTGACAAGTGTTATCAATTTGCCCTTGGACAGGGAACAACACTAAACAACGTGCATTCAAATGACACAGTACGTGATAGGACCCCTTATCGGACCCTATTGATGAATGAGTTAGGTGTTCCTTTTCATCTGGGGACCAAGCAAGTGTGCATAGCATGGTCCAGCTCAAGTTGTCACGATGGAAAAGCATGGCTGCATGTTTGTATAACGGGGGATGATAAAAATGCAACTGCTAGCTTCATTTACAATGGGAGGCTTGTAGATAGTATTGTTTCATGGTCCAAAGAAATCCTCAGGACCCAGGAGTCAGAATGCGTTTGTATCAATGGAACTTGTACAGTAGTAATGACTGATGGGAGTGCTTCAGGAAAAGCTGATACTAAAATACTATTCATTGAGGAGGGGAAAATCGTTCATACTAGCACATTGTCAGGAAGTGCTCAGCATGTCGAGGAGTGCTCCTGCTATCCTCGATATCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGCTCCAATAGGCCCATCGTAGATATAAACATAAAGGATCATAGCATTGTTTCCAGTTATGTGTGTTCAGGACTTGTTGGAGACACACCCAGAAAAAACGACAGCTCCAGCAGTAGCCATTGTTTGGATCCTAACAATGAAGAAGGTGGTCATGGAGTGAAAGGCTGGGCCTTTGATGATGGAAATGACGTGTGGATGGGAAGAACGATCAGCGAGAAGTCACGCTTAGGGTATGAAACCTTCAAAGTCATTGAAGGCTGGTCCAACCCTAAGTCCAAATTGCAGATAAATAGGCAAGTCATAGTTGACAGAGGTAATAGGTCCGGTTATTCTGGTATTTTCTCTGTTGAAGGCAAAAGCTGCATCAATCGGTGCTTTTATGTGGAGTTGATAAGGGGAAGAAAAGAGGAAACTGAAGTCTTGTGGACCTCAAACAGTATTGTTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGATGGGGCGGACATCAATCTCATGCCTATATAA
ATGAGCCTTCTAACCGAGGTCGAAACGTATGTTCTCTCTATCGTTCCATCAGGCCCCCTCAAAGCCGAGATCGCGCAGAGACTTGAAGATGTCTTTGCTGGGAAAAACACAGATCTTGAGGCTCTCATGGAATGGCTAAAGACAAGACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCCTCAATGGGAATGGAGATCCAAATAACATGGACAAAGCAGTTAAACTGTATAGGAAACTTAAGAGGGAGATAACGTTCCATGGGGCCAAAGAAATAGCTCTCAGTTATTCTGCTGGTGCACTTGCCAGTTGCATGGGCCTCATATACAATAGGATGGGGGCTGTAACCACTGAAGTGGCATTTGGCCTGGTATGTGCAACATGTGAGCAGATTGCTGACTCCCAGCACAGGTCTCATAGGCAAATGGTGGCAACAACCAATCCATTAATAAGACATGAGAACAGAATGGTTTTGGCCAGCACTACAGCTAAGGCTATGGAGCAAATGGCTGGATCAAGTGAGCAGGCAGCGGAGGCCATGGAGATTGCTAGTCAGGCCAGGCAGATGGTGCAGGCAATGAGAGCCATTGGGACTCATCCTAGTTCCAGTACTGGTCTAAGAGATGATCTTCTTGAAAATTTGCAGACCTATCAGAAACGAATGGGGGTGCAGATGCAACGATTCAAGTGACCCGCTTGTTGTTGCCGCGAATATCATTGGGATCTTGCACTTGATATTGTGGATTCTTGATCGTCTTTTTTTCAAATGCGTCTATCGACTCTTCAAACACGGCCTTAAAAGAGGCCCTTCTACGGAAGGAGTACCTGAGTCTATGAGGGAAGAATATCGAAAGGAACAGCAGAATGCTGTGGATGCTGACGACAGTCATTTTGTCAGCATAGAGTTGGAGTAA
ATGGATTCCAACACTGTGTCAAGTTTCCAGGTAGATTGCTTTCTTTGGCATATCCGGAAACAAGTTGTAGACCAAGAACTGAGTGATGCCCCATTCCTTGATCGGCTTCGCCGAGATCAGAGGTCCCTAAGGGGAAGAGGCAATACTCTCGGTCTAGACATCAAAGCAGCCACCCATGTTGGAAAGCAAATTGTAGAAAAGATTCTGAAAGAAGAATCTGATGAGGCACTTAAAATGACCATGGTCTCCACACCTGCTTCGCGATACATAACTGACATGACTATTGAGGAATTGTCAAGAAACTGGTTCATGCTAATGCCCAAGCAGAAAGTGGAAGGACCTCTTTGCATCAGAATGGACCAGGCAATCATGGAGAAAAACATCATGTTGAAAGCGAATTTCAGTGTGATTTTTGACCGACTAGAGACCATAGTATTACTAAGGGCTTTCACCGAAGAGGGAGCAATTGTTGGCGAAATCTCACCATTGCCTTCTTTTCCAGGACATACTATTGAGGATGTCAAAAATGCAATTGGGGTCCTCATCGGAGGACTTGAATGGAATGATAACACAGTTCGAGTCTCTAAAAATCTACAGAGATTCGCTTGGAGAAGCAGTAATGAGAATGGGGGACCTCCACTTACTCCAAAACAGAAACGGGAAATGGCGAGAACAGCTAGGTCAAAAGTTTGAAGAGATAAGATGGCTAATTGAAGAAGTGAGACACAGATTAAAAACAACTGAAAATAGCTTTGAACAAATAACATTCATGCAAGCATTACAACTGCTGTTTGAAGTGGAACAGGAGATAAGAACTTTCTCATTTCAGCTTATTTAA
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June 13th, 2011, 10:41 PM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,950
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Re: H3n2
evolution of H3N2 genomes since 2007
---------edit--------------------------------------
4 groups in Texas JMM Dec.2012 ,18+4+12+8 viruses
see below
differences to EI-NA
CZ--:104=24+13+16+19+08+14+04+06
4er-:103=23+14+12+22+08+13+04+07
?---:087=18+20+09+15+05+12+04+04
reas:151=43+28+14+24+12+10+09+11
differences to US-2007
CZ--:161=32+24+23+34+11+21+07+09
4er-:161=33+25+17+38+11+20+07+10
?---:145=28+33+14+29+08+19+07+07
reas:173=36+28+21+36+15+17+12+08
Index_reas_11:110=25+22+11+27+04+08+07+06
Index_EI_2011:106=14+18+14+22+10+16+07+05
EI-NA:61=10+13+07+15+03+07+03+03
EI---:63=10+13+07+15+03+09+03+03
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November 8th, 2011, 04:15 AM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,950
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Re: H3n2
the earliest appearance of the now (since 2007) dominating human
H3N2 strain was in Kolkata(Calcutta) September,2006.
the earliest with A565C,C729T (the two most prevalent mutations) was
in Cheongju,Sept.2007
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January 8th, 2012, 02:27 AM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,950
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Re: H3n2
It seems that we are getting H3N2 this season in USA and Europe.
There is still not much H3N1 from USA 2010/11 at genbank,
which is unusual.
But we have many sequences from Japan's last season.
This showed basically 2 slightly different strains last season.
All recent public viruses descend from the new strain that appeared
in 2006/7 ("Brisbane"-like)
But it's not yet public what will come this season,
we have only 2 HAs since May.
It would be interesting to see, what H3N2 India and China
had this summer.
http://magictour.free.fr/panflu/h3_12ak.GIF
http://www.flutrackers.com/forum/sho...d.php?p=434930
Six genetic groups for the HA gene can be seen in circulating H3N2 viruses.
Within the A/Perth/16/2009 genetic clade there are two genetic groups defined by amino acid substitutions:
(1) P162S, I260M & R261Q, e.g. A/Victoria/210/2009
some E50K, e.g. A/Norway/1186/2011, or N81D, e.g. A/Niigata/510/2011;
(2) N133D , R142G, T212A &V213A, not recent
Four groups, in A/Victoria/208/2009 (K62E, K144N & T212A).
(3) V223I often with N145S, e.g. A/Johannesburg/73/2011
a) N144D , e.g. A/Stockholm/18/2011
b) A198S often with S45, T48I and N312S, e.g. A/Hong Kong/3969/2011;
(4) N312S, e.g. A/Brisbane/11/2010, many T48A & K92R, e.g. A/Rhode Island/01/2010 and A Massachusetts/08/2011
(5) D53N, Y94H, I230V & E280A, e.g. A/Perth/10/2010, some I192T, e.g. A/Athens/108/2011
(6) D53N, Y94H, I230V & E280A, as in (5) but with S199A, e.g. A/Iowa/19/2010, some S45N e.g. A/Hong Kong/3951/2011;
cluster with S45N in South Africa, e.g. A/Johannesburg/114/2011; some L3F & L59I , e.g. A Norway/685/2011;
(1) with E50K,
(3) with 144, or N145S
frequency of the most common mutations:
A522C,684
C729T,525
A565C,514
C318A,412
C660A,373
G232A,362
T480A,360
T615A,358
T615G,329
A682G,326
C483T,326
T686C,166
A983G,128
G205A,118
T328C,118
A736G,114
A108G,109
C690T,109
A887C,108
T291C,108
G540A,104
G830A,095
G837A,092
A555G,089
A712C,088
A828G,077
G382A,077
A672G,076
A939G,075
C186T,071
C532T,070
G182A,065
A479G,047
G196A,046
T643G,044
A445G,040
A190G,036
A521G,036
C543T,035
A721G,034
C447T,031
C393T,029
A231G,026
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March 20th, 2012, 09:09 PM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,950
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Re: H3n2
35 H3N2-genomes from Boston, 2010/2011 season at genbank
basically 2 strains, both reassorted
2.) Egypt/Iowa in segments 1,2,3,4,5,7,8 with a different segment 6,
I haven't found that one elsewhere since 2007, but I haven't looked
much. It's probably still a descendent from the new 2007-H3N2
10/10,12/13,7/7,15/15,3/3,2/4,3/3,3/3
1.) Egypt/Iowa in segments 3,4,5,7 . Segments 2,6 are still
a bit like Egypt/Iowa - an early variation. Segments 1,8 diverged
early in 2006/7 . I don't remember having seen
these segments 1,2,6,8 before.
---segment 1 was in Bogota,Mexico City some months before)
In the 8 segments it has mutations in common with Egypt/Iowa:
1/10,6/13,7/7,15/15,3/3,2/4,3/3,0/3
Code:
>Index/USA-2007 (Brisbane-like) ............................................................................ ...................................................................... -....................................................... ........................................................- ......................................---- .................................................- ..................... ...................
>Index/2009/Egypt/Iowa ....G....G........G....G..A.....C..G..A...A...G............................. .G..G.G........G..................G....A........CAA.A......A......A..G -..C...C....AA..................A..............T...G.... ..........A....TCC.G..AG....T.....A.A..G....AT........AG- .....A....CG..........................---- .........A.......G...............................- ..C....GA............ ........A.G....G...
>Index/Perth-like/2009 ......C...........G.......A........G..A...A......................A....G..... ...TG.............................GT..............A...A.T.........A... -......C..G......A...A.......G.G...................A.A.. ........A.....A.CC.A........T..........G....AT.......TAG- .....A..............A..............ACT---- .....G..AA.......G.....A........GG...............- ..C....GA...AT....... ..............T....
>A/DC/WRAIR0301/2010/11/23 ......C...........G.......A........G..A...A........C.............A....G..... ...TG...A...........G.....CG....C.GT..............A...A.A.........A... .......C..G......A...AT......GCG.............G.....A.A.G ...A....A.....A.CC.A...GC...T..........G....AT.C......AG. ...G.A.....G.......AA..............A.T...- .....G..AA.......G..A..A.........G.............T.. .ACT.A.GA...AT.A..... ..............T....
>A/Boston/DOA71/2011/03/05 ..........A...TGT.G........A...A...............C.......CG.AT..A......A..C... .G..G.G........G..................G....A........CAA.A......A......A..G ...C...C....AA..................A....A.........T...G.... ........A.....A.CC.A....C...T..........G....AT.......TAG. .....A....CG...........................ATA C....G...A.......G....T.............AC....GT....C. ..C..A.GAA......CT... C.....C...........G
>index1(4CA+18BOS+IL+TX+DC) T....A.A..A.T.T.TAGA..A....A...AA......C...A..........ACG.AT.C.......A..CA.. CG..G..A.....A..CGA..........TA..CG..A...T........A......C......TAAAGG ...C...C....AA..C..T............A........TA....T...G.... ..G...A..CA.C..TCC.G.GAG..T.TG.C..AAA..GG...ATC...G.A.AG. ....TA....CG.............................. .........A.......G....T.............ACT....T....C. .ACT.A.GAA........... C...T.C....T....G.G
>A/DC/WRAIR0300/2010/11/17 T....A.A..A.......G..T.GT.A.A.A.C..G..A...A...G....C.......................T .G..G.G........G..........CG....C.G....A........CAA.A...A..A..T...A..G ...CG..CG...AA.C.........T....C.A..............T...G..C. ....A.....A....TCC.G..AG....T.....A.A..G....AT.C......AG. ..T.TA....CG..............T........A.....- C.T......A.......G....T..T..........AC.....T....C. AACT.A.GA.....C.C.... ........A.G....G...
>A/Boston/DOA52/2011/02/18 ....G....G........G..T.GT.A.A.A.C..G..A...A...G............................T .G..G.G........G......A.........C.G....A........CAA.A......A..T...A..G ...CG..CG...AA.C................A..............T...G..C. ....A.....A....TCC.G..AG....T.....A.A..G....AT........AG. ..T..A....TG..............T.C.T....A...... C.T......A.A.....G....T..T..........AC....GT....C. A.C....GA.....C.C.... ........A.G....G...
>index2(17BOS+SC) ...TG....G........G....G..A.....C..G..A...A..CG................G..........C. .G..G.G........GC...........C.....G....ATAA.....CAAAA.....AA......A... ...C...C....AA......A...GTGG....A...G..........T..AG.... C....G.T..AG...TCC.G..AG....T....GA.A.AG...AAT........AG. T....A....CGA.C...A....A.T......C........- ...GA....A.....A.GTA..T....A.......AAC.G.A.T....C. ..C...CGA.TG........G ...A...AA.G....G...
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April 9th, 2012, 03:55 AM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,950
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Re: H3n2
http://www.ncbi.nlm.nih.gov/pmc/arti...7/?tool=pubmed
In contrast, nucleotide sequences of NS gene of A/KOL/536/2007(H1N1),
A/KOL/596/2007(H1N1), A/KOL/968/2007(H1N1), A/KOL/230/2009(H1N1)
and A/KOL/2086/2009(H1N1) were nearly identical with A/Puerto Rico/8/34,
differing at only few nucleotide positions
5 strains [A/KOL/507/2007(H1N1), A/KOL/536/2007(H1N1), A/KOL/596/2007(H1N1),
A/KOL/611/2007(H1N1) and A/KOL/968/2007(H1N1)] clustered with H3N2 strains in group I,
whereas, 6 strains clustered with pH1N1/2009 strains in sub-group 2
To verify possible cross contamination, BLAST search of HA, NA, M1 and NS1 gene
sequences showed only NS1 having sole identity with A/PR/8/34(H1N1). Thus, a chance
of cross contamination with laboratory PR8 strain was ruled out. Though the frequency
of vaccination in India is very low but since the WHO approved vaccines with PR8 backbone
are used, possibility of reassortment with the vaccine strain can not be ruled out.
Of 166 influenza A positive samples, 55 samples were picked randomly (31 H1N1 and 24 H3N2)
for sequencing of PB1-F2 and NS genes. For confirmation, total PB1 gene segment was sequenced
in 19 strains chosen randomly.
Accession Numbers for nucleotide sequences
Accession numbers of all newly reported sequences obtained for full length non-structural
(NS) gene, full length polymerase basic protein 1 (PB1) gene, PB1-F2 gene and
matrix (M1) gene in this study are:
HQ853495,HQ853549,HM460507,HM460510,HQ154076,HQ154 078,HQ154084,HQ853550
HQ853552,HQ853555,HQ853556,HQ853557,HQ853559,HQ853 567,HQ853571,HQ853573
HQ853574,HQ853579,HQ853586,HQ853589,HQ853591,HQ853 551,HQ853553,HQ853554
HQ853558,HQ853560,HQ853566,HQ853568,HQ853570,HQ853 572,HQ853575,HQ853578
HQ853580,HQ853585,HQ853587,HQ853588,HQ853590,HQ853 592,HQ853595,HM460508
HM460509,HM460511,HQ154075,JF903566,JF903570
------------------------------------------------------------------
I think the PR8 is contamination, although they "ruled that out"
The reassortment is hardly verified with just 2 segments.
How do they know what is H1N1 and what H3N2 without sequencing segments 4 and 6 ?
I think it's important enough to sequence at least one of the reassortants fully in all 8 segments
---------------------------------------------------------------
segment 2: 4 groups, group 3 reassorted ? H3-PB2 in H1N1 sequences
Code:
0001
0237
9754
9973
-codon-position--------------------------------
---Index---------------------------------------ATAT
1 >A/******/index/2009/02/01 .... 0 0 , 0 0 1:>A/******/index/2009/02/01
2 >A/KOL/927/2009,2009/08/,H1N1,HQ154084 GCGC 4 4 , 4 4 2:>A/KOL/927/2009,2009/08/,H1N1,HQ154084
3 >A/KOL/2086/2009,2009//,H1N1,HM460507 GC.C 3 3 , 3 3 3:>A/KOL/2086/2009,2009//,H1N1,HM460507
4 >A/KOL/2449/2009,2009//,H1N1,HM460510 GC.C 3 3 , 3 3 4:>A/KOL/2449/2009,2009//,H1N1,HM460510
5 >A/KOL/2465/2009,2009//,H1N1,HM460511 GC.- 3 3 , 2 2 5:>A/KOL/2465/2009,2009//,H1N1,HM460511
6 >A/KOL/230/2009,2009/08/,H1N1,HQ154078 G..C 2 2 , 2 2 6:>A/KOL/230/2009,2009/08/,H1N1,HQ154078
7 >A/KOL/2482/2009,2009/09/,H1N1,HQ154075 G..- 2 2 , 1 1 7:>A/KOL/2482/2009,2009/09/,H1N1,HQ154075
Code:
0000000000000000000000000000000000011111111111111111111111111222222222222222
1111111222222222333344445556788999900011123345666677788889999000001122222222
1455589111122478001423483490413001304523744577678856926891235012595600112377
1101338367923398065502730143701692361021955638847954470497550108217008010734
-codon-position-------------------------------- 1 1 1 21 1 1 1 2 1 2 22
---Index---------------------------------------ACAGATTTACAGGCTACCCGCAAGGGACGAGACAGGGATTAGTTAAGTCAAGATCACAAATCACAACACGAATTGA
1 >A/Brisbane/59/2007/07/01(H1N1) ............................................................................ 0 0 , 0 0 1:>A/Brisbane/59/2007/07/01(H1N1)
4 >A/KOL/2172/2009,2009//,H1N1,HM460508 G....G.......AC.------------------------------------------------------------ 64 64 , 4 4 4:>A/KOL/2172/2009,2009//,H1N1,HM460508
15 >A/KOL/958/2007,2007/07/,H1N1,HQ853565 G....G..C.....-------------------------------------------------------------- 65 65 , 3 3 15:>A/KOL/958/2007,2007/07/,H1N1,HQ853565
16 >A/KOL/2218/2009,2009//,H1N1,HM460509 G....G..CT....C.------------------------------------------------------------ 65 65 , 5 5 16:>A/KOL/2218/2009,2009//,H1N1,HM460509
17 >A/KOL/1065/2009,2009/08/,H1N1,HQ154077 G....G..CT....-------------------------------------------------------------- 66 66 , 4 4 17:>A/KOL/1065/2009,2009/08/,H1N1,HQ154077
18 >A/KOL/301/2009,2009/08/,H1N1,HQ154079 G....G..CT....-------------------------------------------------------------- 66 66 , 4 4 18:>A/KOL/301/2009,2009/08/,H1N1,HQ154079
19 >A/KOL/449/2009,2009/08/,H1N1,HQ154080 G....G..CT....-------------------------------------------------------------- 66 66 , 4 4 19:>A/KOL/449/2009,2009/08/,H1N1,HQ154080
20 >A/KOL/642/2009,2009/08/,H1N1,HQ154083 G....G..CT....-------------------------------------------------------------- 66 66 , 4 4 20:>A/KOL/642/2009,2009/08/,H1N1,HQ154083
21 >A/KOL/1048/2009,2009/08/,H1N1,HQ154085 G....G..CT....-------------------------------------------------------------- 66 66 , 4 4 21:>A/KOL/1048/2009,2009/08/,H1N1,HQ154085
22 >A/KOL/1182/2009,2009/08/,H1N1,HQ154086 G....G..CT....-------------------------------------------------------------- 66 66 , 4 4 22:>A/KOL/1182/2009,2009/08/,H1N1,HQ154086
23 >A/KOL/1299/2009,2009/08/,H1N1,HQ154088 G....G..CT....-------------------------------------------------------------- 66 66 , 4 4 23:>A/KOL/1299/2009,2009/08/,H1N1,HQ154088
24 >A/KOL/105/2009,2009/08/,H1N1,HQ154090 G....G..CT....-------------------------------------------------------------- 66 66 , 4 4 24:>A/KOL/105/2009,2009/08/,H1N1,HQ154090
25 >A/KOL/536/2009,2009/08/,H1N1,HQ154081 G....G..CTG...-------------------------------------------------------------- 67 67 , 5 5 25:>A/KOL/536/2009,2009/08/,H1N1,HQ154081
26 >A/KOL/1225/2009,2009/08/,H1N1,HQ154087 G....G..CTG...-------------------------------------------------------------- 67 67 , 5 5 26:>A/KOL/1225/2009,2009/08/,H1N1,HQ154087
27 >A/KOL/561/2009,2009/08/,H1N1,HQ154082 G....GC.CT....-------------------------------------------------------------- 67 67 , 5 5 27:>A/KOL/561/2009,2009/08/,H1N1,HQ154082
28 >A/KOL/1421/2009,2009/08/,H1N1,HQ154089 G....GC.CT....-------------------------------------------------------------- 67 67 , 5 5 28:>A/KOL/1421/2009,2009/08/,H1N1,HQ154089
34 >A/KOL/46/2009,2009/07/,H1N1,HQ154076 G....GC.CT........TA......G......GAA..CC...C..A..G.AG....TG.........A....... 21 21 , 21 21 34:>A/KOL/46/2009,2009/07/,H1N1,HQ154076
35 >A/KOL/781/2009,2009/08/,H1N1,HQ853571 G....GC.CT........TA......G......GAA..CC...C..A..G.AG....TG.........A....... 21 21 , 21 21 35:>A/KOL/781/2009,2009/08/,H1N1,HQ853571
30 >A/KOL/526/2007,2007/05/,H1N1,HQ853551 G.CCC.........-------------------------------------------------------------- 66 66 , 4 4 30:>A/KOL/526/2007,2007/05/,H1N1,HQ853551
31 >A/KOL/565/2007,2007/06/,H1N1,HQ853553 G.CCC.........-------------------------------------------------------------- 66 66 , 4 4 31:>A/KOL/565/2007,2007/06/,H1N1,HQ853553
32 >A/KOL/918/2007,2007/07/,H1N1,HQ853557 G.CCC.........C...................AA.GC......G......................A....... 11 11 , 11 11 32:>A/KOL/918/2007,2007/07/,H1N1,HQ853557
33 >A/KOL/929/2007,2007/07/,H1N1,HQ853559 G.............C...................AA.GC......G......................A....... 8 8 , 8 8 33:>A/KOL/929/2007,2007/07/,H1N1,HQ853559
5 >A/KOL/919/2007,2007/07/,H1N1,HQ853558 G.............-------------------------------------------------------------- 63 63 , 1 1 5:>A/KOL/919/2007,2007/07/,H1N1,HQ853558
6 >A/KOL/936/2007,2007/07/,H1N1,HQ853560 G.............-------------------------------------------------------------- 63 63 , 1 1 6:>A/KOL/936/2007,2007/07/,H1N1,HQ853560
7 >A/KOL/937/2007,2007/07/,H1N1,HQ853561 G.............-------------------------------------------------------------- 63 63 , 1 1 7:>A/KOL/937/2007,2007/07/,H1N1,HQ853561
8 >A/KOL/943/2007,2007/07/,H1N1,HQ853562 G.............-------------------------------------------------------------- 63 63 , 1 1 8:>A/KOL/943/2007,2007/07/,H1N1,HQ853562
9 >A/KOL/951/2007,2007/07/,H1N1,HQ853563 G.............-------------------------------------------------------------- 63 63 , 1 1 9:>A/KOL/951/2007,2007/07/,H1N1,HQ853563
10 >A/KOL/956/2007,2007/07/,H1N1,HQ853564 G.............-------------------------------------------------------------- 63 63 , 1 1 10:>A/KOL/956/2007,2007/07/,H1N1,HQ853564
11 >A/KOL/964/2007,2007/07/,H1N1,HQ853566 G.............-------------------------------------------------------------- 63 63 , 1 1 11:>A/KOL/964/2007,2007/07/,H1N1,HQ853566
12 >A/KOL/975/2007,2007/07/,H1N1,HQ853568 G.............-------------------------------------------------------------- 63 63 , 1 1 12:>A/KOL/975/2007,2007/07/,H1N1,HQ853568
13 >A/KOL/985/2007,2007/07/,H1N1,HQ853569 G.............-------------------------------------------------------------- 63 63 , 1 1 13:>A/KOL/985/2007,2007/07/,H1N1,HQ853569
14 >A/KOL/990/2007,2007/07/,H1N1,HQ853570 G.............-------------------------------------------------------------- 63 63 , 1 1 14:>A/KOL/990/2007,2007/07/,H1N1,HQ853570
29 >A/KOL/578/2007,2007/06/,H1N1,HQ853554 GT....CG...A..-------------------------------------------------------------- 67 67 , 5 5 29:>A/KOL/578/2007,2007/06/,H1N1,HQ853554
2 >A/Kansas/UR06-0068/2007(H1N1) G.....CG...A....T...A..AA..TA..CT.AA..C.........A.C...T.....C....GT.A.GG..AG 26 26 , 26 26 2:>A/Kansas/UR06-0068/2007(H1N1)
3 >A/New Caledonia/20/1999/// GT....CG...AA..GTT...CG.AA...GACT.AAA.C.GAC.G..GA.C..C.GT..G.TGTG.TCAA..CCAG 44 44 , 44 44 3:>A/New Caledonia/20/1999///
---Index---------------------------------------ACAGATTTACAGGCTACCCGCAAGGGACGAGACAGGGATTAGTTAAGTCAAGATCACAAATCACAACACGAATTGA
-codon-position-------------------------------- 1 1 1 21 1 1 1 2 1 2 22
0000000000000000000000000000000000011111111111111111111111111222222222222222
1111111222222222333344445556788999900011123345666677788889999000001122222222
1455589111122478001423483490413001304523744577678856926891235012595600112377
1101338367923398065502730143701692361021955638847954470497550108217008010734
Code:
000000000000000011111111112222
001111111133469902357778890122
290024556969051855660253850903
890531560527525111567696737304
-codon-position-------------------------------1 1 2 1 21 1 1 11 12
---Index--------------------------------------CAAACCAGAAATACCACGTTGCGGTGGGCA
1 >Index/USA-2007 .............................. 0 0 , 0 0 1:>Index/USA-2007
2 >2007/02/06,14278,AUS,A/Brisbane/10/07 A......A...C..T...C........A.. 6 6 , 6 6 2:>2007/02/06,14278,AUS,A/Brisbane/10/07
3 >Index/Brisbane-like/2007 .............T..............A. 2 2 , 2 2 3:>Index/Brisbane-like/2007
5 >Index/2009/Egypt/Iowa ...G..G..G..G..G.A.CAAA...A.AG 13 13 , 13 13 5:>Index/2009/Egypt/Iowa
6 >A/KOL/507/2007,2007/05/,H1N1,HQ853550 AG..A.....G.............C..A.. 6 6 , 6 6 6:>A/KOL/507/2007,2007/05/,H1N1,HQ853550
7 >A/KOL/611/2007,2007/06/,H1N1,HQ853556 AG........G.............C..A.. 5 5 , 5 5 7:>A/KOL/611/2007,2007/06/,H1N1,HQ853556
9 >A/KOL/596/2007,2007/06/,H1N1,HQ853555 AG......G...............C..A.. 5 5 , 5 5 9:>A/KOL/596/2007,2007/06/,H1N1,HQ853555
8 >A/KOL/536/2007,2007/06/,H1N1,HQ853552 A.C.......G.............C..A.. 5 5 , 5 5 8:>A/KOL/536/2007,2007/06/,H1N1,HQ853552
10 >A/KOL/968/2007,2007/07/,H1N1,HQ853567 A....TG.................C..A.. 5 5 , 5 5 10:>A/KOL/968/2007,2007/07/,H1N1,HQ853567
4 >Index/Perth-like/2009 .....TG........GT....A.A.T..A. 8 8 , 8 8 4:>Index/Perth-like/2009
Code:
00000000000000000000001111111111111111111111122222
01111112333344445677990001122245566677778889900002
60445693346904567503785690815870636700250343901250
05175854883057936125211457281199652147690655576520
-codon-position-------------------------------- 2 2 1 12 11 1
---Index---------------------------------------AACTAGAACGATATCTGCCGCACAGTTAGATTTATCCGCGTGGACGCAGC
18 >A/KOL/2312/2009,2009/09/,H3N2,HQ853589 .G..G.G.....GC.......G.C....A..CC....AAA.....AA.AA 17 17 , 17 17 18:>A/KOL/2312/2009,2009/09/,H3N2,HQ853589
23 >A/KOL/2404/2009,2009/09/,H3N2,HQ853591 .G..G.G.....GC.......G.C....A..CC....AAA.....AA.AA 17 17 , 17 17 23:>A/KOL/2404/2009,2009/09/,H3N2,HQ853591
19 >A/KOL/779/2009,2009/08/,H3N2,HQ853593 -G..G.G....--------------------------------------- 96 43 , 3 3 19:>A/KOL/779/2009,2009/08/,H3N2,HQ853593
20 >A/KOL/857/2009,2009/08/,H3N2,HQ853594 -G..G.G....--------------------------------------- 96 43 , 3 3 20:>A/KOL/857/2009,2009/08/,H3N2,HQ853594
21 >A/KOL/402/2009,2009/08/,H3N2,HQ853595 -G..G.G....--------------------------------------- 96 43 , 3 3 21:>A/KOL/402/2009,2009/08/,H3N2,HQ853595
22 >A/KOL/2321/2009,2009/09/,H3N2,HQ853590 -G..G.G....--------------------------------------- 96 43 , 3 3 22:>A/KOL/2321/2009,2009/09/,H3N2,HQ853590
24 >A/KOL/2309/2009,2009/09/,H3N2,HQ853588 -G..G.G...C--------------------------------------- 97 44 , 4 4 24:>A/KOL/2309/2009,2009/09/,H3N2,HQ853588
5 >Index/2009/Egypt/Iowa .G..G.G.....G........G......A...C....AAA.....A...A 13 12 , 13 12 5:>Index/2009/Egypt/Iowa
25 >A/KOL/1691/2008,2008/06/,H3N2,HQ853582 -...G.....C--------------------------------------- 95 42 , 2 2 25:>A/KOL/1691/2008,2008/06/,H3N2,HQ853582
26 >A/KOL/1708/2008,2008/07/,H3N2,HQ853583 -...G......--------------------------------------- 95 41 , 2 1 26:>A/KOL/1708/2008,2008/07/,H3N2,HQ853583
32 >A/KOL/1687/2008,2008/06/,H3N2,HQ853581 -.T.G......--------------------------------------- 96 42 , 3 2 32:>A/KOL/1687/2008,2008/06/,H3N2,HQ853581
33 >A/KOL/1525/2009,2009/08/,H3N2,HQ853592 -...G.G....--------------------------------------- 96 42 , 3 2 33:>A/KOL/1525/2009,2009/08/,H3N2,HQ853592
15 >A/KOL/994/2007,2007/07/,H3N2,HQ853577 -...G......--------------------------------------- 94 41 , 1 1 15:>A/KOL/994/2007,2007/07/,H3N2,HQ853577
16 >A/KOL/600/2007,2007/06/,H3N2,HQ853572 -...G..G...--------------------------------------- 95 42 , 2 2 16:>A/KOL/600/2007,2007/06/,H3N2,HQ853572
17 >A/KOL/989/2007,2007/07/,H3N2,HQ853578 -...G..G...--------------------------------------- 95 42 , 2 2 17:>A/KOL/989/2007,2007/07/,H3N2,HQ853578
14 >A/KOL/1810/2008,2008/07/,H3N2,HQ853586 ....G.......G........GT...............A..A.......A 8 7 , 8 7 14:>A/KOL/1810/2008,2008/07/,H3N2,HQ853586
4 >Index/Perth-like/2009 ..T.G................GT...............A..A.......A 8 7 , 8 7 4:>Index/Perth-like/2009
10 >A/KOL/1537/2008,2008/05/,H3N2,HQ853579 ..........C....................................... 1 1 , 1 1 10:>A/KOL/1537/2008,2008/05/,H3N2,HQ853579
11 >A/KOL/1822/2008,2008/07/,H3N2,HQ853587 -.........C--------------------------------------- 94 41 , 1 1 11:>A/KOL/1822/2008,2008/07/,H3N2,HQ853587
27 >A/KOL/595/2007,2007/06/,H3N2,HQ853576 -..C.......--------------------------------------- 94 41 , 1 1 27:>A/KOL/595/2007,2007/06/,H3N2,HQ853576
28 >A/KOL/1075/2007,2007/08/,H3N2,HQ853575 -..C.......--------------------------------------- 94 41 , 1 1 28:>A/KOL/1075/2007,2007/08/,H3N2,HQ853575
12 >A/KOL/1690/2008,2008/06/,H3N2,HQ853580 -..........--------------------------------------- 93 40 , 0 0 12:>A/KOL/1690/2008,2008/06/,H3N2,HQ853580
13 >A/KOL/1762/2008,2008/07/,H3N2,HQ853585 -..........--------------------------------------- 93 40 , 0 0 13:>A/KOL/1762/2008,2008/07/,H3N2,HQ853585
1 >Index/USA-2007 .................................................. 0 0 , 0 0 1:>Index/USA-2007
2 >2007/02/06,14278,AUS,A/Brisbane/10/07 .................................................. 6 0 , 6 0 2:>2007/02/06,14278,AUS,A/Brisbane/10/07
3 >Index/Brisbane-like/2007 .................................................A 2 1 , 2 1 3:>Index/Brisbane-like/2007
31 >A/KOL/524/2007,2007/05/,H3N2,HQ853573 ....G......C..T...TAT.....C.AG...G..T...C.AGA..C.. 16 16 , 16 16 31:>A/KOL/524/2007,2007/05/,H3N2,HQ853573
30 >A/KOL/960/2007,2007/07/,H3N2,HQ853574 .....A.....C..T...TAT.....C.AG...G..T...C.AGA..C.. 16 16 , 16 16 30:>A/KOL/960/2007,2007/07/,H3N2,HQ853574
29 >A/KOL/1728/2008,2008/07/,H3N2,HQ853584 -....A.....--------------------------------------- 94 41 , 1 1 29:>A/KOL/1728/2008,2008/07/,H3N2,HQ853584
6 >A/Wisconsin/67/2005/08/ ..............T...T.T........G...G..T.....AG...C.. 15 9 , 15 9 6:>A/Wisconsin/67/2005/08/
7 >A/Index_Fujian/2002(H3N2) C......GTA....TCATT.T...AC.G.GA..GCTT.....AG...C.. 22 22 , 22 22 7:>A/Index_Fujian/2002(H3N2)
8 >A/Index_Fujian/USA/2003(H3N2) C......GTA....TCATT.T...AC.G.GA..GCTT.....AG...C.. 25 22 , 25 22 8:>A/Index_Fujian/USA/2003(H3N2)
9 >A/Index_Fujian_reass./2003/06(H3N2) C....A.GTA....TCA.T.T...AC.G.GA..GCTT...C.AG...... 62 22 , 62 22 9:>A/Index_Fujian_reass./2003/06(H3N2)
---Index---------------------------------------AACTAGAACGATATCTGCCGCACAGTTAGATTTATCCGCGTGGACGCAGC
-codon-position-------------------------------- 2 2 1 12 11 1
00000000000000000000001111111111111111111111122222
01111112333344445677990001122245566677778889900002
60445693346904567503785690815870636700250343901250
05175854883057936125211457281199652147690655576520
--------------------------------------------------------------
segment 8:
Code:
0000000000000000000000000000000000000000000000
0000000001111122222333334444444566667777777788
0555677890146701268234682223379134570134455914
6089505835438190973707623682978538990750769290
-codon-position-------------------------------- 21221 1 2 2 1 1 2 1 2 1 2 211 2
---Index---------------------------------------TAAACGAGCGAGATAACCGAAGAAGGAGCATTGAACGAGCGTGAGG
1 >A/Brisbane/59/2007/07/01(H1N1) .............................................. 0 0 , 0 0 1:>A/Brisbane/59/2007/07/01(H1N1)
2 >A/Kansas/UR06-0068/2007(H1N1) ....T.....G....G........A......A....A......... 6 6 , 6 6 2:>A/Kansas/UR06-0068/2007(H1N1)
3 >A/New Caledonia/20/1999/// ....T...A....C..T.AG..G.......C..C.TA......G.A 13 13 , 13 13 3:>A/New Caledonia/20/1999///
18 >A/KOL/46/2009,2009/07/,H1N1,HQ853516 ............................T................. 1 1 , 1 1 18:>A/KOL/46/2009,2009/07/,H1N1,HQ853516
19 >A/KOL/781/2009,2009/08/,H1N1,HQ853518 ............................T................. 1 1 , 1 1 19:>A/KOL/781/2009,2009/08/,H1N1,HQ853518
20 >A/KOL/927/2009,2009/08/,H1N1,HQ853519 ............................T................. 1 1 , 1 1 20:>A/KOL/927/2009,2009/08/,H1N1,HQ853519
4 >A/KOL/507/2007,2007/05/,H1N1,HQ853495 ....T...............................A......... 2 2 , 2 2 4:>A/KOL/507/2007,2007/05/,H1N1,HQ853495
5 >A/KOL/526/2007,2007/05/,H1N1,HQ853496 ..C.T...............................A..T...... 4 4 , 4 4 5:>A/KOL/526/2007,2007/05/,H1N1,HQ853496
32 >A/KOL/565/2007,2007/06/,H1N1,HQ853498 .TG.T..A............................A......G.. 6 6 , 6 6 32:>A/KOL/565/2007,2007/06/,H1N1,HQ853498
33 >A/KOL/578/2007,2007/06/,H1N1,HQ853499 ....T.........G......A..........A....G...C.... 6 6 , 6 6 33:>A/KOL/578/2007,2007/06/,H1N1,HQ853499
21 >A/KOL/611/2007,2007/06/,H1N1,HQ853501 ....T....................A.................... 2 2 , 2 2 21:>A/KOL/611/2007,2007/06/,H1N1,HQ853501
22 >A/KOL/2172/2009,2009/09/,H1N1,HQ853520 ....T......................T.................. 2 2 , 2 2 22:>A/KOL/2172/2009,2009/09/,H1N1,HQ853520
23 >A/KOL/990/2007,2007/07/,H1N1,HQ853515 ....T.....................C...........A....... 3 3 , 3 3 23:>A/KOL/990/2007,2007/07/,H1N1,HQ853515
6 >A/KOL/943/2007,2007/07/,H1N1,HQ853507 ..C.T.......................T................. 3 3 , 3 3 6:>A/KOL/943/2007,2007/07/,H1N1,HQ853507
7 >A/KOL/918/2007,2007/07/,H1N1,HQ853502 ....T......T................T................. 3 3 , 3 3 7:>A/KOL/918/2007,2007/07/,H1N1,HQ853502
8 >A/KOL/919/2007,2007/07/,H1N1,HQ853503 ....T......T................T................. 3 3 , 3 3 8:>A/KOL/919/2007,2007/07/,H1N1,HQ853503
9 >A/KOL/936/2007,2007/07/,H1N1,HQ853505 ....T.......................T...............A. 3 3 , 3 3 9:>A/KOL/936/2007,2007/07/,H1N1,HQ853505
10 >A/KOL/937/2007,2007/07/,H1N1,HQ853506 C...T.......................T................. 3 3 , 3 3 10:>A/KOL/937/2007,2007/07/,H1N1,HQ853506
11 >A/KOL/956/2007,2007/07/,H1N1,HQ853509 C...T.......................T................. 3 3 , 3 3 11:>A/KOL/956/2007,2007/07/,H1N1,HQ853509
12 >A/KOL/951/2007,2007/07/,H1N1,HQ853508 C...TA......................T................. 4 4 , 4 4 12:>A/KOL/951/2007,2007/07/,H1N1,HQ853508
13 >A/KOL/985/2007,2007/07/,H1N1,HQ853514 C...T.......G...............T................. 4 4 , 4 4 13:>A/KOL/985/2007,2007/07/,H1N1,HQ853514
14 >A/KOL/2218/2009,2009/09/,H1N1,HQ853521 C...T............T..........T................. 4 4 , 4 4 14:>A/KOL/2218/2009,2009/09/,H1N1,HQ853521
15 >A/KOL/2218/2009,2009//,H1N1,HM460502 C...T............T..........T.......---------- 14 14 , 4 4 15:>A/KOL/2218/2009,2009//,H1N1,HM460502
31 >A/KOL/975/2007,2007/07/,H1N1,HQ853513 C...T...............C.......T...........A..... 5 5 , 5 5 31:>A/KOL/975/2007,2007/07/,H1N1,HQ853513
16 >A/KOL/958/2007,2007/07/,H1N1,HQ853510 ....T.......................T............C.... 3 3 , 3 3 16:>A/KOL/958/2007,2007/07/,H1N1,HQ853510
17 >A/KOL/964/2007,2007/07/,H1N1,HQ853511 ....T.......................T.....C........... 3 3 , 3 3 17:>A/KOL/964/2007,2007/07/,H1N1,HQ853511
24 >A/KOL/2172/2009,2009//,H1N1,HM460501 ....T.G..A..................T.......---------- 14 14 , 4 4 24:>A/KOL/2172/2009,2009//,H1N1,HM460501
25 >A/KOL/2449/2009,2009//,H1N1,HM460503 ....T.G..A..................T.......---------- 14 14 , 4 4 25:>A/KOL/2449/2009,2009//,H1N1,HM460503
26 >A/KOL/2465/2009,2009//,H1N1,HM460504 ....T.G..A.............G....T.......---------- 15 15 , 5 5 26:>A/KOL/2465/2009,2009//,H1N1,HM460504
27 >A/KOL/2465/2009,2009/09/,H1N1,HQ853524 ....T.G..A.............G....T............C.... 6 6 , 6 6 27:>A/KOL/2465/2009,2009/09/,H1N1,HQ853524
28 >A/KOL/2449/2009,2009/09/,H1N1,HQ853523 ....T.G..A..................T............CT... 6 6 , 6 6 28:>A/KOL/2449/2009,2009/09/,H1N1,HQ853523
29 >A/KOL/929/2007,2007/07/,H1N1,HQ853504 ..TTT.......................T................. 4 4 , 4 4 29:>A/KOL/929/2007,2007/07/,H1N1,HQ853504
30 >A/KOL/2482/2009,2009/09/,H1N1,HQ853525 ....T..................G....TG................ 4 4 , 4 4 30:>A/KOL/2482/2009,2009/09/,H1N1,HQ853525
---Index---------------------------------------TAAACGAGCGAGATAACCGAAGAAGGAGCATTGAACGAGCGTGAGG
-codon-position-------------------------------- 21221 1 2 2 1 1 2 1 2 1 2 211 2
0000000000000000000000000000000000000000000000
0000000001111122222333334444444566667777777788
0555677890146701268234682223379134570134455914
6089505835438190973707623682978538990750769290
Code:
00000000000000
01113444677777
76788015603335
93866463191581
-codon-position--------------------------------111 222 112 1
---Index---------------------------------------CAGGTGACGATACC
1 >Index/USA-2007 .............. 0 0 , 0 0 1:>Index/USA-2007
3 >2007/02/06,14278,AUS,A/Brisbane/10/07 .............. 1 0 , 1 0 3:>2007/02/06,14278,AUS,A/Brisbane/10/07
4 >Index/Brisbane-like/2007 .............. 0 0 , 0 0 4:>Index/Brisbane-like/2007
5 >Index/Perth-like/2009 .............. 2 0 , 2 0 5:>Index/Perth-like/2009
10 >A/KOL/595/2007,2007/06/,H3N2,HQ853528 .G..........T. 2 2 , 2 2 10:>A/KOL/595/2007,2007/06/,H3N2,HQ853528
11 >A/KOL/1075/2007,2007/08/,H3N2,HQ853532 .G..........T. 2 2 , 2 2 11:>A/KOL/1075/2007,2007/08/,H3N2,HQ853532
12 >A/KOL/1728/2008,2008/07/,H3N2,HQ853538 .G..........T. 2 2 , 2 2 12:>A/KOL/1728/2008,2008/07/,H3N2,HQ853538
13 >A/KOL/1691/2008,2008/06/,H3N2,HQ853536 .G.....T....T. 3 3 , 3 3 13:>A/KOL/1691/2008,2008/06/,H3N2,HQ853536
14 >A/KOL/1822/2008,2008/07/,H3N2,HQ853540 .G.....T....T. 3 3 , 3 3 14:>A/KOL/1822/2008,2008/07/,H3N2,HQ853540
15 >A/KOL/1537/2008,2008/05/,H3N2,HQ853533 .G.....T...... 2 2 , 2 2 15:>A/KOL/1537/2008,2008/05/,H3N2,HQ853533
16 >A/KOL/1687/2008,2008/06/,H3N2,HQ853534 .G.....T....T. 4 3 , 4 3 16:>A/KOL/1687/2008,2008/06/,H3N2,HQ853534
17 >A/KOL/1690/2008,2008/06/,H3N2,HQ853535 .G...AGT...G.. 5 5 , 5 5 17:>A/KOL/1690/2008,2008/06/,H3N2,HQ853535
18 >A/KOL/1525/2009,2009/08/,H3N2,HQ853545 .....AG....G.. 3 3 , 3 3 18:>A/KOL/1525/2009,2009/08/,H3N2,HQ853545
19 >A/KOL/402/2009,2009/08/,H3N2,HQ853542 .....AG....G.. 3 3 , 3 3 19:>A/KOL/402/2009,2009/08/,H3N2,HQ853542
20 >A/KOL/779/2009,2009/08/,H3N2,HQ853543 .....AG....G.. 3 3 , 3 3 20:>A/KOL/779/2009,2009/08/,H3N2,HQ853543
21 >A/KOL/857/2009,2009/08/,H3N2,HQ853544 .....AG....G.. 3 3 , 3 3 21:>A/KOL/857/2009,2009/08/,H3N2,HQ853544
22 >A/KOL/2309/2009,2009/09/,H3N2,HQ853546 .....AG....G.. 3 3 , 3 3 22:>A/KOL/2309/2009,2009/09/,H3N2,HQ853546
23 >A/KOL/2312/2009,2009/09/,H3N2,HQ853547 .....AG....G.. 3 3 , 3 3 23:>A/KOL/2312/2009,2009/09/,H3N2,HQ853547
24 >A/KOL/2321/2009,2009/09/,H3N2,HQ853548 .....AG....G.. 3 3 , 3 3 24:>A/KOL/2321/2009,2009/09/,H3N2,HQ853548
25 >A/KOL/2404/2009,2009/09/,H3N2,HQ853549 .....AG....G.. 3 3 , 3 3 25:>A/KOL/2404/2009,2009/09/,H3N2,HQ853549
6 >Index/2009/Egypt/Iowa .....AG....G.. 3 3 , 3 3 6:>Index/2009/Egypt/Iowa
26 >A/KOL/1708/2008,2008/07/,H3N2,HQ853537 TG............ 3 2 , 3 2 26:>A/KOL/1708/2008,2008/07/,H3N2,HQ853537
27 >A/KOL/1762/2008,2008/07/,H3N2,HQ853539 T...C........T 3 3 , 3 3 27:>A/KOL/1762/2008,2008/07/,H3N2,HQ853539
28 >A/KOL/1810/2008,2008/07/,H3N2,HQ853541 ....C......... 3 1 , 3 1 28:>A/KOL/1810/2008,2008/07/,H3N2,HQ853541
29 >A/KOL/524/2007,2007/05/,H3N2,HQ853527 ....C...AGC... 4 4 , 4 4 29:>A/KOL/524/2007,2007/05/,H3N2,HQ853527
30 >A/KOL/960/2007,2007/07/,H3N2,HQ853529 ....C...AGC... 4 4 , 4 4 30:>A/KOL/960/2007,2007/07/,H3N2,HQ853529
31 >A/KOL/989/2007,2007/07/,H3N2,HQ853530 ....C...AGC... 4 4 , 4 4 31:>A/KOL/989/2007,2007/07/,H3N2,HQ853530
32 >A/KOL/600/2007,2007/06/,H3N2,HQ853526 ..AA...TAGC... 6 6 , 6 6 32:>A/KOL/600/2007,2007/06/,H3N2,HQ853526
33 >A/KOL/994/2007,2007/07/,H3N2,HQ853531 ..AA...TAGC... 6 6 , 6 6 33:>A/KOL/994/2007,2007/07/,H3N2,HQ853531
7 >A/Index_Fujian/2002(H3N2) ........AGC... 3 3 , 3 3 7:>A/Index_Fujian/2002(H3N2)
8 >A/Index_Fujian/USA/2003(H3N2) ........AGC... 3 3 , 3 3 8:>A/Index_Fujian/USA/2003(H3N2)
9 >A/Index_Fujian_reass./2003/06(H3N2) ........AGCG.T 18 5 , 18 5 9:>A/Index_Fujian_reass./2003/06(H3N2)
2 >A/Wisconsin/67/2005/08/ ........AGC... 4 3 , 4 3 2:>A/Wisconsin/67/2005/08/
---Index---------------------------------------CAGGTGACGATACC
-codon-position--------------------------------111 222 112 1
00000000000000
01113444677777
76788015603335
93866463191581
Code:
00000000000000000000000000000000000000000000000000000000000
00000001111111112222222333333333344444455555556666667777888
00366882334456790145679000113477711123313346991466782238023
79634143184703468038431378781028904906822799493301007974338
-codon-position--------------------------------1 1 2 1 11 122 11 12 2 1 21 2 211 1121 21211
---Index---------------------------------------TCCGTGTGGACTTGCGAGTTCTGCTTTGGTGGATCGGCAAGGAAAGACGAAATGAACGA
8 >A/Brevig Mission/1/1918,1918// ........................................................... 0 0 , 0 0 8:>A/Brevig Mission/1/1918,1918//
6 >A/Index/early human C.TAGA......C.....G...A......C....T..T.........A..GGC...... 15 15 , 15 15 6:>A/Index/early human
1 >A/KOL/536/2007,2007/06/,H1N1,HQ853497 CATAGA.A.G....A..AGGT.A..C.A.C....T..TGC.A.CT..AAGGGCA.T..G 33 33 , 33 33 1:>A/KOL/536/2007,2007/06/,H1N1,HQ853497
2 >A/KOL/596/2007,2007/06/,H1N1,HQ853500 CATAGA.A.G....A..AGGTCAA.C.A.C.A..T..TGC.A.....AAGGGCAGT.A. 35 35 , 35 35 2:>A/KOL/596/2007,2007/06/,H1N1,HQ853500
3 >A/KOL/968/2007,2007/07/,H1N1,HQ853512 CATAGA.A.G....A..AGGTCAA.C.A.C.A..T..TGC.A.....AAGGGCAGT.A. 35 35 , 35 35 3:>A/KOL/968/2007,2007/07/,H1N1,HQ853512
4 >A/KOL/230/2009,2009/08/,H1N1,HQ853517 CATAGA.A.G....A..AGGTCAA.C.A.C.A..T..TGC.A.....AAGGGCAGT.A. 35 35 , 35 35 4:>A/KOL/230/2009,2009/08/,H1N1,HQ853517
5 >A/KOL/2086/2009,2009/09/,H1N1,HQ853522 CATAGA.A.G....A..AGGTCAA.C.A.C.A..T..TGC.A.....AAGGGCAGT.A. 35 35 , 35 35 5:>A/KOL/2086/2009,2009/09/,H1N1,HQ853522
11 >A/Puerto Rico/8/1934,1934// CATAGA.A.G....A..AGGTCAA.C.A.C.A..T..TGC.A.....AAGGGCAGT.A. 35 35 , 35 35 11:>A/Puerto Rico/8/1934,1934//
12 >A/Puerto Rico/8/1934,1934// CATAGA.A.GT.CAA..AGGT.A..C.A.C....T..TGC.A.....AAGGGCA.T..G 34 34 , 34 34 12:>A/Puerto Rico/8/1934,1934//
22 >A/Melbourne/1/1946,1946// C.TAGA......C..AG.GG..A.C...ACA...TAAT.GA....ACA..GGC....A. 28 28 , 28 28 22:>A/Melbourne/1/1946,1946//
20 >A/Phila/1935,1935// C.TAGA.AA...C.A...GG..A...G..C..G.T..TG.A......A.GGGC..GA.- 27 27 , 26 26 20:>A/Phila/1935,1935//
17 >A/Puerto Rico/8-1/1934,1934// ..TAGA.A.G..C.A..AGGT.A..C.A.C....T..TGC.A.....AAGGGCA.T..G 30 30 , 30 30 17:>A/Puerto Rico/8-1/1934,1934//
7 >A/Puerto Rico/8-1/1934(H1N1) ..TAGA.A.G..C.A..AGGT.A..C.A.C....T..TGC.A.....AAGGGCA.T..G 30 30 , 30 30 7:>A/Puerto Rico/8-1/1934(H1N1)
10 >A/Puerto Rico/8/1934,1934// CATAGA.A.G.CC.A..AGGT.A..C.A.C...AT..TGC.AG....AAGGGCA.T..G 35 35 , 35 35 10:>A/Puerto Rico/8/1934,1934//
13 >A/Puerto Rico/8/34/Mount Sinai,1934// CATAGA.A.G.CC.A..AGGT.A..C.A.C....T..TGC.AG....AAGGGCA.T... 33 33 , 33 33 13:>A/Puerto Rico/8/34/Mount Sinai,1934//
15 >A/Puerto Rico/8/1934,1934// CATAGA.A.GTCC.A..AGGT.A..C.A.C....T..TGC.AG....AAGGGCA.T..G 35 35 , 35 35 15:>A/Puerto Rico/8/1934,1934//
11 >A/Puerto Rico/8/1934,1934// CATAGA.A.G....A..AGGTCAA.C.A.C.A..T..TGC.A.....AAGGGCAGT.A. 35 35 , 35 35 11:>A/Puerto Rico/8/1934,1934//
23 >A/Leningrad/1954/1,1954// CATAGA.A.GT.CAA..AGGTCA..C.A.C....T..TGC.A.....AAGGGCA.T..G 35 35 , 35 35 23:>A/Leningrad/1954/1,1954//
14 >A/Puerto Rico/8/1934,1934// CATAGA.A.GT.CAA..AGGT.A..C.A.C....T..TGC.A.....AAGGGCA.T..G 34 34 , 34 34 14:>A/Puerto Rico/8/1934,1934//
16 >A/Puerto Rico/8-SV14/1934,1934// CATAGACA.GT.CAA..AGGT.A..C.A.C....T..TGC.A.....AAGGGCA.T..G 35 35 , 35 35 16:>A/Puerto Rico/8-SV14/1934,1934//
18 >A/Puerto Rico/8-WG/1934,1934// CATAGACA.GT.CAA..AGGT.A..C.A.C....T..TGC.A.....AAGGGCA.T..G 35 35 , 35 35 18:>A/Puerto Rico/8-WG/1934,1934//
19 >A/Alaska/1935,1935// CATAGA.A.GT.CAA..AGGT.A..C.A.C....T..TGC.A.....AAGGGCA.T... 33 33 , 33 33 19:>A/Alaska/1935,1935//
21 >A/Henry/1936,1936// CATAGA.A.G..C.A...GG..A..C.A.C....T..TG........A.GGGCAGT... 27 27 , 27 27 21:>A/Henry/1936,1936//
---Index---------------------------------------TCCGTGTGGACTTGCGAGTTCTGCTTTGGTGGATCGGCAAGGAAAGACGAAATGAACGA
-codon-position--------------------------------1 1 2 1 11 122 11 12 2 1 21 2 211 1121 21211
00000000000000000000000000000000000000000000000000000000000
00000001111111112222222333333333344444455555556666667777888
00366882334456790145679000113477711123313346991466782238023
79634143184703468038431378781028904906822799493301007974338
---------------------------------------------------------------
Pune India, 10 flu-outbreaks 1978-1990, 10 in Jun-Sep,3 in Mar-May,1 in Nov-Feb,2 in Feb-Mar
------------------------------------------------------------------
A/KOL/968/2007/07(H1N1) segment 2 (H3N2-like)
has C141T and A155G just as Perth-like/2009
but also C28A,T1887C,G2193A just like the other KOL-H1N1 sequences.
Looks like another "dirty-chromatogram"-pseudo recombination,presumably they
had sequenced other Perth-like H3N2s before with that machine/procedure.
A/KOL/1762/2008/07/(H3N2) and A/KOL/1819/2008/07(H3N2) had T386C in segment 8,
like 3 of the other KOL-2007 sequences, which however were the old Wisconsin/2005 strain
while the 2 former were the new 2007-strain.
This could be another "dirty-chromatogram"-pseudo recombination, but less clear with
just one mutation.
A/KOL/1690/2008/06/(H3N2) has A163G and C453T in segment 8 like 4 of the other KOL
non-Egypt/Iowa sequences from summer 2008, but then it also has the 3 Egypt/Iowa
mutations G404A,A416G,A735G, so this looks like another clear "dirty chromatogram"-
pseudo-recombination
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May 16th, 2012, 07:33 AM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,950
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Re: H3n2
>12000 H3N2-HA at genbank. Lots from Malaysia since 1995 yesterday.
trying to detect, where/when those mutations that are established today
emerged first :
Code:
monthly appearances of current ("Egypt/Iowa") H3N2-HA mutations in quantity > 0.1% of all mutations
program 32s4db2.bas
CTCCCGCGCAAGATGGACAGTGGACGGAAAGAATGGGTTTTGCCCTTAGATTCGGTCGGTGGGAAAGCGGGCGTCCCAACGGAAGCTTGCCATCAACACAACAGTGGCGGGAAGCTGGGCGTTTGGGGATTATCCCTGCCGTATCCTTGCTCATAACAGCGGGCCAAACCCTCCATCGGAAGGACGACCATTCTTCGGGGGACCCTAGGTCTATATACGCTCGG
00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000111111111111111111111111111111111111111111111111111111111111111
00000000000000111111111111112222222222222223333333344444444444444444444444445555555555555555555666666666666666666777777777777777777777888888888888889999999999999000000001111111111222222222223333333334444444445555555555566666
03344445567999002233445789990011333467888990122599911112234455555677778888990111222222333366677001111222345666788001122222356777888999011233567777782233455666689013458892346788999000133357891233466780023477880124566778923467
91313782408369580189476432565989235643125269879703903780554701278725892349294468012347167845779460358356582089825252412467292278069128419813572356914706447038973519467928097389478059203945404058725463681636450278706587607280
TCATTCTAATGTGCAAGAGACATGTATGGGAGGAAAAGGCCAATACAGACAAAAACAAACAACTCTATAAATACTTTCCTAACTTACCATACATGGTGAGCTTTCAAAAAAGGATAAAAACCCAAATTGCCCATTACAAGACGCAACAAACTGCGCTGATAAAATGGGTAGCATGCTATGGACGTACTTGACTCCTAAAAAGTTTCGAACTCGAGAGTATCTAA
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
1968/01 00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
1980/06 00000000000000000000000000000000000000000000000000101111110000010001011011001100010001000000001001100001000010000010000000011101000000101100001100110000000000000000000000000000000000000000000000000000000000000000000000000000
1981/02 00000000000000000000000000000000000000000000000110101111110000011001011011001100010001000000001001100001000010000010000000111101000001100000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
1982/06 10011101010000101011000111101100011010111011000010101101110000010001111011000100010001000000111001100001000010001010000000011101001100101100001100110000001011010001001000001001100001000000100100110110110010101000001100100011
1985/01 10011101110000101011000111101100011010111011000110101101110000010001011011011110010001010000111001100001000010001010000000011101101100101100001100111001001011010001001000001001101001000000100101110110110010101000001100100011
1989/12 00011101110100101011110111111100011010111111001110101101110000010001011011011000010111010000111001100001000011001010000000011101101110101110011100111001101011111001001000001001101001000000100100110110110011101001001100100011
1990/01 00011101110100101011110111111100011010111111001110101100110000010001011011011100010111010000111001100001000011001010000000011101101110101110011100111001101011111001001000001001101001000000100100110110110011101001001100100011
1991/11 10111101110000101011010111101100011010111111001110111101110000110001011111111100011111010000111001100000000011101000000000011111101110101110111100111100101011111001001000001001101001000000100111110110110011101001001101100011
1991/12 10111101110000101011010111101100011010111111001110111101110000110001011111111100011111010000111001100000000011101000000000011111101110101110111100111100101011111001001000001001101001000000100111110110110011101001001101100011
1992/01 10111101110010101011010111101100011010111111001110111101110000110001011111111100011111010000111001100000000011101000000000011111101110101110111100111101101011111001001000001001101001000000100111110110110011101001001101100011
1992/02 10111111110010101011010111101100011010111111001110101101110000110001011111111100010111010000111001100000000011101000000000011111101111101110011100111101101011111001001000001001101001000000100111110110110011101001001101100011
1992/03 01101101110000101011010111101100011010111111001110111101110000110001011111111100011111010000111001100000000011101000000000011111101110101110111100111100101011111101001000001001101001000000100111110110110011101001001101100011
1992/04 10111101110000101011010111101100011010111111001110111101110000110001011111111100011111010000111001100000000011101100000000011111101110101110111100111100101011111001001000001001101001000000100111110110110011101001001101100011
1992/11 10111111110010101011010111101100011010111111001110101101110000110001011111111100010111010000111001111000000011101010000000011111101111101111011100111101101111111001001000001001101001000100100111111110110011101001001101100011
1993/01 10111111110000101011010111101100011010111111001110101101110000010001011011111001010111010000111001111000000011101010000000011111101111101111011110111101101101111001001000001001101001000110100111111110110011101001001101100011
1993/02 10111111110001101011010111101100011010111111001110101101110001110001011011111001010111010000111001111000000011101010000000011111101111101111011110111101101101111001001000001001101001000100100111111110110011101001001101100011
1993/03 10111111110001101011010111101100011010111111001110101101110001110001011011111001010111010000111001111000000011101010000000011111101111101111011110111101101101111001001000001001101001000100100111111110110011101001001101100011
1993/04 10111111110001101011010111101100011010111111001110101101110001110001011111111001011111010000111001111000000011101010000000011111101111101111111110111101101101111001001000001001101001000100100111111110110011101001001101100011
1993/11 10111111110001101011010111101100011010111111001110111101110001110001011011111001010111010000111001111000000011101010000000011111101111101111011110111101101101111001001000001001101001000100100111111110110011101001001101100011
1993/12 10111111110001101011010111101100011010111111001110111101110001110001011111111001010111010000111001111000000011101010000000011111101111101111011110111101101101111001001000001001101001000100100111111110110011101001001101100011
1994/01 10111111110001101011010111101100011010111111001110101101110001110001011011111001010111010000111001111000000011101010000000011111101111101111011110111101101101110001001000001001101001000100100111111110110011101001001101100011
1994/02 10111111110001101011010111101100011010111111001110101101110001110001011011111001010111010000111001111000000011101010000000011111101111101111011110111101101101110001001000001001101001000100100111111110110011101001001101100011
1994/03 10111111110001101011010111101100011010111111001110101101110001110001011011111001010111010000111001111000000011101010000000011111101111101111011110111101101101110001001000001001101001000100100111111110110011101001001101100011
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1995/07 10101111110001101011010111101100011010111111001110111101110001110001011011111001010111011000111001111000000011101000000110011111111111101111010110111101101111111001001000001101101001000100100111011110110011101001001101100011
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1995/09 10111111111001101011110111101100111010111111001111111101110011110001011111111001010111011000111011111100100011101010000110111111111111101111011110111101101111111001001000001001101001000101100111111110110011101011001101100011
1995/11 10111111110001101011010111101100011010111111001110111101110001110001011011111001010111011000101001111000000011101000000110011111111111101111010110111101101111111001001000001101101001000110100111011110110011101001001101100011
1995/12 10111111110001101011010111101100011110111111001110111101110001110001011111111001010111011000111001111000000011101000000110011111111111101111010110111101101111111001001000001101101001000110100111011110110011101001001101100011
1996/01 10111111111001101011110111101100011010111111001111111111110011110001011111111001010111011000111011111000000011101010000110111111111111101111011110111101101111111001001000001101101001000110100111011110110011101001001101100011
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2004/04 11111111111111111111111111111111111111111111011111111111111011111011111111111111110111111110111111111100111011101111001111111111111111101111111111111101101111111011111100011001101011111100111111111111111111101011001101111111
2004/05 11111111111111111111111111111111111111111111011111111111111011111011111111111111110111111110111111111100111011101111001111111111111111101111111111111101101111111011111100011001101011111100111111111111111111101011001101111111
2004/06 11111111111111111111111111111111111111111111011111111111111011111011111111111111110111111110111111111100111011101111001111111111111111101111111111111101101111111011111100011001101011111100111111111111111111101011001101111111
2004/07 11111111111111111111111111111111111111111111011111111111111011111011111011111111110111111110111111111100111011101111001111111111111111101111111111111101101111111011111100011001101011111100111111111111111111101011001101111111
2004/08 11111111111111111111111111111111111111111111011111111111111011111011111011111111110111111110111111111100111011101111001111111111111111101111111111111101101111111011111111111011101111111100111111111111111111101011001101111111
2004/09 11111111111111111111111111111111111111111111011111111111111011111011111011111111110111111110111111111100111011101111001111111111111111101111111111111101101111111011111111111011101111111100111111111111111111101011001101111111
2004/10 11111111111111111111111111111111111111111111011111111111111011111011111011111111110111111110111111111100111011101111001111111111111111101111111111111101101111111011111111111011101111111100111111111111111111101011001101111111
2004/11 11111111111111111111111111111111111111111111011111111111111011111011111011111111110111111110111111111100111011101111001111111111111111101111111111111101101111111011111111111011101111111100111111111111111111101011001101111111
2004/12 11111111111111111111111111111111111111111111011111111111111011111011111011111111110111111110111111111100111011101111001111111111111111101111111111111101101111111011111111111011101111111100111111111111111111101011001101111111
2005/01 11111111111111111111111111111111111111111111011111111111111011111011111011111111110111111110111111111100111011101111001111111111111111101111111111111101101111111011111111111011101111111100111111111111111111101011001101110111
2005/02 01111111111111111111111111111111111111111111011111111111111011111011111011111111110111111110111111111100111011101111001111111111111111101111111111111101101111111011101100011001101011111100111111111111111111101011001101110111
2005/03 11111111111111111111111111111111111111111111011111111111111011111011111011111111110111111110111111111100111011101111001111111111111111101111111111111101101111111011111101011011101111111100111111111111111111101011001101111111
2005/04 11111111111111111111111111111111111111111111011111111111111011111011111011111111110111111111111111111111111011101111111111111111111111111111111111111101101111111011111111111011101111111100111111111111111111101011001101111111
2005/05 11111111111111111111111111111111111111111111011111111111111011111011111011111111110111111110111111111111111011101111111111111111111111111111111111111101101111111011111111111111101111111100111111111111111111111011011101111111
2005/06 11111111111111111111111111111111111111111111011111111111111011111011111011111111110111111111111111111111111011101111111111111111111111111111111111111101101111111011111111111111101111111100111111111111111111111011011101111111
2005/07 11111111111111111111111111111111111111111111011111111111111011111011111011111111110111111111111111111111111011101111111111111111111111111111111111111101101111111011111111111111101111111100111111111111111111111011011101111111
2005/08 11111111111111111111111111111111111111111111011111111111111011111011111011111111110111111111111111111111111011101111111111111111111111111111111111111101101111111011111111111011101111111100111111111111111111101011001101111111
2005/09 00011111111111111111111111111111111111111111011111111111111011111011111011111111110111111111111111111111111011101111111111111111111111111111111111111101101111111011110000000000000000000000000000000000000000000000000000000000
2005/10 11111111111111111111111111111111111111111111011111111111111011111011111011111111110111111110111111111111111011101111111111111111111111111111111111111101101111111011111111111011101111111100111111111111111111101011001101111111
2005/11 01111111111111111111111111111111111111111111011111111111111011111011111011111111110111111110111111111111111011101111111111111111111111111111111111111101101111111010000000000000000000000000000000000000000000000000000000000000
2005/12 00000001111111111111111111111111111111111111011111111111111011111011111011111111110111111111111111111111111011101111111111111111111111111111111111111101101111111011100000000000000000000000000000000000000000000000000000000000
2006/01 00000001111111111111111111111111111111111111011111111111111011111011111011111111110111111111111111111111111011101111111111111111111111111111111111111101101111111010000000000000000000000000000000000000000000000000000000000000
2006/02 01111111111111111111111111111111111111111111011111111111111011111011111011111111110111111110111111111111111011101111111111111111111111111111111111111101101111111010000000000000000000000000000000000000000000000000000000000000
2006/03 11111111111111111111111111111111111111111111011111111111111011111011111011111111110111111110111111111111111011101111111111111111111111111111111111111101101111111011111111111111101111111100111111110111111111111011011101110111
2006/04 11111111111111111111111111111111111111111111011111111111111011111011111011111111110111111111111111111111111011101111111111111111111111111111111111111101101111111011111111111111101111111100111111111111111111111011011101110111
2006/05 00000001111111111111111111111111111111111111011111111111111111111011111011111111110111111110111111111111111011101111111111111111111111111111111111111101111111111010000000000000000000000000000000000000000000000000000000000000
2006/06 00000001111111111111111111111111111111111111011111111111111111111011111011111111110111111110111111111111111011101111111111111111111111111111111111111101111111111011110000000000000000000000000000000000000000000000000000000000
2006/07 00000001111111111111111111111111111111111111011111111111111011111011111011111111110111111110111111111111111011101111111111111111111111111111111111111101111111111010000000000000000000000000000000000000000000000000000000000000
2006/08 00000001111111111111111111111111111111111111011111111111111111111011111011111111110111111110111111111111111011101111111111111111111111111111111111111101111111111010000000000000000000000000000000000000000000000000000000000000
2006/09 00000001111111111111111111111111111111111111011111111111111111111011111011111111110111111110111111111111111011101111111111111111111111111111111111111101111111111011100000000000000000000000000000000000000000000000000000000000
2006/10 00000001111111111111111111111111111111111111011111111111111111111011111011111111110111111111111111111111111011101111111111111111111111111111111111111101111111111011111110000000000000000000000000000000000000000000000000000000
2006/11 00000001111111111111111111111111111111111111011111111111111111111011111011111111110111111111111111111111111011101111111111111111111111111111111111111101111111111010000000000000000000000000000000000000000000000000000000000000
2006/12 00000001111111111111111111111111111111111111011111111111111111111111111011111111110111111111111111111111111011101111111111111111111111111111111111111111111111111010000000000000000000000000000000000000000000000000000000000000
2007/01 11111111111111111111111111111111111111111111011111111111111111111111111011111111110111111111111111111111111011101111111111111111111111111111111111111111111111111011111111111111101111111100111111111111111111111010111101111111
2007/02 11111111111111111111111111111111111111111111011111111111111111111111111011111111110111111111111111111111111011101111111111111111111111111111111111111111111111111011111111111111101111111111111111111111111111111111111101111111
2007/03 11111111111111111111111111111111111111111111011111111111111111111111111011111111110111111111111111111111111011101111111111111111111111111111111111111111111111111011111111111111101111111111111111111111111111111111111101111111
2007/04 11111111111111111111111111111111111111111111011111111111111111111111111011111111110111111110111111111111111011101111111111111111111111111111111111111111111111111011111111111111101111111110111111111111111111111111111101111111
2007/05 11111111111111111111111111111111111111111111011111111111111111111111111011111111110111111110111111111111111011101111111111111111111111111111111111111111111111111011111111111111101111111111111111111111111111111111111101111111
2007/06 11111111111111111111111111111111111111111111011111111111111111111111111011111111110111111110111111111111111011101111111111111111111111111111111111111111111111111011111111111111101111111111111111111111111111111111111101111111
2007/07 11111111111111111111111111111111111111111111011111111111111111111111111011111111110111111110111111111111111011101111111111111111111111111111111111111111111111111011111111111111101111111111111111111111111111111111111101111111
2007/08 11111111111111111111111111111111111111111111011111111111111111111111111011111111110111111110111111111111111011101111111111111111111111111111111111111111111111111011111111111111101111111111111111111111111111111111111101111111
2007/09 11111111111111111111111111111111111111111111011111111111111111111111111011111111110111111111111111111111111011101111111111111111111111111111111111111111111111111011111111111111101111111111111111111111111111111111111101111111
2007/10 11111111111111111111111111111111111111111111011111111111111111111111111011111111110111111111111111111111111011101111111111111111111111111111111111111111111111111011111111111111101111111111111111111111111111111111111101111111
2007/11 11111111111111111111111111111111111111111111011111111111111111111111111011111111110111111111111111111111111011101111111111111111111111111111111111111111111111111011111111111111101111111111111111111111111111111111111101111111
2007/12 11111111111111111111111111111111111111111111011111111111111111111111111011111111110111111111111111111111111011101111111111111111111111111111111111111111111111111011111111111111101111111111111111111111111111111111111101111111
2008/01 11111111111111111111111111111111111111111111011111111111111111111111111011111111110111111111111111111111111011101111111111111111111111111111111111111111111111111011111111111111101111111111111111111111111111111111111101111111
2008/02 11111111111111111111111111111111111111111111011111111111111111111111111011111111110111111111111111111111111011101111111111111111111111111111111111111111111111111011111111111111101111111111111111111111111111111111111101111111
2008/03 11111111111111111111111111111111111111111111011111111111111111111111111011111111110111111111111111111111111011101111111111111111111111111111111111111111111111111011111111111111101111111111111111111111111111111111111101111111
2008/04 11111111111111111111111111111111111111111111011111111111111111111111111011111111110111111111111111111111111011101111111111111111111111111111111111111111111111111011111111111111101111111111111111111101111111111111011101110111
2008/05 11111111111111111111111111111111111111111111011111111111111111111111111011111111110111111111111111111111111011101111111111111111111111111111111111111111111111111011111111111111101111101110111111111111111111111111111101111111
2008/06 00000001111111111111111111111111111111111111011111111111111111111111111011111111110111111111111111111111111011101111111111111111111111111111111111111111111111111011111000000000000000000000000000000000000000000000000000000000
2008/07 00000001111111111111111111111111111111111111011111111111111111111111111011111111110111111111111111111111111011101111111111111111111111111111111111111111111111111011111000000000000000000000000000000000000000000000000000000000
2008/08 11111111111111111111111111111111111111111111011111111111111111111111111011111111110111111111111111111111111011101111111111111111111111111111111111111111111111111011111111111111111111111111111111111111111111111111111111111111
2008/09 11111111111111111111111111111111111111111111011111111111111111111111111011111111110111111111111111111111111011101111111111111111111111111111111111111111111111111011111111111111101111111111011111111111101111111111111101111111
2008/10 00000001111111111111111111111111111111111111011111111111111111111111111011111111110111111111111111111111111011101111111111111111111111111111111111111111111111111011111111111111111111111111111111110111111111111111111111111111
2008/11 00000001111111111111111111111111111111111111011111111111111111111111111011111111110111111111111111111111111011101111111111111111111111111111111111111111111111111011111111111111111111111111111111110111111111111111111111111111
2008/12 11111111111111111111111111111111111111111111011111111111111111111111111011111111110111111111111111111111111011101111111111111111111111111111111111111111111111111011111111111111111111111111111111111111111111111111111111111111
2009/01 00000111111111111111111111111111111111111111011111111111111111111111111011111111110111111111111111111111111011101111111111111111111111111111111111111111111111111011111010000000000000000000000000000000000000000000000000000000
2009/02 11111111111111111111111111111111111111111111011111111111111111111111111011111111110111111111111111111111111011101111111111111111111111111111111111111111111111111011111111111111111111111111111111111111111111111111111111111111
2009/03 11111111111111111111111111111111111111111111011111111111111111111111111011111111110111111111111111111111111011101111111111111111111111111111111111111111111111111011111111111111111111111111111111111111111111111111111111111111
2009/04 11111111111111111111111111111111111111111111011111111111111111111111111011111111111111111111111111111111111011101111111111111111111111111111111111111111111111111011111111111111111111111111111111111111111111111111111111111111
2009/05 11111111111111111111111111111111111111111111011111111111111111111111111011111111111111111111111111111111111011101111111111111111111111111111111111111111111111111011111111111111111111111111111111111111111111111110111111111111
2009/06 11111111111111111111111111111111011111111111011111111111111111111111111011111111111111111111111111101111111011101111111111111111111111111111111111111111111111111011111111111111111111111111111111111111111111111110111111111111
2009/07 11111111111111111111111111111111011111111111011111111111111111111111111011111111111111111111111111101111111011101111111111111111111111111111111111111111111111111011111111111111111111111111111111111111111111111110111111111111
2009/08 11111111111111111111111111111111111111111111011111111111111111111111111011111111111111111111111111111111111011101111111111111111111111111111111111111111111111111011111111111111111111111111111111111111111111111110111111111111
2009/09 11111111111111111111111111111111011111111111011111111111111111111111111011111111111111111111111111101111111011101111111111111111111111111111111111111111111111111011111111111111111111111111111111111111111111111110111111111111
2009/10 11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111110111111111111
2009/11 11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
2009/12 11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
2010/01 11111111111111111111111111111111111111111111011111111111111111111111111011111111110111111111111111111111111011101111111111111111111111111111111111111111111101111011111111111111111111111111111111111111111111111111111111111111
2010/02 00000000001111111111111111111110111111111111111111111111111111111111111111111111111111111111111000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
2010/03 11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
2010/04 11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
2010/05 11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111100000000000000000000000000000000000000000000
2010/06 11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
2010/07 11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
2010/08 11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111110111111111111
2010/09 11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
2010/10 11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
2010/11 11111111111111101111111111110111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
2010/12 11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
2011/01 11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
2011/02 01111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
2011/03 11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
2011/04 11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
2011/07 10111111111001100110110111110110011000111111111111111111111111110101011011111011111111010000111111111001000011101010000110111111111111101111110011111101000111101101001000001001110001100101000111111110010011111001001101100011
2011/08 10111111111001100110110111110110011000111111111111111111111111110101011011111011111111010000111111111001000011101010000110111111111111101111110011111101000011101101000000000000000000000000000000000000000000000000000000000000
2011/10 10111111111001100110110111100110011000111111111011111111111111110101011011111011111111010000111111111001000011101010000110111111111111101111110011111101000111101101001000001001110001000101000111111110010011111001001101100011
2011/11 11111111111001100110110111100110011000111111111011111111111111110101011011111011111111011000111111111001000011101110000110111111111111101111110011111101000111101101001000001001110001000101000111111110010011111001001101100011
2011/12 11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111100000000000000000000000000000000000000000000
2012/01 11111111111111111111111111111111111111111111111111111111111111111111110111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111100000000000000000000000000000000000000000000
2012/02 11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111100000000000000000000000000000000000000000000
2012/03 11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111100000000000000000000000000000000000000000000
first appearances of >02 new mutations (of the current Egypt/Iowa strain)
Code:
107 >1970/06/14,A/Bcm/1/1970,USA, 5 ,G139A,C183T,G235A,T285C,G762A
172 >1973/01/15,A/Bcm/1/1973,USA, 19 ,A174G,T281G,T282C,C413A,G417A,T420C,G479A,A610G,G668A,G678A,C705T,G772A,C804T,A872G,T873C,T879C,A957G,C963T,G969A
191 >1974/09/09,A/Bcm/1/1974,USA, 4 ,C121A,C425A,G478A,C1039A
210 >1975/01/11,A/Bcm/3/1975,USA, 9 ,A120G,A138G,G195T,A205G,C296A,G482A,C613A,T819C,C987T
253 >1977/12/30,A/Bcm/3/1977,USA, 14 ,G105A,G192A,A209G,T233A,C309T,A457T,G484A,T489C,G521A,A579G,T759A,G778T,G828A,T867C
262 >1978/01/03,A/Bcm/1/1978,USA, 3 ,G264A,C527A,T786C
290 >1980/02/26,A/Bcm/1/1980,USA, 6 ,G418A,G435A,C475T,C504T,T732C,C936T
293 >1980/12/01,A/Netherlands/209/1980,Netherlands, 26 ,C9T,C41T,C43T,G47C,G52A,T99C,C660A,G1005A,G1011A,A1087G,C1167A,T1189C,C1194T,G1209A,T1320C,T1347C,C1362T,G1386A,A1428G,C1473T,A1484G,G1500A,A1566G,T1575A,G1668A,G1670A
339 >1982/04/01,A/Netherlands/233/1982,Netherlands, 10 ,G390A,T567A,C577T,A685G,T789C,A791C,A968G,C1284T,G1374A,G1406A
408 >1984/01/ ,A/Taiwan/VGHYM0109-12/1984,Taiwan, 2 ,A357G,C499T
455 >1985/01/01,A/Netherlands/330/1985,Netherlands, 7 ,C54A,T536C,A780G,G924A,G1198T,T1338C,G1596A
456 >1985/02/01,A/Netherlands/333/1985,Netherlands, 2 ,G993A,G1485A
533 >1988/02/05,A/Siena/3/1988,Italy, 3 ,T329A,A523T,T1548C
535 >1988/12/ ,A/Taiwan/VGHYM1220-03/1988,Taiwan, 3 ,C492T,G669A,C831A
681 >1989/01/28,A/Beijing/57/1989,China, 4 ,T144C,G147A,G292A,A944G
746 >1990/10/ ,A/Taiwan/VGHYM1001-06/1990,Taiwan, 2 ,A618C,G777T
811 >1991/09/15,A/England/260/1991,United Kingdom, 6 ,C33A,A96G,C798T,C1335T,T1476C,C1587T
824 >1991/12/17,A/Stockholm/20/1991,Sweden, 2 ,T31C,G855A
956 >1992/11/01,A/Stockholm/12/1992,Sweden, 7 ,C48T,C518T,T792A,C875A,A960C,G1239A,G1365A
1125 >1993/02/03,A/New York/758/1993,USA, 2 ,T531C,C1527T
1165 >1993/03/26,A/New York/757/1993,USA, 2 ,G451A,C833G
1281 >1994/01/02,A/New York/723/1994,USA, 2 ,G450A,A1230G
1328 >1994/06/01,A/Hong Kong/1/1994,Hong Kong, 2 ,A1188G,C1446T
1333 >1994/07/29,A/New York/715/1994,USA, 2 ,T635C,C1642T
1334 >1994/08/02,A/Hong Kong/56/1994,Hong Kong, 5 ,G702A,C724A,G726C,T881A,A1089G
1335 >1994/11/03,A/New York/654/1994,USA, 3 ,A514C,G520A,C1275T
1336 >1994/11/17,A/New York/655/1994,USA, 2 ,T327C,C564A
1337 >1994/12/02,A/New York/657/1994,USA, 4 ,A219G,T399A,C1044T,G1403A
1458 >1995/01/06,A/New York/671/1995,USA, 2 ,G537A,A1578G
1508 >1995/04/06,A/Guangxi/42/1995,China, 4 ,A78G,A393C,G452C,C606T
1519 >1995/09/27,A/Malaysia/07832/1995,Malaysia, 2 ,A232G,C623T
1526 >1995/12/02,A/Netherlands/271/1995,Netherlands, 2 ,G524T,C1173T
1709 >1996/04/ ,A/Fujian/124/1996,China, 4 ,T410A,T447C,G472A,C927A
1719 >1996/05/20,A/Fujian/152/1996,China, 2 ,G218A,G444A
1735 >1996/08/26,A/Malaysia/10675/1996,Malaysia, 8 ,G246A,A458C,C876A,A1056G,C1233T,A1290G,C1431T,C1620T
1930 >1997/03/14,A/Malaysia/12106/1997,Malaysia, 2 ,G108A,A1205G
1981 >1997/12/20,A/Malaysia/14712/1997,Malaysia, 2 ,A1200G,A1557G
2238 >1998/08/31,A/Hong Kong/CUHK18036/1998,Hong Kong, 2 ,A60T,C1092T
2839 >2000/03/01,A/Hong Kong/CUHK22072/2000,Hong Kong, 2 ,A196G,G722A
2903 >2000/09/14,A/Canterbury/75/2000,New Zealand, 2 ,T1149C,T1314A
3053 >2001/07/19,A/Hong Kong/CUHK24749/2001,Hong Kong, 4 ,G93T,C538T,G652A,T1637C
3087 >2001/10/14,A/Guangzhou/1237/2001,China, 2 ,G714A,T727C
3088 >2001/10/23,A/Okinawa/208/2001,Japan, 2 ,A516C,A604G
3606 >2002/06/01,A/Hong Kong/CUHK24044/2002,Hong Kong, 4 ,G156T,T273G,G648A,T712A
5071 >2003/12/30,A/Hong Kong/CUHK83422/2003,Hong Kong, 2 ,C1128A,G1212C
5595 >2004/03/11,A/Jeonnam/336/2004,South Korea, 4 ,A625T,G626T,G721A,C811A
7264 >2005/10/ ,A/Kolkata/43/2005,India, 3 ,A467T,T930C,T954C
8243 >2006/12/08,A/Colorado/05/2006,USA, 2 ,A1254C,T1512C
9280 >2007/07/24,A/LangSon/LS218/2007,Viet Nam, 4 ,A565C,C1130G,G1197A,T1560A
11140 >2009/04/10,A/Nanjing/1/2009,China, 5 ,C318A,C483T,A522C,A615G,A682G
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September 10th, 2012, 02:10 AM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,950
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Re: H3n2
we have 2 major strains in H3-HA, both descending from Egypt/Iowa/2009
2 out of 405 viruses are not Egypt/Iowa, but both are Perth/~2008
> Index USA/2007 (H3N2)
>Index/Brisbane-like/2007,1,1-1701,1,
A622G
>Index/Perth-like/2009,12,1-1701,12,
G232A,T480A,A522C,A565C,T615A,C729T
T1130G,G1197A,C1296T,C1548T,C1560A,A1578G
>Index/2009/Egypt/Iowa,15,1-1701,15,
C318A,C483T,A522C,A565C,T615G,C660A
A682G,C729T,G1005A,C1053A,T1130G,G1197A
C1296T,C1560A,A1578G
--------------------------------------------------------
Germany,2011/12
group 3(85%)
3C: 51% A/HK/3969/2011 S45N,T48I,A198S,V223I,N312S (Victoria/361/2011)
3B: 24% A/England/259/2011 N145S,A198S,V223I,N312S,D487N
3A: 10% A/Stockholm/18/2011 N145S,V223I,D487N (add 16 to get the real positions)
2: A/Norway/1330/2010 N133D,R142G,T212A,V213A
1: A/Victoria/210/2009 P162S,I260M,R261Q {C532T,A828G,G830A}
4: A/Serbia/71/2011 N312S
5: A/Perth/10/2011 D53N,Y94H,I230V,E280A
6: A/Iowa/19/2010 D53N,Y94H,S199A,I230V,E280A
7: A/Alabama/04/2011 S45N
(these viruses are not at genbank)
I can't find the separation into groups ("3A,3B,3C,6,5,..."), what mutations determine those groups
------------------
found it on page 8 here: http://www.nimr.mrc.ac.uk/documents/...t-feb-2012.pdf
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September 10th, 2012, 01:13 PM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,950
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Re: H3n2
ahh, Egypt/Iowa(2009) had reassorted with another virus that I hadn't
seen before. That virus could still have been a descendent from
the USA/2007-index to which all current human H3N2 (except H3N2v)
goes back to. Or close to that one, maybe mrcat=2006
that virus contributed segments 1,2,6,8 while a descendent
of Egypt/Iowa contributed 3,4,5,7
we have particularly few mutations in segment 5 since 2007
besides that reassortant we have another H3N2 that could be a descendent
of Egypt/Iowa/2009 in all segments except 6 (NA)
that NA also goes back to the the 2007-USA-index
we no longer have descendents from the Wisconsin/2005 vaccine strain
or similar
--------------------------------------
I forgot what I had written before here: Feb.28.2011
http://www.flutrackers.com/forum/showpost.php?p=396272
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December 6th, 2012, 12:24 AM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,950
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Re: H3n2
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January 4th, 2013, 09:57 PM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,950
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Re: H3n2
bump----------------------
> that virus contributed segments 1,2,6,8 while a descendent
> of Egypt/Iowa contributed 3,4,5,7
it's a pity that we have no recent H3N2 at genbank.
The last is from Czechia last season
we need India,China
what had Australia last season ?
Just one genome would be fine
And not only HA, I feel that it's not HA that is responsible
for this bad flu-season in USA
--------------------------------------------------
http://www.ncbi.nlm.nih.gov/pubmed/23201458
http://www.flutrackers.com/forum/att...9&d=1354703360
--------------------------------------------------
file 3212c7 , 2012.09.12 , m=5450 n=1703
file 3212c7.iow , 2012.09.12 , m=1468 , n=1703
file 3212s1 , 2012.09.11 , m=1092 , n=2282
file 3212i , 2012.09. m=361 , n=2282+2276+2153+1703+1499+1412+984+840
file 3213 , 2013.01.05 m=5461 , n=2350+2353+
file 3213v , 2013.01.05 , m=992 , n=2282+2276+2153+1703+1499+1412+984+840
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January 14th, 2013, 08:04 AM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,950
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Re: H3n2
here the 2 strains that were circulating in 2011
(and uploaded to genbank)
Code:
>Index/H3N3-2011-reassortedEI/2011(H3N2)
ATGGAAAGAATAAAAGAATTACGGAATCTGATGTCGCAGTCTCGCACTCGCGAGATACTGACAAAAACCACAGTGGACCATATGGCCATAATTAAGAAGTACACATCGGGGAGACAGGAAAAGAACCCGTCACTTAGGATGAAATGGATGATGGCAATGAAATACCCAATCACTGCTGACAAAAGGATAACAGAAATGGTTCCAGAGAGAAATGAACAAGGACAAACTCTATGGAGTAAAATAAGTGATGCTGGATCAGATAGAGTGATGGTATCACCTTTGGCTGTAACATGGTGGAATAGAAATGGACCCGTGACAAGTACGGTCCATTACCCAAAAGTGTACAAAACTTATTTCGACAAAGTCGAAAGGTTAAAACATGGAACCTTTGGCCCTGTTCATTTTAGAAATCAAGTCAAGATACGCAGAAGAGTAGACATAAATCCTGGTCATGCAGACCTCAGTGCCAAAGAGGCACAAGATGTAATTATGGAAGTTGTTTTTCCCAATGAAGTGGGAGCCAGGATACTAACATCAGAATCACAATTAACAATAACTAAAGAGAAAAAAGAAGAACTCCGAGATTGTAAAATTTCTCCCTTGATGGTTGCATACATGTTAGAGAGAGAACTTGTACGAAAAACAAGATTTCTCCCAGTTTCTGGAGGAACAAGCAGTATATACATTGAAGTTTTACATTTGACTCAGGGAACGTGTTGGGAACAAATGTACACTCCAGGTGGAGGAGTGAGGAATGACGATATTGACCAAAGCCTAATTATTGCGGCCAGGAACATAGTAAGAAGAGCCGCAGTATCAGCAGATCCACTAGCATCTTTATTGGAAATGTGCCACAGCACACAAATTGGCGGGACAAAGATGGTGGACATTCTTAGACAGAACCCGACTGAAGAACAAGCTGTGGATATATGCAAGGCTGCAATGGGATTGAGAATCAGCTCATCATTCAGCTTTGGTGGATTTACATTTAAAAGAACAAGCGGGTCATCAGTCAAAAAAGAAGAAGAGGTGCTTACAGGCAATCTCCAAACATTGAAAATAAGAGTACATGAGGGGTATGAGGAGTTCACAATGGTGGGGAAAAGAGCAACAGCTATACTAAGAAAAGCAACCAGAAGATTGGTTCAGCTCATAGTGAGTGGAAGAGACGACCAGTCAATAGCCGAAGCAATAATCGTGGCCATGGTGTTTTCACAAGAGGATTGCATGATAAAAGCAGTTAGAGGTGACCTGAATTTCGTCAACAGAGCAAATCAGCGGTTAAACCCCATGCATCAGCTTTTAAGGCATTTTCAGAAAGATGCGAAAGTGCTTTTTCAAAATTGGGGAGTTGAACACATCGACAGTGTGATGGGAATGATTGGAGTATTACCAGATATGACTCCAAGCACAGAGATGTCAATGAGAGGAATAAGAGTCAGCAAAATGGGTGTGGATGAATACTCCAGTACAGAGAGGGTGGTGGTTAGCATTGATCGGTTTTTGAGAGTTCGAGACCAACGTGGGAATGTATTATTATCTCCTGAGGAGGTCAGTGAAACACAGGGAACTGAGAGACTGACAATAACTTATTCATCGTCGATGATGTGGGAGATTAACGGTCCTGAATCGGTTCTGGTCAATACCTATCAGTGGATCATCAGAAATTGGGAAGCTATTAAAATTCAATGGTCTCAGAATCCTGCAATGTTGTACAACAAAATGGAATTTGAACCATTTCAATCCTTAGTCCCCAAGGCCATTAGAAGCCAATACAGTGGGTTTGTCAGAACTCTATTCCAACAAATGAGAGACGTACTTGGGACATTTGACACCACCCAGATAATAAAGCTTCTCCCTTTTGCAGCTGCTCCACCAAAGCAAAGCAGAATGCAGTTCTCTTCACTGACTGTGAATGTGAGGGGATCAGGGATGAGAATACTTGTAAGGGGCAATTCTCCTGTATTCAACTACAACAAGACCACTAAAAGACTAACAATTCTCGGAAAAGATGCCGGCACTTTAATTGAAGACCCAGATGAAAGCACATCCGGAGTGGAATCCGCCGTCTTGAGAGGGTTTCTCATTATAGGTAAGGAAGACAGAAGATACGGACCAGCATTAAGCATCAATGAACTGAGCAACCTTGCAAAAGGGGAAAAGGCTAATGTGCTAATAGGGCAAGGAGACGTGGTGTTGGTAATGAAACGAAAACGGGACTCTAGCATACTTACTGACAGCCAGACAGCGACCAAAAGAATTCGGATGGCCATCAATTAA
ATGGATGTCAATCCGACTCTACTGTTCCTAAAGGTTCCAGCGCAAAATGCCATAAGCACAACATTCCCTTATACTGGAGACCCTCCATACAGCCATGGAACAGGGACAGGGTACACCATGGACACAGTCAACAGAACACACCAATATTCAGAGAGGGGGAAGTGGACGACAAATACAGAAACTGGGGCACCCCAACTAAACCCAATTGATGGACCACTACCTGAGGATAATGAACCAAGTGGATATGCACAAACAGACTGTGTCCTGGAGGCTATGGCCTTCCTTGAAGAATCCCACCCAGGTATCTTTGAGAACTCATGCCTTGAAACAATGGAAGCCGTTCAACAGACAAGGGTGGACAAACTAACCCAAGGTCGCCAAACTTATGATTGGACATTAAACAGAAATCAACCGGCAGCAACTGCATTAGCCAACACCATAGAAGTCTTTAGATCGAACGGATTGACAGCTAATGAATCAGGAAGACTAATAGATTTCCTCAAGGATGTGATGGAATCAATGGATAAAGAGGAAATGGAGATAACAACACACTTTCAAAGAAAAAGGAGAGTAAGGGACAACATGACCAAGAAAATGGTCACACAAAGAACAATAGGGAAGAAAAAACAAAGAGTGAATAAGAGAGGCTACCTAATAAGAGCTTTGACATTGAACACGATGACCAAAGATGCAGAGAGAGGCAAATTAAAAAGAAGGGCTATTGCAACACCCGGGATGCAAATTAGAGGGTTCGTGTACTTCGTTGAAACTTTAGCTAGAAGCATTTGTGAAAAGCTTGAACAGTCTGGACTTCCAGTTGGGGGTAATGAAAAGAAGGCCAAACTGGCAAATGTTGTGAGAAAAATGATGACTAATTCACAAGACACAGAGCTTTCTTTCACAATCACTGGGGACAACACTAAGTGGAATGAAAATCAAAACCCTCGAATGTTTCTGGCGATGATTACATACATCACAAAGAATCAACCTGAGTGGTTCAGAAACATCCTGAGCATCGCACCAATAATGTTCTCAAACAAAATGGCAAGACTGGGAAAAGGATACATGTTCGAGAGTAAGAAAATGAAGCTCCGGACACAAATACCTGCAGAAATGCTAGCAAGCATTGACCTGAAGTATTTCAATGAATCAACAAGGAAGAAAATTGAGAAAATAAGGCCTCTTCTAATAGATGGCACAGCATCATTGAGCCCTGGAATGATGATGGGCATGTTCAACATGCTAAGTACGGTTTTAGGAGTCTCGATACTGAATCTTGGACAAAAGAAATACACCAAGACAACATACTGGTGGGATGGGCTCCAATCCTCCGACGATTTTGCTCTCATAGTGAATGCACCAAATCATGAGGGAATACAAGCAGGAGTGGATAGATTCTACAGGACCTGCAAGTTAGTGGGAATCAACATGAGCAAAAAGAAGTCCTATATAAATAAAACAGGGACATTTGAATTCACTAGCTTTTTTTATCGATATGGATTTGTGGCTAATTTTAGCATGGAGCTGCCCAGTTTTGGAGTGTCTGGAATAAACGAGTCAGCTGATATGAGCATTGGAGTAACAGTGATAAAGAACAACATGATAAACAATGACCTTGGACCAGCAACAGCCCAAATGGCTCTCCAATTGTTCATCAAAGATTACAGATACACATATAGGTGCCATAGAGGAGACACACAAATCCAGACGAGAAGATCATTCGAGATAAAGAAGCTGTGGGATCAAACCCAATCAAGGGCAGGACTATTGGTATCAGATGGGGGACCAAACTTATACAATATCCGGAATCTTCACATCCCTGAAGTCTGCTTAAAGTGGGAGCTGATGGATGAGAATTATCGGGGAAGACTTTGTAATCCCCTGAATCCCTTTGTCAGCCATAAAGAAATTGAGTCTGTAAACAATGCTGTAGTAATGCCAGCCCATGGTCCGGCCAAAAGTATGGAATATGATGCCGTTGCAACCACACACTCCTGGATTCCCAAGAGGAACCGCTCTATTCTAAACACAAGCCAAAGGGGAATTCTTGAGGATGAACAGATGTACCAGAAGTGCTGCAACTTGTTCGAGAAATTTTTCCCTAGTAGTTCATATAGGAGACCTATTGGAATTTCTAGCATGGTGGAGGCAATGGTGTCTAGGGCCCGGATTGATGCCAGAATTGACTTCGAGTCTGGAAGGATTAAGAAAGAGGAGTTCTCTGAGATCATGAGGATCTGTTCCACCATTGAAGAACTCAGACGGCAAAAATAA
ATGGAAGATTTTGTGCGACAATGCTTCAACCCGATGATTGTCGAACTTGCAGAAAAAGCAATGAAAGAGTATGGGGAGGATCTGAAAATTGAAACCAACAAATTTGCAGCAATATGCACTCACTTGGAGGTGTGTTTCATGTATTCAGATTTCCATTTCATCAATGAACAAGGCGAATCAATAGTGGTAGAACTTGACGATCCAAATGCACTGTTAAAGCACAGATTTGAAATAATCGAGGGGAGAGACAGAACAATGGCCTGGACAGTAGTAAACAGTATCTGCAACACTACTGGAGCTGGAAAACCGAAGTTTCTACCAGATTTGTATGATTACAAAGAGAACAGATTCATCGAAATTGGAGTGACAAGGAGAGAAGTCCACATATATTACCTTGAAAAGGCCAACAAGATTAAATCTGAGAACACACACATTCACATTTTCTCATTCACTGGGGAGGAAATGGCCACAAAGGCAGACTACACTCTTGACGAGGAAAGCAGGGCTAGGATTAAGACCAGGCTGTTTACCATAAGACAAGAAATGGCCAACAGAGGCCTCTGGGATTCCTTTCGTCAGTCCGAAAGAGGCGAAGAAACAATTGAAGAAAAATTTGAAATCACAGGAACTATGCGTAGGCTTGCCGACCAAAGTCTCCCACCGAACTTCTCCTGCCTTGAGAATTTTAGAGCCTATGTGGATGGATTCGAACCGAACGGCTGCATTGAGGGCAAGCTTTCTCAAATGTCCAAAGAAGTGAATGCCCAAATTGAACCTTTTCTGAAGACAACACCAAGACCAATCAAACTTCCGAATGGACCTCCTTGTTATCAGCGGTCCAAATTCCTCCTGATGGATGCTTTAAAATTGAGCATTGAAGACCCAAGTCACGAAGGAGAAGGGATCCCATTATATGATGCGATCAAGTGCATAAAAACATTCTTTGGATGGAAAGAACCTTATATAGTCAAACCACACGAAAAGGGAATAAATTCAAATTACCTGCTGTCATGGAAGCAAGTACTGTCAGAATTGCAGGACATTGAAAATGAGGAGAAGATTCCAAGAACTAAAAACATGAAGAAAACGAGTCAACTGAAGTGGGCTCTTGGTGAAAACATGGCACCAGAGAAGGTAGACTTTGAAAACTGCAGAGACATAAGCGATTTGAAGCAATATGATAGTGACGAACCTGAATTAAGGTCACTTTCAAGCTGGATACAGAATGAGTTCAACAAGGCCTGTGAGCTAACTGATTCAGTCTGGATAGAGCTCGATGAAATTGGAGAGGATGTAGCCCCAATTGAGCACATTGCAAGCATGAGAAGAAATTATTTCACAGCAGAGGTGTCCCATTGTAGAGCTACTGAATACATAATGAAGGGGGTATACATTAACACTGCCCTGCTCAATGCATCCTGTGCAGCAATGGACGATTTTCAACTAATTCCCATGATAAGCAAGTGCAGAACTAAAGAGGGAAGGCGAAAAACCAATTTATATGGATTCATCATAAAGGGAAGATCTCATTTAAGGAATGACACAGACGTGGTAAATTTTGTGAGCATGGAGTTTTCTCTCACTGACCCGAGACTTGAGCCACATAAATGGGAGAAATACTGTGTCCTTGAGATAGGAGATATGTTACTAAGAAGTGCCATAGGCCAAATTTCAAGGCCGATGTTCTTGTATGTGAGGACAAACGGAACATCAAAGGTCAAAATGAAATGGGGAATGGAGATGAGACGTTGCCTCCTTCAGTCACTCCAGCAGATCGAGAGCATGATTGAAGCCGAGTCCTCGGTTAAAGAGAAAGACATGACCAAAGAGTTTTTTGAGAATAAATCAGAAGCATGGCCCATTGGGGAGTCCCCCAAGGGAGTGGAAGAAGGTTCCATTGGGAAAGTCTGTAGGACTCTATTGGCTAAGTCAGTATTCAATAGCCTGTATGCATCACCACAATTGGAAGGATTTTCAGCGGAGTCAAGAAAACTGCTCCTTGTTGTTCAGGCTCTTAGGGACAACCTCGAACCTGGGACCTTTGATCTTGGGGGGCTATATGAAGCAATTGAGGAGTGCCTGATTAATGATCCCTGGGTTTTGCTCAATGCGTCTTGGTTCAACTCCTTCCTGACACATGCATTAAAATAG
ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTGCCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTGAAATATGCAACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAACAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCCACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGCTCTGCTTGCATAAGGAGATCTAATAATAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAACTTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAAGGACCAAATCTTCCTGTATGCTCAAGCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAATTCCGAATATCGGATCTAGACCCAGAGTAAGGAATATCCCTAGCAGAGTAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAATTCTGCATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGAATGAGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGGGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATAGATTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTCGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACACACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTGTACAGAGATGAAGCATTAAACAACCGATTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATTTGA
ATGGCGTCCCAAGGCACCAAACGGTCTTATGAACAGATGGAAACTGATGGGGATCGCCAGAATGCAACTGAGATTAGGGCATCCGTCGGGAAGATGATTGATGGAATTGGGAGATTCTACATCCAAATGTGCACTGAACTTAAACTCAGTGATCATGAAGGGCGTTTGATCCAGAACAGCTTGACAATAGAGAAAATGGTACTCTCTGCTTTTGATGAAAGAAGGAATAAATACCTGGAAGAACACCCCAGCGCGGGGAAAGATCCCAAGAAAACTGGGGGGCCCATATACAGGAGAGTCGATGGGAAATGGATGAGGGAACTCGTCCTTTATGACAAAGAAGAAATAAGGCGAATCTGGCGCCAAGCCAACAATGGTGAGGATGCTACATCTGGTCTAACTCACATAATGATTTGGCATTCCAATTTGAATGATGCAACATACCAGAGGACAAGAGCTCTTGTTCGAACTGGAATGGATCCCAGAATGTGCTCTCTGATGCAGGGCTCGACTCTCCCTAGAAGGTCCGGAGCTGCAGGTGCTGCAGTCAAAGGAATCGGGACAATGGTGATGGAACTGATCAGAATGGTCAAACGGGGGATCAACGATCGAAATTTTTGGAGAGGTGAGAATGGGCGGAAAACAAGAAGTGCTTATGAGAGAATGTGCAACATTCTTAAAGGAAAATTTCAAACAGCTGCACAAAGAGCAATGGTGGATCAAGTGAGAGAAAGTCGGAACCCAGGAAACGCTGAGATCGAAGATCTCATATTTTTAGCAAGATCTGCATTGATATTGAGAGGATCAGTTGCTCACAAATCTTGCCTACCTGCCTGTGCGTATGGACCTGCAGTATCCAGTGGGTACGACTTCGAAAAAGAGGGATATTCCTTGGTGGGAATAGACCCTTTCAAACTACTTCAAAATAGCCAAATATACAGCTTAATCAGACCTAACGAGAATCCAGCACACAAGAGTCAGCTGGTGTGGATGGCATGCCATTCTGCTGCATTTGAAGATTTAAGATTGTTAAGCTTCATCAGAGGGACAAAAGTATCTCCTCGGGGGAAACTGTCAACTAGAGGAGTACAAATTGCTTCAAATGAGAACATGGATAATATGGGATCGAGCACTCTTGAACTGAGAAGCGGGTACTGGGCCATAAGGACCAGGAGTGGAGGAAACACTAATCAACAGAGGGCCTCCGCAGGCCAAACCAGTGTGCAACCTACGTTTTCTGTACAAAGAAACCTCCCATTTGAAAAGTCAACCATCATGGCAGCATTCACTGGAAATACGGAGGGAAGAACTTCAGACATGAGGGCAGAAATCATAAGAATGATGGAAGGTGCAAAACCAGAAGAAGTGTCATTCCGGGGGAGGGGAGTTTTCGAGCTCTCAGACGAGAAGGCAACGAACCCGATCGTGCCCTCTTTTGATATGAGTAATGAAGGATCTTATTTCTTCGGAGACAATGCAGAAGAGTACGACAATTAA
ATGAATCCAAATCAAAAGATAATAACGATTGGCTCTGTTTCTCTCACCATTTCCACAATATGCTTCTTCATGCAAATTGCCATCTTGATAACTACTGTAACATTGCATTTCAAGCAATATGAATTCAACTCCCCCCCAAACAACCAAGTGATGCTGTGTGAACCAACAATAATAGAAAGAAACATAACAGAGATAGTGTATCTGACCAACACCACCATAGAGAAGGAAATATGCCCCAAACTAGCAGAATACAGAAATTGGTCAAAGCCGCAATGTGACATTACAGGATTTGCACCTTTTTCTAAGGACAATTCGATTAGGCTTTCCGCTGGTGGGGACATCTGGGTGACAAGAGAACCTTATGTGTCATGCGATCCTGACAAGTGTTATCAATTTGCCCTTGGACAGGGAACAACACTAAACAACGTGCATTCAAATAACACAGTACGTGATAGGACCCCTTATCGGACCCTATTGATGAATGAGTTAGGTGTTCCTTTTCATCTGGGGACCAAGCAAGTGTGCATAGCATGGTCCAGCTCAAGTTGTCACGATGGAAAAGCATGGCTGCATGTTTGTATAACGGGGGATGATAAAAATGCAACTGCTAGCTTCATTTACAATGGGAGGCTTGTAGATAGTGTTGTTTCATGGTCCAAAGAAATCCTCAGGACCCAGGAGTCAGAATGCGTTTGTATCAATGGAACTTGTACAGTAGTAATGACTGATGGGAGTGCTTCAGGAAAAGCTGATACTAAAATACTATTCATTGAGGAGGGGAAAATCGTTCATACTAGCACATTGTCAGGAAGTGCTCAGCATGTCGAGGAGTGCTCTTGCTATCCTCGATATCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGCTCCAATAGGCCCATCGTAGATATAAACATAAAGGATCATAGCATTGTTTCCAGTTATGTGTGTTCAGGACTTGTTGGAGACACACCCAGAAAAAACGACAGCTCCAGCAGTAGCCATTGTTTGGATCCTAACAATGAAGAAGGTGGTCATGGAGTGAAAGGCTGGGCCTTTGATGATGGAAATGACGTGTGGATGGGAAGAACGATCAACGAGACGTCACGTTTAGGGTATGAAACCTTCAAAGTCATTGAAGGCTGGTCCAACCCTAAGTCCAAATTGCAGATAAATAGGCAAGTCATAGTTGACAGAGGTAATAGGTCCGGTTATTCTGGTATTTTCTCTGTTGAAGGCAAAAGCTGCATCAATCGGTGCTTTTATGTGGAGTTGATTAGGGGAAGAAAAGAGGAAACTGAAGTCTTGTGGACCTCAAACAGTATTGTTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGATGGGGCGGACCTCAATCTCATGCCTATATAA
ATGAGCCTTCTAACCGAGGTCGAAACGTATGTTCTCTCTATCGTTCCATCAGGCCCCCTCAAAGCCGAGATCGCGCAGAGACTTGAAGATGTCTTTGCTGGGAAAAACACAGATCTTGAGGCTCTCATGGAATGGCTAAAGACAAGACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGCCAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCCTCAATGGGAATGGAGACCCAAATAATATGGACAAAGCAGTTAAACTGTATAGGAAACTTAAGAGAGAGATAACGTTCCATGGGGCCAAAGAAATAGCTCTCAGTTATTCTGCTGGTGCACTTGCCAGTTGCATGGGCCTCATATACAATAGGATGGGGGCTGTAACCACTGAAGTGGCATTTGGCCTGGTATGTGCAACATGTGAGCAGATTGCTGACTCCCAGCACAGGTCTCATAGGCAGATGGTGGCAACAACCAATCCATTAATAAAACATGAGAACAGAATGGTTTTGGCAAGCACTACAGCTAAGGCTATGGAGCAAATGGCTGGATCAAGTGAGCAGGCAGCGGAGGCCATGGAGATTGCTAGTCAGGCCAGGCAGATGGTGCAGGCAATGAGAGCCATTGGGACTCATCCTAGTTCCAGTACTGGTCTAAGAGATGATCTTCTTGAAAATTTGCAGACCTATCAGAAACGAATGGGGGTGCAGATGCAACGATTCAAGTGACCCGCTTGTTGTTGCCGCGAATATCATTGGGATCTTGCACTTGATATTGTGGATTCTTGATCGTCTTTTTTTCAAATGCGTCTATCGACTCTTCAAACACGGCCTTAAAAGAGGCCCTTCTACGGAAGGAGTACCTGAGTCTATGAGGGAAGAATATCGAAAGGAACAGCAGAATGCTGTGGATGCTGACGACAGTCATTTTGTCAGCATAGAGTTGGAGTAA
ATGGACTCCAACACTGTGTCAAGTTTCCAGGTAGATTGCTTTCTTTGGCATATCCGGAAACAAGTTGTAGACCAAGAACTGAGTGATGCCCCATTCCTTGATCGGCTTCGCCGAGATCAGAGGTCCCTAAGGGGAAGAGGCAATACTCTTGGTCTAGACATCAAAGCAGCCACCCATGTTGGAAAGCAAATTGTAGAAAAGATTCTGAAAGAAGAATCTGATGAGGCACTTAAAATGACCATGGTCTCCACACCTGCTTCGCGATACATAACTGACATGACTATTGAGGAATTGTCAAGAAACTGGTTCATGCTAATGCCCAAGCAGAAAGTGGAAGGACCTCTTTGCATCAGAATGGACCAGGCAATCATGGAGAAAAACATCACGTTGAAAGCGAATTTCAGTGTGATTTTTGACCGACTAGAGACTATAGTATTACTAAGGGCTTTCACCGAAGAGGGAGCAATTGTTGGCGAAATCTCACCATTGCCTTCTTTTCCAGGACATACTATTGAGGATGTCAAAAATGCAATTGGGGTCCTCATCGGAGGACTTGAATGGAATGATAACACAGTTCGAGTCTCTAAAAATCTACAGAGATTCGCTTGGAGAAGCAGTAATGAGAATGGGGGACCTCCACTTACTCCAAAACAGAAACGGGAAATGGCGAGAACAGCTAGGTCAAAAGTTTGAAGAGATAAGATGGCTAATTGAAGAAGTGAGACACAGATTAAAAACAACTGAAAGTAGCTTTGAACAAATAACATTCATGCAAGCATTACAACTGCTGTTTGAGGTGGAACAGGAGATAAGAACTTTCTCATTTCAGCTTATTTAA
>Index/H3N2-2011-normalEI/2011(H3N2)
ATGGAAAGAATAAAAGAACTACGGAATCTGATGTCGCAGTCTCGCACTCGCGAGATACTGACAAAAACCACAGTGGACCATATGGCCATAATTAAGAAGTACACATCGGGGAGACAGGAAAAGAACCCGTCACTTAGGATGAAATGGATGATGGCAATGAAATATCCAATCACTGCTGACAAAAGGGTAACAGAAATGGTTCCGGAGAGAAATGAACAAGGACAAACTCTATGGAGTAAAATGAGTGATGCTGGATCAGATAGAGTGATGGTATCACCTTTGGCTGTAACATGGTGGAATAGGAATGGACCCGTGACAAGTACGGTCCATTACCCAAAAGTGTACAAGACTTATTTCGACAAAGTCGAAAGGTTAAAACATGGAACCTTTGGCCCTGTTCATTTTAGAAATCAAGTCAAGATACGCAGAAGAGTAGACATAAACCCTGGTCATGCAGACCTCAGTGCCAAAGAGGCACAAGATGTAATTATGGAAGTTGTTTTTCCCAATGAAGTGGGAGCCAGGATACTAACATCAGAATCACAATTAACAATAACTAAAGAGAAAAAAGAAGAACTCCGAGATTGCAAAATTTCTCCCTTGATGGTTGCATACATGTTAGAGAGAGAACTTGTACGAAAAACAAGATTTCTCCCAGTTGCTGGCGGAACAAGCAGTATATACATTGAAGTTTTACATTTGACTCAGGGAACGTGTTGGGAACAAATGTACACTCCAGGTGGAGGAGTGAGGAATGACGATGTTGACCAAAGCCTAATTATTGCGGCCAGGAACATAGTAAGAAGAGCCGCAGTATCAGCAGATCCACTAGCATCTTTATTGGAGATGTGCCACAGCACGCAAATTGGCGGAACAAGGATGGTGGACATTCTTAGACAGAACCCGACTGAAGAACAAGCTGTGGATATATGCAAGGCTGCAATGGGATTGAGAATCAGCTCATCCTTCAGCTTTGGTGGCTTTACATTTAAAAGAACAAGCGGGTCATCAGTCAAAAAAGAAGAAGAGGTGCTTACAGGCAATCTCCAAACATTGAGAATAAGAGTACATGAGGGGTATGAGGAGTTCACAATGGTGGGGAAAAGAGCAACAGCTATACTAAGAAAAGCAACCAGAAGATTGGTTCAACTCATAGTGAGTGGAAGAGACGAACAGTCAATAGCCGAAGCAATAATCGTGGCCATGGTGTTTTCACAAGAAGATTGCATGATAAAAGCAGTTAGAGGTGACCTGAATTTCGTCAACAGAGCAAATCAGCGGTTGAACCCCATGCATCAGCTTTTAAGGCATTTTCAGAAAGATGCGAAAGTGCTCTTTCAAAATTGGGGAGTTGAACACATCGACAGTGTGATGGGAATGGTTGGAGTATTACCAGATATGACTCCAAGCACAGAGATGTCAATGAGAGGAATAAGAGTCAGCAAAATGGGTGTGGATGAATACTCCAGTACAGAGAGGGTGGTGGTTAGCATTGATCGGTTTTTGAGAGTTCGAGACCAACGTGGGAATGTATTATTATCTCCTGAGGAGGTCAGTGAAACACAGGGAACTGAGAGACTGACAATAACTTATTCATCGTCGATGATGTGGGAGATTAACGGTCCTGAGTCGGTTTTGGTCAATACCTATCAATGGATCATCAGAAATTGGGAAGCTGTCAAAATTCAATGGTCTCAGAATCCTGCAATGTTGTACAACAAAATGGAATTTGAACCATTTCAATCTTTAGTCCCCAAGGCCATTAGAAGCCAATACAGTGGGTTTGTCAGAACTCTATTCCAACAAATGAGAGACGTACTTGGGACATTTGACACCACCCAGATAATAAAGCTTCTCCCTTTTGCAGCTGCTCCACCGAAGCAAAGCAGAATGCAGTTCTCTTCACTGACTGTGAATGTGAGGGGATCAGGGATGAGAATACTTGTAAGGGGCAATTCTCCTGTATTCAACTACAACAAGACCACTAAAAGACTAACAATTCTCGGAAAAGATGCCGGCACTTTAATTGAAGACCCAGATGAAAGCACATCCGGAGTGGAGTCCGCCGTCTTGAGAGGGTTTCTCATTATAGGTAAGGAAGACAGAAGATACGGACCAGCATTAAGCATCAATGAACTGAGTAACCTTGCAAAAGGGGAAAAGGCTAATGTGCTAATCGGGCAAGGAGACGTGGTGTTGGTAATGAAACGAAAACGGGACTCTAGCATACTTACCGACAGCCAGACAGCGACCAAAAGAATTCGGATGGCCATCAATTAA
ATGGATGTCAATCCGACTCTACTGTTCCTAAAGGTTCCAGCGCAAAATGCCATAAGCACAACATTCCCTTATACTGGAGATCCTCCATACAGCCATGGAACAGGGACAGGGTACACCATGGACACAGTCAACAGAACACACCAATATTCAGAGAGGGGGAAGTGGACGACAAATACAGAAACTGGGGCACCCCAGCTCAACCCAATTGATGGACCACTACCTGAGGATAATGAACCAAGTGGATATGCACAAACAGACTGTGTCCTGGAGGCTATGGCCTTCCTTGAAGAATCCCACCCAGGTATCTTTGAGAACTCATGCCTTGAAACAATGGAAGCCGTTCAACAGACAAGGGTGGACAAACTAACCCAAGGTCGCCAGACTTATGATTGGACATTAAACAGGAATCAACCGGCAGCAACTGCATTAGCCAACACCATAGAAGTCTTTAGATCGAACGGATTAACAGCTAATGAATCAGGAAGGCTAATAGATTTCCTCAAGGATGTGATGGAATCAATGGATAAAGAGGAAATGGAGATAACAACACACTTTCAAAGAAAAAGGAGAGTAAGGGACAACATGACCAAGAAAATGGTCACACAAAGAACAATAGGGAAGAAAAAACAAAGAGTGAATAAGAGAGGCTACCTAATAAGAGCTTTGACATTGAACACGATGACCAAAGATGCAGAGAGAGGCAAATTAAAAAGAAGGGCTATTGCAACACCCGGGATGCAAATTAGAGGGTTCGTGTACTTCGTTGAAACTCTAGCTAGAAGCATTTGCGAAAAGCTTGAACAGTCTGGACTTCCGGTTGGGGGTAATGAAAAGAAGGCCAAACTGGCAAATGTTGTGAGAAAAATGATGACTAATTCACAAGACACAGAGCTTTCTTTCACAATCACTGGGGACAACACTAAGTGGAATGAAAATCAAAACCCTCGAATGTTTTTGGCGATGATTACATACATCACAAAGAATCAACCTGAGTGGTTCAGAAACATCCTGAGCATCGCACCAATAATGTTCTCAAACAAAATGGCAAGACTGGGAAAAGGATACATGTTCGAGAGTAAGAGAATGAAGCTCCGGACACAAATACCTGCAGAAATGCTAGCAAGCATTGACCTGAAGTATTTCAATGAATCAACAAGGAAGAAAATTGAGAAAATAAGGCCTCTTCTAATAGATGGCACAGCATCATTGAGCCCTGGAATGATGATGGGCATGTTCAACATGCTAAGTACAGTTTTAGGAGTCTCGATACTGAATCTTGGACAAAAGAAATACACCAAGACAACATACTGGTGGGATGGGCTCCAATCCTCCGACGATTTTGCACTCATAGTGAATGCACCAAATCATGAGGGAATACAAGCAGGAGTAGATAGATTCTACAGGACCTGCAAGTTAGTGGGAATCAACATGAGCAAAAAGAAGTCCTATATAAATAAAACAGGGACATTTGAATTCACTAGCTTTTTTTATCGATATGGATTTGTGGCTAATTTTAGCATGGAGCTGCCCAGTTTTGGAGTGTCTGGAATAAACGAGTCAGCTGACATGAGCATTGGAGTAACAGTGATAAAGAACAACATGATAAACAATGACCTTGGACCAGCAACAGCCCAAATGGCTCTCCAATTGTTCATCAAAGATTACAGATACACATATAGGTGCCATAGAGGAGACACACAAATCCAAACGAGAAGATCATTCGAGATAAAGAAGCTGTGGGATCAAACCCAATCAAAGACAGGACTATTGGTATCAGATGGGGGACCAAACTTATACAATATCCGGAATCTTCACATCCCTGAAGTCTGCTTAAAGTGGGAGCTGATGGATGAGAATTATCGGGGAAGACTTTGTAATCCCCTGAATCCCTTTGTCAGCCATAAAGAAATTGAGTCTGTAAACAATGCTGTAGTAATGCCAGCCCATGGTCCGGCCAAAAGTATGGAATATGATGCCGTTGCAACTACACACTCATGGATTCCCAAAAGGAACCGCTCTATTCTAAACACAAGCCAAAGGGGAATTCTTGAGGATGAACAGATGTACCAGAAGTGCTGCAACTTGTTCGAGAAATTTTTCCCTAGTAGTTCATATAGGAGACCGATTGGAATTTCTAGCATGGTGGAGGCCATGGTGTCTAGGGCCCGGATTGATGCCAGAATTGACTTCGAGTCTGGAAGGATTAAGAAGGAAGAGTTCTCTGAGATCATGAAGATCTGTTCCACCATTGAAGAACTCAGACGGCAAAAATAA
ATGGAAGATTTTGTGCGACAATGCTTCAACCCGATGATTGTCGAACTTGCAGAAAAAGCAATGAAAGAGTATGGGGAGGATCTGAAAATTGAAACCAACAAATTTGCAGCAATATGCACTCACTTGGAGGTGTGTTTCATGTATTCAGATTTCCATTTCATCAATGAACAAGGCGAATCAATAGTGGTAGAACTTGACGATCCAAATGCACTGTTAAAGCACAGATTTGAAATAATCGAGGGGAGAGACAGAACAATGGCCTGGACAGTAGTAAACAGTATCTGCAACACTACTGGAGCTGGAAAACCGAAGTTTCTACCAGATTTGTATGATTACAAAGAGAACAGATTCATCGAAATTGGAGTGACAAGGAGAGAAGTCCACATATATTACCTTGAAAAGGCCAATAAGATTAAATCTGAGAACACACACATTCACATTTTCTCATTCACTGGGGAGGAAATGGCCACAAAGGCAGACTACACTCTCGACGAGGAAAGCAGGGCTAGGATTAAAACCAGGCTGTTTACCATAAGACAAGAAATGGCCAACAGAGGCCTCTGGGATTCCTTTCGTCAGTCCGAAAGAGGCGAAGAAACAATTGAAGAAAAATTTGAAATCACAGGAACTATGCGTAGGCTTGCCGACCAAAGTCTCCCACCGAACTTCTCCTGCCTTGAGAATTTTAGAGCCTATGTGGATGGATTCGAACCGAACGGCTGCATTGAGGGCAAGCTTTCTCAAATGTCCAAAGAAGTGAATGCCCAAATTGAACCTTTTCTGAAGACAACACCGAGACCAATCAAACTTCCTAATGGACCTCCTTGTTATCAGCGGTCCAAATTCCTCCTGATGGATGCTTTAAAATTGAGCATTGAAGACCCAAGTCACGAAGGAGAAGGGATCCCATTATATGATGCGATCAAGTGCATAAAAACATTCTTTGGATGGAAAGAACCTTGTATAGTCAAACCACACGAAAAGGGGATAAATTCAAATTACCTGCTGTCATGGAAGCAAGTACTGTCAGAATTGCAGGACATTGAAAATGAGGAGAAGATTCCAAGAACTAAAAACATGAAGAAAACGAGTCAACTGAAGTGGGCTCTTGGTGAAAACATGGCACCAGAGAAGGTAGACTTTGAAAACTGCAGAGACATAAGCGATTTGAAGCAATATGATAGTGACGAACCTGAATTAAGGTCACTTTCAAGCTGGATACAGAGTGAGTTCAACAAGGCCTGTGAGCTAACTGATTCAGTCTGGATAGAGCTCGATGAAATTGGAGAGGACGTAGCCCCAATTGAGCACATTGCAAGCATGAGAAGGAATTATTTCACAGCAGAGGTGTCCCATTGTAGAGCTACTGAATACATAATGAAGGGGGTATACATTAACACTGCCCTGCTCAATGCATCCTGTGCAGCAATGGACGATTTTCAACTAATTCCCATGATAAGCAAGTGCAGAACTAAAGAGGGAAGGCGAAAAACCAATTTATATGGATTCATCATAAAGGGAAGATCTCATTTAAGGAATGACACAGACGTGGTAAATTTTGTGAGCATGGAGTTTTCTCTCACTGACCCGAGACTTGAGCCACATAAATGGGAGAAATACTGTGTCCTTGAGATAGGAGATATGTTACTAAGAAGTGCCATAGGCCAAATTTCAAGACCGATGTTCTTGTATGTGAGGACAAACGGAACATCAAAGGTCAAAATGAAATGGGGAATGGAGATGAGACGTTGCCTCCTTCAGTCACTCCAGCAGATCGAGAGCATGATTGAAGCCGAGTCCTCGGTTAAAGAGAAAGACATGACCAAAGAGTTTTTTGAGAATAAATCAGAAGCATGGCCCATTGGGGAGTCCCCCAAGGGAGTGGAAGAAGGTTCCATTGGGAAAGTCTGTAGGACTCTATTGGCTAAGTCAGTATTCAATAGCCTGTATGCATCACCACAATTGGAAGGATTTTCAGCGGAGTCAAGAAAACTGCTCCTTGTTGTTCAGGCTCTTAGGGACAACCTCGAACCTGGGACCTTTGATCTTGGGGGGCTATATGAAGCAATTGAGGAGTGCCTGATTAATGATCCCTGGGTTTTGCTCAATGCGTCTTGGTTCAACTCCTTCCTGACACATGCATTAAAATAG
ATGAAGACCATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAGCAGGTGAAATATGCGACAGTCCTCATCATATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGAAGCAGAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGCTCTGCTTGCATAAGGAGATCTAATAATAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAACTTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAAGGACCAAATCTTCCTGTATGCTCAAGCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAATCCCGAATATCGGATCTAGACCCAGAGTAAGGAATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAATTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAGCACTCTGAAATTGGCAACAGGAATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGATGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGAAAGCTGAATAGATTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTCGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGAGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATTTGA
ATGGCGTCTCAAGGCACCAAACGGTCTTATGAACAGATGGAAACTGATGGGGATCGCCAGAATGCAACTGAGATTAGGGCATCCGTCGGGAAGATGATTGATGGAATTGGGAGATTCTACATCCAAATGTGCACTGAACTTAAACTCAGTGATCATGAAGGGCGGTTGATCCAGAACAGCTTGACAATAGAGAAAATGGTACTCTCTGCTTTTGATGAAAGAAGGAATAAATACCTGGAAGAACACCCCAGCGCGGGGAAAGATCCCAAGAAAACTGGGGGGCCCATATACAGGAGAGTCGATGGGAAATGGATGAGGGAACTCGTCCTTTATGACAAAGAAGAAATAAGGAGAATCTGGCGCCAAGCCAACAATGGTGAGGATGCTACATCTGGTCTAACCCACATAATGATTTGGCATTCCAATTTGAATGATGCAACATACCAGAGGACAAGAGCTCTTGTTCGAACTGGAATGGATCCCAGAATGTGCTCTCTGATGCAGGGCTCGACTCTCCCTAGAAGGTCCGGAGCTGCAGGTGCTGCAGTCAAAGGAATCGGAACAATGGTGATGGAACTGATCAGAATGGTCAAACGGGGGATCAACGATCGAAATTTTTGGAGAGGTGAGAATGGGCGGAAAACAAGAAGTGCTTATGAGAGAATGTGCAACATTCTTAAAGGAAAATTTCAAACAGCTGCACAAAGAGCAATGGTGGATCAAGTGAGAGAAAGTCGAAACCCAGGAAACGCTGAGATCGAAGATCTCATATTTTTAGCAAGATCTGCATTGATATTGAGAGGATCAGTTGCTCACAAATCTTGTCTACCTGCCTGTGCGTATGGACCTGCAGTATCCAGTGGGTACGACTTCGAAAAAGAGGGATATTCCTTGGTGGGAATAGACCCTTTCAAACTACTTCAAAATAGCCAAATATACAGCTTAATCAGACCTAACGAGAATCCAGCACACAAGAGTCAGCTGGTGTGGATGGCATGCCATTCTGCTGCATTTGAAGATTTAAGATTGTTAAGCTTCATCAGAGGGACAAAAGTATCTCCTCGGGGGAAACTGTCAACTAGAGGAGTACAAATTGCTTCAAATGAGAACATGGATAATATGGGATCGAGCACTCTTGAACTGAGAAGCGGGTACTGGGCCATAAGGACCAGGAGTGGAGGAAACACTAATCAACAGAGGGCCTCCGCAGGCCAAACCAGTGTGCAACCTACGTTTTCTGTACAAAGAAACCTCCCATTTGAAAAGTCAACCATCATGGCCGCATTCACTGGAAATACGGAGGGAAGAACTTCAGACATGAGGGCAGAAATCATAAGAATGATGGAAGGTGCAAAACCAGAAGAAGTGTCATTCCGGGGGAGGGGAGTTTTCGAGCTCTCAGACGAGAAGGCAACGAACCCGATCGTGCCCTCTTTTGATATGAGTAATGAAGGATCTTATTTCTTCGGAGACAATGCAGAAGAGTACGACAATTAA
ATGAATCCAAATCAAAAGATAATAACGATTGGCTCTGTTTCTCTCACCATTTCCACAATATGCTTCTTCATGCAAATTGCCATCTTGATAACTACTGTAACATTGCATTTCAAGCAATATGAATTCAACTCCCCCCCAAACAACCAAGTGATGCTGTGTGAACCGACAATAATAGAAAGAAACATAACAGAGATAGTGTATCTGACCAACACCACCATAGAGAAGGAAATATGCCCCAAACTAGCAGAATACAGAAATTGGTCAAAACCGCAATGTGACATTACAGGATTTGCACCTTTTTCTAAGGACAATTCGATTAGGCTTTCCGCTGGTGGGGACATCTGGGTGACAAGAGAACCTTATGTGTCATGCGATCCTGACAAGTGTTATCAATTTGCCCTTGGACAGGGAACAACACTAAACAACGTGCATTCAAATAACACAGTACGTGATAGGACCCCTTATCGGACCCTATTGATGAATGAGTTAGGTGTTCCTTTTCATCTGGGGACCAAGCAAGTGTGCATAGCATGGTCCAGCTCAAGTTGTCACGATGGAAAAGCATGGCTGCATGTTTGTATAACGGGGGATGATAAAAATGCAACTGCAAGCTTCATTTACAATGGGAGGCTTGTAGATAGTGTTGTTTCATGGTCCAAAGAAATTCTCAGGACCCAGGAGTCAGAATGCGTTTGTATCAATGGAACTTGTACAGTAGTAATGACTGATGGAAGTGCTTCAGGAAAAGCTGATACTAAAATACTATTCATTGAGGAGGGGAAAATCGTTCATACTAGCACATTGTCAGGAAGTGCTCAGCATGTCGAGGAGTGCTCTTGCTATCCTCGATATCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGCTCCAATAGGCCCATCGTAGATATAAACATAAAGGATCATAGCATAGTTTCCAGTTATGTGTGTTCAGGACTTGTTGGAGACACACCCAGAAAAAACGACAGCTCCAGCAGTAGCCATTGTTTGGATCCTAACAATGAAGAAGGTGGTCATGGAGTGAAAGGCTGGGCCTTTGATGATGGAAATGACGTGTGGATGGGAAGAACAATCAACGAGACGTCACGCTTGGGGTATGAAACCTTCAAAGTCATTGAAGGCTGGTCCAACCCTAAGTCCAAATTGCAGATAAATAGGCAAGTCATAGTTGACAAAGGTAATAGGTCCGGTTATTCTGGTATTTTCTCTGTTGAAGGCAAAAGCTGCATCAATCGGTGCTTTTATGTGGAGTTGATTAGGGGAAGAAAAGAGGAAACTGAAGTCTTGTGGACCTCAAACAGTATTGTTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGATGGGGCGGACCTCAATCTCATGCCTATATAA
ATGAGCCTTCTAACCGAGGTCGAAACGTATGTTCTCTCTATCGTTCCATCAGGCCCCCTCAAAGCCGAGATCGCGCAGAGACTTGAAGATGTCTTTGCTGGGAAAAACACAGATCTTGAGGCTCTCATGGAATGGCTAAAGACAAGACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCCTCAATGGGAATGGAGACCCAAATAACATGGACAAAGCAGTTAAACTGTATAGGAAACTTAAGAGGGAGATAACGTTCCATGGGGCCAAAGAAATAGCTCTCAGTTATTCTGCTGGTGCACTTGCCAGTTGCATGGGCCTCATATACAATAGGATGGGGGCTGTAACCACCGAAGTGGCATTTGGCCTGGTATGTGCAACATGTGAGCAGATTGCTGACTCCCAGCACAGGTCTCATAGGCAGATGGTGGCAACAACCAATCCATTAATAAAACATGAGAACAGAATGGTTTTGGCCAGCACTACTGCTAAGGCTATGGAGCAAATGGCTGGGTCAAGTGAGCAGGCAGCGGAGGCCATGGAGATTGCTAGTCAGGCCAGGCAGATGGTGCAGGCAATGAGAGCCATTGGGACTCATCCTAGTTCCAGTACTGGTCTAAGAGATGATCTTCTTGAAAATTTGCAGACCTATCAGAAACGAATGGGGGTGCAGATGCAACGATTCAAGTGACCCGCTTGTTGTTGCCGCGAATATCATTGGGATCTTGCACTTGATATTGTGGATTCTTGATCGTCTTTTTTTCAAATGCGTCTATCGACTCTTCAAACACGGCCTTAAAAGAGGCCCTTCTACGGAAGGAGTACCTGAGTCTATGAGGGAAGAATATCGAAAGGAACAGCAGAGTGCTGTGGATGCTGACGACAGTCATTTTGTCAGCATAGAGTTGGAGTAA
ATGGATTCCAACACTGTGTCAAGTTTCCAGGTAGATTGCTTTCTTTGGCATATCCGGAAACAAGTTGTAGACCAAGAAATGAGTGATGCCCCATTCCTTGATCGGCTTCGCCGAGATCAGAGGTCCCTAAGGGGAAGAGGCAATACTCTCGGTCTAGACATCAAAGCAGCCACCCATGTTGGAAAGCAAATTGTAGAAAAGATTCTGAAAGAAGAATCTGATGAGGCACTTAAAATGACCATGGTCTCCACACCTGCTTCGCGATACATAACTGACATGACTATTGAGGAATTGTCAAGAAACTGGTTCATGCTAATGCCCAAGCAGAAAGTGGAAGGACCTCTTTGCATCAGAATGGACCAGGCAATCATGGAGAAAAACATCATGTTAAAAGCGAATTTCAATGTGATTTTTGGCCGACTAGAGACCATAGTATTACTAAGGGCTTTCACCGAAGAGGGAGCAATTGTTGGCGAAATCTCACCATTGCCTTCTTTTCCAGGACATACTATTGAGGATGTCAAAAATGCAATTGGGGTCCTCATCGGAGGACTTGAATGGAATGATAACACAGTTCGAGTCTCTAAAAATCTACAGAGATTCGCTTGGAGAAGCAGTAATGAGAATGGGGGACCTCCACTTACTCCAAAACAGAAACGGGAAATGGCGAGAACAGCTAGGTCAAAAGTTTGAAGAGATAAGATGGCTAATTGAAGAAGTGAGACACAGATTAAGAACAACTGAAAATAGCTTTGAACAAATAACATTCATGCAAGCATTACAACTGCTGTTTGAAGTGGAACAGGAGATAAGAACTTTCTCATTTCAGCTTATTTAA
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January 20th, 2013, 02:30 AM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,950
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Re: H3n2
summary, Jan.2013
-----------------------------
all current human H3N2 (except swinish H3N2v) goes back in all 8 segments to one ancester
from ~mid 2006 ("US-Index/2007" , one of the dominant strains in seasonal US-flu 2006/7)
similar to the "Brisbane" vax-strain.
Then we had the Perth-vax strain which was prevalent until Egypt/Iowa appeared
and is now no longer found.
then we had Egypt/Iowa which separated from Perth in most segments in ~2008,
was first seen in ~mid 2009 in Egypt,Kenya,Djibuti,Iowa and was dominant in ~2010
Egypt/Iowa has 63=10+13+7+15+3+9+3+3 mutations (as compared to US-Index/2007)
In NA,segment 6 we have a common ancestor from ~2009 with 7 mutations which later
reassorted with Egypt/Iowa to form the ancestor(~2010) of current human seasonal H3N2
("Egypt_Iowa+NA")
In genbank 2011 we see basically 2 strains that emerged from US-Index/2007:
1.) Index1/2011 = normal Egypt_Iowa+NA with meanwhile 106=14+18+14+22+10+16+7+5
mutations as compared to US-Index/2007, including all the 61 of Egypt_Iowa+NA.
2.) Index2/2011 = reassortant Egypt-Iowa+NA in segments 3,4,5,6,7 plus one other new virus
from ~2007, also a descendent of US-Index/2007.
It has 110=25+22+11+27+4+8+7+6 mutations as compared toi US-Index/2007 including
all the 35=7+15+3+7+3 Egyt_Iowa+NA mutations from segments 3,4,5,6,7 and also
2+6+0 of the 10+13+3 Egypt/Iowa mutations from segments 1,2,8. So it separated from the
forming Egypt/Iowa in ~2008.
--------------edit--------------
3.) Index3/2011 = A/Czech Republik/121/2012/03/06(H3N2) -like , see below
Now as of Jan.2013 we have segments 4,6,7 from 2 recent H3N2 viruses from USA at genbank:
A/Georgia/3058/2012/09/26 and A/Oklahoma/3059/2012/10/05
GA3058 is a direct descendent of Index2/2011 in segments 4,6,7 (and in the other 5 segments too ?)
It has those 27+8+7 mutations plus 9+10+5 further,others mutations for a total of
36+18+12=66 (as compared to US-Index/2007, as usual)
OK3059 is a completely different virus, it descends from Egypt_Iowa+NA, but not from Index1/2011
nor from Index2/2011. It has 34+20+7 mutations in segments 4,6,7 including the 15+7+3
from Egypt_Iowa+NA and further 2+4+0 from Index1/2011 to which it is therefore a bit more related
then to Index2/2011
================================================== ===============================
here the mentioned strains and their mutations:
Code:
21,>2007/02/06,14278,AUS,A/Brisbane/10/07
T735C(1),A1026G(1),G1029A(1),C1227T(1),T1794C(1)
C28A(2),G156A(2),T397C(2),C915T(2),T1365C(2),G2193A(2)
A1371G(3)
G46A(4),T60C(4),T903C(4)
A648G(5)
T935C(6),A1110G(6)
T354C(7),T540C(7)
A703G(8)
------------------------------------------------------------
9,>Index/Brisbane-like/2007
C652T(2),C2200A(2)
G129A(3),C1353T(3),A1377C(3)
A622G(4)
T27A(5),T513C(5),T1440G(5)
--------------------------------------------------------------
8+8+8+12+5+7+5+2=55,>Index/Perth-like/2009
T228C(1),A708G(1),G873A(1),A1058G(1),G1149A(1),G1221A(1),G1920A(1),A2109G(1)
C141T(2),A155G(2),A981G(2),C1051T(2),C1726A(2),G1836A(2),G1953T(2),C2200A(2)
T153C(3),A303G(3),G456A(3),C561A(3),A1042G(3),A1060G(3),T1680A(3),G1689A(3)
G232A(4),T480A(4),A522C(4),A565C(4),T615A(4),C729T(4),T1130G(4),G1197A(4)
C1296T(4),C1548T(4),C1560A(4),A1578G(4)
G201A(5),G636A(5),G1348A(5),T1389C(5),C1488T(5)
A288G(6),G429A(6),G439A(6),A643G(6),C891A(6),A1029G(6),A1044G(6)
T267C(7),A492G(7),G521A(7),G591A(7),C685T(7)
G331A(8),C634T(8)
----------------------------------------------------------------
10+13+7+15+3+9+3+3=63,>Index/2009/Egypt/Iowa
A187G(1),A303G(1),A708G(1),A861G(1),G873A(1),G981C(1),A1058G(1),G1149A(1)
G1221A(1),A1381G(1)
A105G(2),A155G(2),A195G(2),A405G(2),A981G(2),G1251A(2),T1566C(2),G1707A(2)
C1726A(2),G1759A(2),G2007A(2),C2200A(2),A2234G(2)
A96C(3),T153C(3),G339A(3),G363A(3),G1068A(3),C1365T(3),T1680G(3)
C318A(4),C483T(4),A522C(4),A565C(4),T615G(4),C660A(4),A682G(4),C729T(4)
G1005A(4),C1053A(4),T1130G(4),G1197A(4),C1296T(4),C1560A(4),A1578G(4)
G201A(5),A300C(5),A306G(5)
T77C(6),T78C(6),T85C(6),A119G(6),G439A(6),C471T(6),A643G(6),G1107A(6)
A1290G(6)
T267C(7),A492G(7),G521A(7)
G404A(8),A416G(8),A735G(8)
------------------------------------------------------------------
10+13+7+15+3+7+3+3=61,>Index/2009/Egypt_Iowa+NA
A187G(1),A303G(1),A708G(1),A861G(1),G873A(1),G981C(1),A1058G(1),G1149A(1)
G1221A(1),A1381G(1)
A105G(2),A155G(2),A195G(2),A405G(2),A981G(2),G1251A(2),T1566C(2),G1707A(2)
C1726A(2),G1759A(2),G2007A(2),C2200A(2),A2234G(2)
A96C(3),T153C(3),G339A(3),G363A(3),G1068A(3),C1365T(3),T1680G(3)
C318A(4),C483T(4),A522C(4),A565C(4),T615G(4),C660A(4),A682G(4),C729T(4)
G1005A(4),C1053A(4),T1130G(4),G1197A(4),C1296T(4),C1560A(4),A1578G(4)
G201A(5),A300C(5),A306G(5)
G439A(6),A643G(6),C837T(6),G1100A(6),A1106C(6),A1281T(6),A1390C(6)
T267C(7),A492G(7),G521A(7)
G404A(8),A416G(8),A735G(8)
------------------------------------------------------------------
vaccine strain A/Victoria/210/2009:
P162S=P187S=C532T,I260M=I276M=A828G,R261Q=R277Q=G830A
-----------------------------------------------------------------
25+22+11+27+4+8+7+6=110,>Index2/2011-reassortedEI/2011
C19T(1),G204A(1),G243A(1),G348A(1),C444T(1),C588T(1),G661T(1),C666A(1)
A708G(1),G763A(1),G846A(1),G878A(1),C966A(1),G981A(1),A1173C(1),G1284A(1)
G1629A(1),T1636C(1),A1653G(1),G1678A(1),C1680T(1),T1746C(1),G2061A(1),T2142C(1)
C2178A(1)
T81C(2),A105G(2),A155G(2),C198A(2),G381A(2),T447C(2),A465G(2),G486A(2)
C789T(2),G816A(2),T955C(2),A981G(2),G1082A(2),C1344T(2),C1726A(2),T1986C(2)
G2124T(2),C2151A(2),C2200A(2),G2211A(2),A2214G(2),A2234G(2)
A96C(3),T153C(3),G339A(3),G363A(3),T408C(3),C489T(3),G1068A(3),C1293T(3)
G1329A(3),C1365T(3),T1680G(3)
A108G(4),G205A(4),T291C(4),C318A(4),T328C(4),C483T(4),A522C(4),A565C(4)
T615G(4),C660A(4),A682G(4),C690T(4),C729T(4),A736G(4),A887C(4),G1005A(4)
C1009A(4),C1053A(4),T1130G(4),A1131G(4),G1197A(4),C1296T(4),T1353C(4),A1518G(4)
G1545A(4),C1560A(4),A1578G(4)
G165T(5),G201A(5),A300C(5),A306G(5)
G439A(6),A643G(6),C837T(6),G1100A(6),A1106C(6),C1113T(6),A1281T(6),A1390C(6)
C207A(7),T267C(7),C276T(7),G315A(7),A492G(7),G521A(7),C546A(7)
T6C(8),C150T(8),T386C(8),C429T(8),A747G(8),A796G(8)
-----------------------------------------------------------------
14+18+14+22+10+16+7+5=106,>Index1/2011-normalEIN/2011
C165T(1),A187G(1),A303G(1),A708G(1),A861G(1),G873A(1),G981C(1),A1058G(1)
G1149A(1),G1221A(1),T1335C(1),A1381G(1),A1878G(1),T2235C(1)
A105G(2),A155G(2),A195G(2),A405G(2),T447C(2),T772C(2),A981G(2),G1251A(2)
C1344A(2),G1389A(2),T1566C(2),G1707A(2),C1726A(2),G1757A(2),G1759A(2),C1995A(2)
G2007A(2),C2200A(2)
A96C(3),T153C(3),G339A(3),G363A(3),G516A(3),A795G(3),G813T(3),A962G(3)
A987G(3),G1068A(3),A1226G(3),C1365T(3),G1677A(3),T1680G(3)
T9C(4),A190G(4),G219T(4),C318A(4),A323G(4),C483T(4),A522C(4),A565C(4)
T615G(4),C660A(4),A682G(4),C729T(4),A983G(4),G1005A(4),C1053A(4),G1087A(4)
T1130G(4),G1185A(4),G1197A(4),C1296T(4),C1560A(4),A1578G(4)
C9T(5),G201A(5),A300C(5),A306G(5),C352A(5),T402C(5),G561A(5),G738A(5)
C825T(5),A1281C(5)
A165G(6),G267A(6),G439A(6),T609A(6),A643G(6),C666T(6),G732A(6),C837T(6)
T936A(6),G1095A(6),G1100A(6),A1106C(6),A1116G(6),G1199A(6),A1281T(6),A1390C(6)
T267C(7),T420C(7),A492G(7),G521A(7),A555T(7),A582G(7),A933G(7)
C79A(8),G390A(8),G404A(8),A416G(8),A735G(8)
-------------------------------------------------------------
34+20+7=61,>A/Oklahoma/3059/2012,2012/10/05
C72T(4),A146G(4),G182A(4),C191T(4),C285T(4),C318A(4),A430G(4),C456T(4)
A472G(4),A482G(4),C483T(4),G501A(4),A522C(4),A565C(4),T615G(4),G640T(4)
C660A(4),A682G(4),G715A(4),C729T(4),T882G(4),A983G(4),G1005A(4),C1053A(4)
G1087A(4),T1130G(4),A1195C(4),G1197A(4),C1254A(4),C1296A(4),A1524G(4),C1560A(4)
A1578G(4),A1671G(4)
A25T(6),C63T(6),T242C(6),G267A(6),A278G(6),T300C(6),G439A(6),C471T(6)
A489G(6),A643G(6),C666T(6),G732A(6),G828A(6),C837T(6),G1095A(6),G1100A(6)
A1106C(6),A1204G(6),A1281T(6),A1390C(6)
G180A(7),G189T(7),T267C(7),A441G(7),C468T(7),A492G(7),G521A(7)
-------------------------------------------------------------------
36+18+12=66,>A/Georgia/3058/2012,2012/09/26
T9C(4),A33T(4),G39A(4),A52G(4),A70G(4),A108G(4),G205A(4),T291C(4)
C318A(4),T328C(4),C483T(4),A522C(4),A565C(4),T615G(4),C660A(4),A682G(4)
C690T(4),C729T(4),A736G(4),G765A(4),A887C(4),T975C(4),G1005A(4),C1009A(4)
C1053A(4),T1130G(4),A1131G(4),G1197A(4),C1296T(4),T1353C(4),C1509T(4),A1518G(4)
G1545A(4),G1557A(4),C1560A(4),A1578G(4)
G204A(6),T242C(6),C399T(6),G439A(6),A643G(6),C837T(6),C903T(6),T945G(6)
A1016G(6),T1062C(6),G1100A(6),A1106C(6),C1113T(6),A1185G(6),A1204G(6),A1281T(6)
T1326C(6),A1390C(6)
C207A(7),T267C(7),C276T(7),G315A(7),G438A(7),C468T(7),A492G(7),G521A(7)
C546A(7),G839A(7),C859T(7),C874T(7),
-----------------------------------------------------
divide nucleotide-positions by 3 to get the amino-acid positions.
numbering the nucleotides of the coding region, other people often use
another numbering, e.g. substract 16 from the amino-acid positions to get the WHO numbering
mutations A<->G or C<->T at positions divisible by 3 are usually synonymous.
It would be useful to have a typical virus from the current outbreak with all 8 segments at genbank
-------------------------------------------------------------------------
there are currently 10 human HAs at genbank from June 2012 or later
3 are similar to GA3058 (Index2/2011,reassortant , 7 are similar to OK3059, new strain, now called "sgp11",
first seen in Singapore,July 2011 , see below
this could have led to reassortment between these 2
>A/Sao Paulo/49663/2012,2012/07/17
>A/Georgia/3058/2012,2012/09/26
>A/California/NHRC362744/2012,2012/11/06
>A/Guam/3049/2012,2012/08/08
>A/Guam/3050/2012,2012/06/15
>A/Guam/3057/2012,2012/08/24
>A/Japan/3060/2012,2012/10/17
>A/South Carolina/NHRC358725/2012,2012/08/24
>A/California/NHRC362154/2012,2012/10/25
>A/Oklahoma/3059/2012,2012/10/05
----------------------------------------------------------------------------
sgp11 HAs at genbank:
Code:
>A/Singapore/TT430/2011,2011/07/29
>A/Singapore/GP1490/2011,2011/09/08
>A/Singapore/GP1503/2011,2011/09/13
>A/Singapore/KK398/2011,2011/09/19
>A/Singapore/TT654/2011,2011/10/04
>A/Singapore/GP1575/2011,2011/10/06
>A/Singapore/TT662 /2011,2011/10/11
>A/Singapore/TT663/2011,2011/10/11
>A/Singapore/KK445/2011,2011/10/17
>A/Singapore/GP1655/2011,2011/10/20
>A/Singapore/H2011.808bC/2011,2011/10/22
>A/Singapore/GP1669/2011,2011/10/24
>A/Singapore/KK459/2011,2011/10/24
>A/Singapore/TT717/2011,2011/11/01
>A/Singapore/GP1703/2011,2011/11/03
>A/Singapore/KK482/2011,2011/11/08
>A/Singapore/KK505/2011,2011/11/17
>A/Singapore/GP1760/2011,2011/11/18
>A/Singapore/GP1810/2011,2011/12/01
>A/Singapore/KK535/2011,2011/12/05
>A/Singapore/GP1846/2011,2011/12/09
>A/Singapore/TT815/2011,2011/12/13
>A/Singapore/TT827/2011,2011/12/13
>A/Singapore/GP1905/2011,2011/12/21
>A/Singapore/TT837/2011,2011/12/22
>A/Singapore/TT879/2011,2011/12/30
>A/Korea/AF2784/2012,2012/01/19
>A/Korea/AF2785/2012,2012/01/20
>A/Korea/AF2781/2012,2012/01/24
>A/Kyrgyzstan/3056/2012,2012/01/26
>A/Novosibirsk/RII09/2012,2012/01/29
>A/Novosibirsk/155/2012,2012/01/29
>A/Tyumen/03/2012,2012/01/30
>A/Moscow/02/2012,2012/02/01
>A/Novosibirsk/RII08/2012,2012/02/02
>A/Novosibirsk/13/2012,2012/02/02
>A/Pavia/81/2012,2012/02/07
>A/Pavia/95/2012,2012/02/09
>A/Krasnoyarsk/10/2012,2012/02/09
>A/Korea/AF2857/2012,2012/02/13
>A/Japan/AF2846/2012,2012/02/14
>A/Kyrgyzstan/3053/2012,2012/02/18
>A/Novosibirsk/26k/2012,2012/02/19
>A/Novosibirsk/22/2012,2012/02/20
>A/Korea/AF2856/2012,2012/02/21
>A/Novosibirsk/RII14/2012,2012/02/24
>A/Novosibirsk/16/2012,2012/02/24
>A/North Carolina/AF2843/2012,2012/02/28
>A/Korea/2970/2012,2012/03/01
>A/Nevada/3001/2012,2012/03/03
>A/Illinois/AF2867/2012,2012/03/05
>A/Saint Petersburg/RII16/2012,2012/03/05
>A/Huzhou/1113/2012,2012/03/05
>A/New York/AF2868/2012,2012/03/06
>A/Czech Republic/121/2012,2012/03/06
>A/Novosibirsk/RII25/2012,2012/03/06
>A/Kaliningrad/RII02/2012,2012/03/07
>A/Kyrgyzstan/3051/2012,2012/03/12
>A/Ohio/3029/2012,2012/03/14
>A/Ohio/3027/2012,2012/03/14
>A/Novosibirsk/59d/2012,2012/03/14
>A/Ekaterinburg/RII06/2012,2012/03/20
>A/Japan/2974/2012,2012/03/21
>A/Kyrgyzstan/3048/2012,2012/03/22
>A/Ohio/2992/2012,2012/03/26
>A/Ohio/3015/2012,2012/04/23
>A/Ohio/3016/2012,2012/04/23
>A/Guam/3050/2012,2012/06/15
>A/Guam/3049/2012,2012/08/08
>A/South Carolina/NHRC358725/2012,2012/08/24
>A/Guam/3057/2012,2012/08/24
>A/Oklahoma/3059/2012,2012/10/05
>A/Japan/3060/2012,2012/10/17
>A/California/NHRC362154/2012,2012/10/25
--------------------------------------------------------------------------
we had this HA in Russia, i.e. Novosibirsk , Feb.Mar 2012 , several viruses are at genbank
with segments 4,5,6,7,8 - 1,2,3 missing.
There are many mutations in that strain, at least 12,6,6,5,3 more than in Index1/2011
from which it seems to descend. Almost double as many as I'd expect in 1 year.
so it seems that USA now has this strain: (from which only segments 4,5,6,7,8 are available)
-------edit--------no, we have one virus with these mutations and all 8 segments at genbank !
It's A/Czech Republik/121/2012/03/06(H3N2) it has 156=28+27+23+33+10+19+10+6
mutations , descends from Egypt_Iowa+NA but not from Index1/2011 nor Index2/2011
and is similar to OK3059 in segments 4,6,7
A/Novosibirsk/RII08/2012,2012/02/02
A/Novosibirsk/RII09/2012,2012/01/29
A/Novosibirsk/13/2012,2012/02/02
A/Novosibirsk/155/2012,2012/01/29
A/Kaliningrad/RII02/2012,2012/03/07
A/Krasnoyarsk/10/2012,2012/02/09
A/Novosibirsk/RII14/2012,2012/02/24
A/Novosibirsk/22/2012,2012/02/20
A/Novosibirsk/16/2012,2012/02/24
A/Novosibirsk/26k/2012,2012/02/19
A/Novosibirsk/RII25/2012,2012/03/06
A/Saint Petersburg/RII16/2012,2012/03/05
A/Saint Petersburg/RII50/2012,2012/04/10
A/Moscow/02/2012,2012/02/01
A/Ekaterinburg/RII06/2012,2012/03/20
A/Tyumen/03/2012,2012/01/30,H3N2
A/Novosibirsk/59d/2012,2012/03/14
--------------------------------------------------------------------------
2013-01-25 : fludb uses the 5 available HAs for an antigenic analysis
A/Victoria/361/2011
A/Japan/3060/2012
A/Oklahoma/3059/2012
A/California/NHRC/362744/2012
A/California/NHRC/362154/2012
http://www.fludb.org/brcDocs/documen...content_v1.pdf
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February 5th, 2013, 06:12 AM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,950
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Re: H3n2
82 H3N2-HAs from Canada, this season, today at genbank
(segment 4 only)
I count ~4(10) different introductions
82=7+32+11+32=7+(6+6+4+16)+(9+2)+(22+8+2)
7 are from the reassorted strain 2011-reassorted-EI, index2-2011
the other 75 are similar to CZ121 in HA, "index3-2011"
Code:
000000000000000000000000000000000000000000000000000000111111111111111111111111111111111
000111111111222222222333444444555566666667777788889999000000001111222222333334555555666
357023466889001446789224123578019900244990113625880188001134580139145699235671112347167
952802625021589077651185900622181439203035456594273537591487671315554936383716384057321
-codon-position------------------------------------ 1 2 2211 1 1 2 1 12 2 111 11 12 2 2 1 1 1 2 1 22
---Index-------------------------------------------GCCAGAATTGGCGAGCACTCTCTTGCACAAGTGTGGAGTCGTAGAGCGTATCATACATCCGGCTAACCCGCTGCTCCGGAAAGGTCA
1 >Index/2009/Egypt/Iowa ....................................................................................... 0 0 , 0 0 1:>Index/2009/Egypt/Iowa
2 >Index/H3N3-2011-reassortedEI/2011(H3N2) ...G........A.......C.C................T....G....C.....A........G.........C....G..A.... 12 12 , 12 12 2:>Index/H3N3-2011-reassortedEI/2011(H3N2)
3 >Index/H3N2-2011-normalEI/2011(H3N2) ..............T.....................................G........A......................... 7 3 , 7 3 3:>Index/H3N2-2011-normalEI/2011(H3N2)
4 >KC526210,A/Ontario/004/2013(H3N2) ...G.G...A..A.......C.CC........A.....GT.CG.G....CC....A....T.T.G.........C.T..G..A.C.. 24 24 , 24 24 4:>KC526210,A/Ontario/004/2013(H3N2)
5 >KC535039,A/Quebec/016/2012(H3N2) ...G.G...A..A.......C.CC........A....AGT.CG.G....CC....A....T.T.G.......--------------- 38 35 , 20 20 5:>KC535039,A/Quebec/016/2012(H3N2)
6 >KC535052,A/Quebec/030/2012(H3N2) ...G.G...A..A.......C.CC........A....AGT.CG.G....CC....A....T.T.G........-------------- 38 34 , 21 20 6:>KC535052,A/Quebec/030/2012(H3N2)
7 >KC535043,A/Quebec/020/2012(H3N2) ...G.G...A..A.......C.CC........A.....GT.CG.G....CC....A....T.T.G.......--------------- 38 34 , 20 19 7:>KC535043,A/Quebec/020/2012(H3N2)
8 >KC535060,A/Quebec/039/2012(H3N2) ...G.G...A..A.......C.CC........A.....GT.CG.G....CC....A....T.T.G........-------------- 37 33 , 20 19 8:>KC535060,A/Quebec/039/2012(H3N2)
9 >KC539120,A/Alberta/054/2012(H3N2) ...G.....A..A.......C.CC........A.....GT.CG.G....CC....A....T.T.G.........CYT..G..A.C.. 26 24 , 25 24 9:>KC539120,A/Alberta/054/2012(H3N2)
10 >KC535055,A/Quebec/034/2012(H3N2) ...G.G...A..A.......C.CC........A....AGT.CG.G....CC....A....T.T.G.....----------------- 43 37 , 22 20 10:>KC535055,A/Quebec/034/2012(H3N2)
11 >KC539119,A/Alberta/053/2012(H3N2) ..T...G...AT.....T.........T..A......T.....A....G...G............C..A........A.....A..G 16 16 , 16 16 11:>KC539119,A/Alberta/053/2012(H3N2)
12 >KC539134,A/Alberta/068/2012(H3N2) ..T...G...AT.....T.........T..A..C...T.....A....G...G............C..A........A.....A..G 17 17 , 17 17 12:>KC539134,A/Alberta/068/2012(H3N2)
13 >KC535022,A/British Columbia/023/2012(H3N2) A.T...G...AT...............T..AC.....T.....A....G.C.G......T.A.C.C.TA...--------------- 37 34 , 19 19 13:>KC535022,A/British Columbia/023/2012(H3N2)
14 >KC535045,A/Quebec/022/2012(H3N2) A.T...G...AT...............T..AC.....T.....A....G.C.G......T.A.C.C.TA...--------------- 37 34 , 19 19 14:>KC535045,A/Quebec/022/2012(H3N2)
15 >KC535046,A/Quebec/023/2012(H3N2) A.T...G...AT...............T..AC.....T.....A....G.C.G......T.A.C.C.TA...--------------- 38 34 , 20 19 15:>KC535046,A/Quebec/023/2012(H3N2)
16 >KC535042,A/Quebec/019/2012(H3N2) A.T...G...AT...............T..AC.....T.....A....G...G......T.A.C.C.TA.----------------- 40 35 , 20 18 16:>KC535042,A/Quebec/019/2012(H3N2)
17 >KC526204,A/Ontario/030/2012(H3N2) ..T...G.C.AT......CT.......T.GA......T..A..A....G...G...G..T.....C..AA........AGG....AG 25 25 , 25 25 17:>KC526204,A/Ontario/030/2012(H3N2)
18 >KC526209,A/Ontario/003/2013(H3N2) ..T...G.C.AT......CT.......T.GA......T..A..A....G...G...G..T.....C..AA........AGG..---- 29 27 , 23 23 18:>KC526209,A/Ontario/003/2013(H3N2)
19 >KC526212,A/Ontario/006/2013(H3N2) ..T...G.C.AT......CT.......T.GA......T..A..A....G...G...G..T.....C..AA........AGG....AG 25 25 , 25 25 19:>KC526212,A/Ontario/006/2013(H3N2)
20 >KC535044,A/Quebec/021/2012(H3N2) ..T...G.C.AT......CT.......T.GA......T..A..A....G...G...G..T.....C..AA..--------------- 38 35 , 20 20 20:>KC535044,A/Quebec/021/2012(H3N2)
21 >KC535030,A/British Columbia/005/2013(H3N2) ..T...G.C.AT......CT.......T.GA......T..A..A....G...G...G..T.....C..AA...-------------- 38 34 , 21 20 21:>KC535030,A/British Columbia/005/2013(H3N2)
22 >KC526208,A/Ontario/002/2013(H3N2) ..T...G.C.AT......CT.......T.GA......T..A..A....G...G...G..T.....C..AA..........G.....G 23 22 , 23 22 22:>KC526208,A/Ontario/002/2013(H3N2)
23 >KC535027,A/British Columbia/002/2013(H3N2) ..T...G...AT.......T.......T.GA.A....T..A..A....G...G............C..A...--------------- 35 31 , 17 16 23:>KC535027,A/British Columbia/002/2013(H3N2)
24 >KC535049,A/Quebec/026/2012(H3N2) ..T...G...AT.......T.......T.GA...A..T..A..A....G...G.......A....C..A...--------------- 37 32 , 19 17 24:>KC535049,A/Quebec/026/2012(H3N2)
25 >KC526207,A/Ontario/001/2013(H3N2) ..T...G...AT.......T.......T.GA......T.....A....G...G............C..A..........GG.....G 21 17 , 21 17 25:>KC526207,A/Ontario/001/2013(H3N2)
26 >KC535061,A/Manitoba/001/2012(H3N2) ..T...G...AT....G..T.......T.GA......T.....A....G...G.G..........C..A.T---------------- 36 33 , 17 17 26:>KC535061,A/Manitoba/001/2012(H3N2)
27 >KC535062,A/Manitoba/002/2012(H3N2) ..T...G...AT....G..T.......T.GA......T.....A....G...G.G..........C..A.T---------------- 37 33 , 18 17 27:>KC535062,A/Manitoba/002/2012(H3N2)
28 >KC539115,A/Alberta/049/2012(H3N2) ..T...G...AT....G..T.......T.GA......T.....A....G...G.G..........C..A.T.T......GGG....G 22 22 , 22 22 28:>KC539115,A/Alberta/049/2012(H3N2)
29 >KC539116,A/Alberta/050/2012(H3N2) ..T...G...AT....G..T.......T.GA......T.....A....G...G.G..........C..A.T.T......GGG....G 22 22 , 22 22 29:>KC539116,A/Alberta/050/2012(H3N2)
30 >KC539117,A/Alberta/051/2012(H3N2) ..T...G...AT....G..T.......T.GA......T.....A....G...G.G..........C..A.T.T......GGG...-- 24 23 , 21 21 30:>KC539117,A/Alberta/051/2012(H3N2)
31 >KC539121,A/Alberta/055/2012(H3N2) ..T...G...AT....G..T.......T.GA......T.....A....G...G.G..........C..A.T.T......GGG...-- 24 23 , 21 21 31:>KC539121,A/Alberta/055/2012(H3N2)
32 >KC539122,A/Alberta/056/2012(H3N2) ..T...G...AT....G..T.......T.GA......T.....A....G...G.G..........C..A.T.T......GGG....G 22 22 , 22 22 32:>KC539122,A/Alberta/056/2012(H3N2)
33 >KC539124,A/Alberta/058/2012(H3N2) ..T...G...AT....G..T.......T.GA......T.....A....G...G.G..........C..A.T.T......GGG....G 22 22 , 22 22 33:>KC539124,A/Alberta/058/2012(H3N2)
34 >KC539127,A/Alberta/061/2012(H3N2) ..T...G...AT....G..T.......T.GA......T.....A....G...G.G..........C..A.T.T......GGG....G 22 22 , 22 22 34:>KC539127,A/Alberta/061/2012(H3N2)
35 >KC539128,A/Alberta/062/2012(H3N2) ..T...G...AT....G..T.......T.GA......T.....A....G...G.G..........C..A.T.T......GGG....G 23 22 , 22 22 35:>KC539128,A/Alberta/062/2012(H3N2)
36 >KC539130,A/Alberta/064/2012(H3N2) ..T...G...AT....G..T.......T.GA......T.....A....G...G.G..........C..A.T.T......GGG....G 22 22 , 22 22 36:>KC539130,A/Alberta/064/2012(H3N2)
37 >KC539132,A/Alberta/066/2012(H3N2) ..T...G...AT....G..T.......T.GA......T.....A....G...G.G..........C..A.T.T......GGG....G 22 22 , 22 22 37:>KC539132,A/Alberta/066/2012(H3N2)
38 >KC539133,A/Alberta/067/2012(H3N2) ..T...G...AT....G..T.......T.GA......T.....A....G...G.G..........C..A.T.T......GGG....G 22 22 , 22 22 38:>KC539133,A/Alberta/067/2012(H3N2)
39 >KC539123,A/Alberta/057/2012(H3N2) ..T...G...AT....G..T.......T.GA......T.....A....G...G.G..........C..A.T.T......GGG....G 23 22 , 23 22 39:>KC539123,A/Alberta/057/2012(H3N2)
40 >KC539131,A/Alberta/065/2012(H3N2) ..T...G...AT....G..T.......T.GA......T.....A....G...G.G..........C..A.T.T......GGG....G 23 22 , 23 22 40:>KC539131,A/Alberta/065/2012(H3N2)
41 >KC539112,A/Alberta/046/2012(H3N2) ..T...G...AT....G..T.......T.GA......T.....A....G...G.G..........C..A.T.T......GGG...-- 25 23 , 22 21 41:>KC539112,A/Alberta/046/2012(H3N2)
42 >KC535026,A/British Columbia/001/2013(H3N2) ..T...G...AT..A....T....A..T.GA......T.....A....G...G............C..A.----------------- 40 33 , 19 16 42:>KC535026,A/British Columbia/001/2013(H3N2)
43 >JX913034,A/Czech Republic/121/2012(H3N2) ..T...G...AT............A..T..A......T.....A....G...G............C..A.................G 18 14 , 18 14 43:>JX913034,A/Czech Republic/121/2012(H3N2)
44 >KC535035,A/Quebec/012/2012(H3N2) ..T...G...AT...T...T.......T.GA......T.....A.A..G..AG............C..A...--------------- 37 32 , 19 17 44:>KC535035,A/Quebec/012/2012(H3N2)
45 >KC539118,A/Alberta/052/2012(H3N2) ..T...G...AT...T...T.T.....T.GA......T.....A.A..G..AG............C..A....T......G.....G 21 21 , 21 21 45:>KC539118,A/Alberta/052/2012(H3N2)
46 >KC539135,A/Alberta/069/2012(H3N2) ..T...G...AT...T...T.T.....T.GA......T.....A.A..G..AG............C..A....T......G.....G 21 21 , 21 21 46:>KC539135,A/Alberta/069/2012(H3N2)
47 >KC526213,A/Ontario/007/2013(H3N2) ..T...G...AT...T...T.T.....T.GA......T.....A.A..G..AG............C..A....T......G.....G 22 21 , 22 21 47:>KC526213,A/Ontario/007/2013(H3N2)
48 >KC539113,A/Alberta/047/2012(H3N2) ..T...G...AT...T...T.T.....T.GA......T.....A.A..G..AGC...........C..A....T......G.....G 22 22 , 22 22 48:>KC539113,A/Alberta/047/2012(H3N2)
49 >KC539114,A/Alberta/048/2012(H3N2) ..T...G...AT...T...T.T.....T.GA......T.....A.A..G..AG............C..A....T......G.....G 22 21 , 22 21 49:>KC539114,A/Alberta/048/2012(H3N2)
50 >KC539125,A/Alberta/059/2012(H3N2) ..T...G...AT...T...T.T.....T.GA......T.....A.A..G..AG............C..A....T......G.....G 22 21 , 22 21 50:>KC539125,A/Alberta/059/2012(H3N2)
51 >KC539136,A/Alberta/070/2012(H3N2) ..T...GC..AT...T...T.......T.GA....T.T.....A.A..G..AG....C.......C..A...........G.....G 23 22 , 23 22 51:>KC539136,A/Alberta/070/2012(H3N2)
52 >KC535063,A/Manitoba/003/2012(H3N2) ..T...GC..AT...T...T.......T.GA....T.T.....A.A..G..AG....C.......C.-------------------- 49 39 , 21 19 52:>KC535063,A/Manitoba/003/2012(H3N2)
53 >KC539129,A/Alberta/063/2012(H3N2) .AT...G...AT.GAT...T.......T.GA......T.....A.AA.G..AG............CT.A...........G.....G 24 24 , 24 24 53:>KC539129,A/Alberta/063/2012(H3N2)
54 >KC539126,A/Alberta/060/2012(H3N2) .AT...G...AT.GAT...T.......T.GA......T.....A.AA.G..AG............CT.A......Y....G.....G 26 25 , 26 25 54:>KC539126,A/Alberta/060/2012(H3N2)
55 >KC526211,A/Ontario/005/2013(H3N2) ..T...G...AT.......T......GTGGA......T.....A....G...G........A...C..A..A........G.....G 20 20 , 20 20 55:>KC526211,A/Ontario/005/2013(H3N2)
56 >KC526214,A/Ontario/008/2013(H3N2) ..T...G...AT.......T......GTGGA......T.....A....G...G........A...C..A..A........G.....G 20 20 , 20 20 56:>KC526214,A/Ontario/008/2013(H3N2)
57 >KC535025,A/British Columbia/026/2012(H3N2) ..T...G...AT.......T......GTGGA......T.....A....G...G........A...C..A.----------------- 38 34 , 17 17 57:>KC535025,A/British Columbia/026/2012(H3N2)
58 >KC535036,A/Quebec/013/2012(H3N2) ..T...G...AT.......T......GTGGA......T.....A....G...G........A...C..A.----------------- 37 34 , 17 17 58:>KC535036,A/Quebec/013/2012(H3N2)
59 >KC535037,A/Quebec/014/2012(H3N2) ..T...G...AT.......T......GTGGA......T.....A....G...G........A...C..A..---------------- 36 33 , 17 17 59:>KC535037,A/Quebec/014/2012(H3N2)
60 >KC535038,A/Quebec/015/2012(H3N2) ..T...G...AT.......T......GTGGA......T.....A....G...G........A...C..A..---------------- 36 33 , 17 17 60:>KC535038,A/Quebec/015/2012(H3N2)
61 >KC535040,A/Quebec/017/2012(H3N2) ..T...G...AT.......T......GTGGA......T.....A....G...G........A...C..A.----------------- 38 34 , 17 17 61:>KC535040,A/Quebec/017/2012(H3N2)
62 >KC535041,A/Quebec/018/2012(H3N2) ..T...G...AT.......T......GTGGA......T.....A....G...G........A...C..A..---------------- 36 33 , 17 17 62:>KC535041,A/Quebec/018/2012(H3N2)
63 >KC535047,A/Quebec/024/2012(H3N2) ..T...G...AT.......T......GTGGA......T.....A....G...G........A...C..A..---------------- 36 33 , 17 17 63:>KC535047,A/Quebec/024/2012(H3N2)
64 >KC535048,A/Quebec/025/2012(H3N2) ..T...G...AT.......T......GTGGA......T.....A....G...G........A...C..A..A--------------- 36 33 , 18 18 64:>KC535048,A/Quebec/025/2012(H3N2)
65 >KC535054,A/Quebec/033/2012(H3N2) ..T...G...AT.......T......GTGGA......T.....A....G...G........A...C..A..A--------------- 36 33 , 18 18 65:>KC535054,A/Quebec/033/2012(H3N2)
66 >KC535058,A/Quebec/037/2012(H3N2) ..T...G...AT.......T......GTGGA......T.....A....G...G........A...C..A..---------------- 36 33 , 17 17 66:>KC535058,A/Quebec/037/2012(H3N2)
67 >KC526205,A/Ontario/031/2012(H3N2) ..T...G...AT.......T.....AGTGGA......T.....A....G...G........A...C..A..A........G.....G 21 21 , 21 21 67:>KC526205,A/Ontario/031/2012(H3N2)
68 >KC526206,A/Ontario/032/2012(H3N2) ..T...G...AT.......T.....AGTGGA......T.....A....G...G........A...C..A..A........G.....G 21 21 , 21 21 68:>KC526206,A/Ontario/032/2012(H3N2)
69 >KC535034,A/Quebec/011/2012(H3N2) ..T...G...AT.......T......GTGGA......T.....A....G...G........A...C..A..---------------- 37 33 , 18 17 69:>KC535034,A/Quebec/011/2012(H3N2)
70 >KC535050,A/Quebec/028/2012(H3N2) ..T...G...AT.......T......GTGGA.....GT.....A....G...G........A...C..A..A--------------- 37 34 , 19 19 70:>KC535050,A/Quebec/028/2012(H3N2)
71 >KC535059,A/Quebec/038/2012(H3N2) ..T...G...AT.......T......GTGGA.....GT.....A....G...G........A...C..A..---------------- 37 34 , 18 18 71:>KC535059,A/Quebec/038/2012(H3N2)
72 >KC535051,A/Quebec/029/2012(H3N2) ..T...G...AT.......T......GTGGA......T.....A....G...G........A...C..A..A--------------- 37 33 , 19 18 72:>KC535051,A/Quebec/029/2012(H3N2)
73 >KC535053,A/Quebec/031/2012(H3N2) ..T...G...AT.......T......GTGGA......T.....A....G...G........A...C..A..A--------------- 37 33 , 19 18 73:>KC535053,A/Quebec/031/2012(H3N2)
74 >KC535064,A/Manitoba/004/2012(H3N2) ..T...G...AT.......T......GTGGA......T.....A....G...G........A...C..A.----------------- 38 34 , 18 17 74:>KC535064,A/Manitoba/004/2012(H3N2)
75 >KC535056,A/Quebec/035/2012(H3N2) ..T...G...AT.......T......GTGGA......T.....A...AG...G........A...C..A.----------------- 40 35 , 19 18 75:>KC535056,A/Quebec/035/2012(H3N2)
76 >KC535021,A/British Columbia/022/2012(H3N2) ..T...G...AT.......T......GTGGA......T.....A....G...G............C..A..---------------- 36 32 , 17 16 76:>KC535021,A/British Columbia/022/2012(H3N2)
77 >KC535028,A/British Columbia/003/2013(H3N2) ..T.A.G...AT.......T......GTGGA......T.....A....G...GA....A......C..A..---------------- 38 35 , 19 19 77:>KC535028,A/British Columbia/003/2013(H3N2)
78 >KC535032,A/British Columbia/007/2013(H3N2) ..T.A.G...AT.......T......GTGGA......T.....A....G...GA....A.....----------------------- 57 40 , 17 17 78:>KC535032,A/British Columbia/007/2013(H3N2)
79 >KC535033,A/British Columbia/008/2013(H3N2) ..T.A.G...AT.......T......GTGGA......T.....A....G...GA....A......C..A..---------------- 38 35 , 19 19 79:>KC535033,A/British Columbia/008/2013(H3N2)
80 >KC535020,A/British Columbia/021/2012(H3N2) ..T.A.G...AT.......T......GTGGA......T.....A....G...GA....A......C..A..---------------- 39 35 , 20 19 80:>KC535020,A/British Columbia/021/2012(H3N2)
81 >KC535029,A/British Columbia/004/2013(H3N2) ..T.A.G...AT.......T......GTGGA......T.....A....G...GA....A......C..A..---------------- 39 35 , 20 19 81:>KC535029,A/British Columbia/004/2013(H3N2)
82 >KC535019,A/British Columbia/020/2012(H3N2) -.T.A.G...AT.......T......GTGGA......T.....A....G...GA....A......C..A..A........G....-- 28 24 , 23 21 82:>KC535019,A/British Columbia/020/2012(H3N2)
83 >KC535023,A/British Columbia/024/2012(H3N2) ..T.A.G...AT.......T......GTGGA......T.....A....G...GA....A......C..A..---------------- 40 35 , 21 19 83:>KC535023,A/British Columbia/024/2012(H3N2)
84 >KC535024,A/British Columbia/025/2012(H3N2) ..T.A.G...AT.......T......GTGGA......T.....A...AG...GA....A......C..A.----------------- 42 37 , 21 20 84:>KC535024,A/British Columbia/025/2012(H3N2)
85 >KC535031,A/British Columbia/006/2013(H3N2) ..T.......AT.......T......GTGGA......T.....A....G...G............C..A..---------------- 37 31 , 18 15 85:>KC535031,A/British Columbia/006/2013(H3N2)
86 >KC535057,A/Quebec/036/2012(H3N2) ..T...G...AT.......T......GTGGA..CA..T.....A....A...G............C..A..---------------- 39 34 , 20 18 86:>KC535057,A/Quebec/036/2012(H3N2)
---Index-------------------------------------------GCCAGAATTGGCGAGCACTCTCTTGCACAAGTGTGGAGTCGTAGAGCGTATCATACATCCGGCTAACCCGCTGCTCCGGAAAGGTCA
-codon-position------------------------------------ 1 2 2211 1 1 2 1 12 2 111 11 12 2 2 1 1 1 2 1 22
000000000000000000000000000000000000000000000000000000111111111111111111111111111111111
000111111111222222222333444444555566666667777788889999000000001111222222333334555555666
357023466889001446789224123578019900244990113625880188001134580139145699235671112347167
952802625021589077651185900622181439203035456594273537591487671315554936383716384057321
amino acids:
(same positions-numeration as in the pdf from fludb above
but substract 16 to get the WHO-enumeration (in the first part) )
Code:
000000000000000000000000000000000000000000000000
000000000000011111111112222222223333333334445555
124456666777800134456780113488990122677890290236
963991469038348070481378459658468708324452745681
------------------------------------------------
LTKQVSTEDSQEIVKYNSTRNLNIASVIRANEKTANVQSKGGKIDGIR
>Index/2009/Egypt/Iowa ................................................
>Index/H3N3-2011-reassortedEI/2011(H3N2) ........N......H...........V...A................
>Index/H3N2-2011-normalEI/2011(H3N2) ......A...H...R....................SM...........
>KC526210,A/Ontario/004/2013(H3N2) ........N......H.........A.V...A..............T.
>KC535039,A/Quebec/016/2012(H3N2) ........N......H........TA.V...A...........-----
>KC535052,A/Quebec/030/2012(H3N2) ........N......H........TA.V...A...........-----
>KC535043,A/Quebec/020/2012(H3N2) ...H....N......H.........A.V...A...........-----
>KC535060,A/Quebec/039/2012(H3N2) ........N......H.........A.V...A.I.........-----
>KC539120,A/Alberta/054/2012(H3N2) ........N......H.........A.V...A..D...........T-
>KC535055,A/Quebec/034/2012(H3N2) ........N......Q........TA.V...A..........------
>KC539119,A/Alberta/053/2012(H3N2) ...R.NI.................S.I...K....S.........E.-
>A/Victoria/361(vaccine-strain)/2011(H3N2) .....NI.................S.I........S............
>KC539134,A/Alberta/068/2012(H3N2) ...R.NI.................S.I...K....S.........E..
>KC535022,A/British Columbia/023/2012(H3N2) ...R.NI..............S..S.I...K....SM......-----
>KC535045,A/Quebec/022/2012(H3N2) ...R.NI..............S..S.I...K....SM......-----
>KC535046,A/Quebec/023/2012(H3N2) ...R.NI..............S..S.I...K....SM......-----
>KC535042,A/Quebec/019/2012(H3N2) ...R.NI..............S..S.I...K....SM......-----
>KC526204,A/Ontario/030/2012(H3N2) ...R.NI.............S...S.I...K....S........N...
>KC526209,A/Ontario/003/2013(H3N2) ...R.NI.............S...S.I...K....S........N---
>KC526212,A/Ontario/006/2013(H3N2) ...R.NI.............S...S.I...K....S........N...
>KC535044,A/Quebec/021/2012(H3N2) ...R.NI.............S...S.I...K....S.......-----
>KC535030,A/British Columbia/005/2013(H3N2) ...R.NI....K........S...S.I...K....S.......-----
>KC526208,A/Ontario/002/2013(H3N2) ...R.NI.............S...S.I...K....S............
>KC535027,A/British Columbia/002/2013(H3N2) ...R.NI.............S...S.I...K....S.......-----
>KC535049,A/Quebec/026/2012(H3N2) ...R.NI.............S...S.I...K....S.......-----
>KC526207,A/Ontario/001/2013(H3N2) ...R.NI.........S...S...S.I...K....S.......M....
>KC535061,A/Manitoba/001/2012(H3N2) ...R.NI.....V.......S...S.I...K....S.......-----
>KC535062,A/Manitoba/002/2012(H3N2) ...R.NI.....V.......S...S.I...K....S.......-----
>KC539115,A/Alberta/049/2012(H3N2) ...R.NI.....V.......S...S.I...K....S............
>KC539116,A/Alberta/050/2012(H3N2) ...R.NI.....V.......S...S.I...K....S............
>KC539117,A/Alberta/051/2012(H3N2) ...R.NI.....V.......S...S.I...K....S...........-
>KC539121,A/Alberta/055/2012(H3N2) ...R.NI.....V.......S...S.I...K....S...........-
>KC539122,A/Alberta/056/2012(H3N2) ...R.NI.....V.......S...S.I...K....S............
>KC539124,A/Alberta/058/2012(H3N2) ...R.NI.....V.......S...S.I...K....S............
>KC539127,A/Alberta/061/2012(H3N2) ...R.NI.....V.......S...S.I...K....S............
>KC539128,A/Alberta/062/2012(H3N2) ...R.NI.....V.......S...S.I...K....S...........-
>KC539130,A/Alberta/064/2012(H3N2) ...R.NI.....V.......S...S.I...K....S...........-
>KC539132,A/Alberta/066/2012(H3N2) ...R.NI.....V.......S...S.I...K....S...........-
>KC539133,A/Alberta/067/2012(H3N2) ...R.NI.....V.......S...S.I...K....S............
>KC539123,A/Alberta/057/2012(H3N2) ...R.NI.....V.......S...S.I...K....S...........-
>KC539131,A/Alberta/065/2012(H3N2) ...R.NI.....V.......S...S.I...K....S............
>KC539112,A/Alberta/046/2012(H3N2) ...R.NI.....V.......S...S.I...K....S...........-
>KC535026,A/British Columbia/001/2013(H3N2) ...R.NI..........N..S...S.I...K.R..S......------
>JX913034,A/Czech Republic/121/2012(H3N2) ...R.NIK.........N....D.S.I...K....S............
>KC535035,A/Quebec/012/2012(H3N2) ..ER.NI......I......S...S.I...K....S.......-----
>KC539118,A/Alberta/052/2012(H3N2) ...R.NI.............S...S.I...K....S............
>KC539135,A/Alberta/069/2012(H3N2) ...R.NI.............S...S.I...K....S...........-
>KC526213,A/Ontario/007/2013(H3N2) ...R.NI.............S...S.I...K....S............
>KC539113,A/Alberta/047/2012(H3N2) ...R.NI.............S...S.I...K....S............
>KC539114,A/Alberta/048/2012(H3N2) .K.R.NI.............S...S.I...K....S............
>KC539125,A/Alberta/059/2012(H3N2) ...R.NI.............S...S.I...K....S............
>KC539136,A/Alberta/070/2012(H3N2) ...R.NI.............S...S.I...K....S...........M
>KC535063,A/Manitoba/003/2012(H3N2) ...R.NI.............S...S.I...K....S.....R------
>KC539129,A/Alberta/063/2012(H3N2) I..R.NI..G..........S...S.I...K....S............
>KC539126,A/Alberta/060/2012(H3N2) I..R.NI..G..........S...S.I...K....S............
>KC526211,A/Ontario/005/2013(H3N2) ...R.NI...........AGS...S.I...K....SM...........
>KC526214,A/Ontario/008/2013(H3N2) ...R.NI...........AGS...S.I...K....SM...........
>KC535025,A/British Columbia/026/2012(H3N2) ...R.NI...........AGS...S.I...K....SM.....------
>KC535036,A/Quebec/013/2012(H3N2) ...R.NI...........AGS...S.I...K....SM......-----
>KC535037,A/Quebec/014/2012(H3N2) ...R.NI...........AGS...S.I...K....SM......-----
>KC535038,A/Quebec/015/2012(H3N2) ...R.NI...........AGS...S.I...K....SM......-----
>KC535040,A/Quebec/017/2012(H3N2) ...R.NI...........AGS...S.I...K....SM.....------
>KC535041,A/Quebec/018/2012(H3N2) ...R.NI...........AGS...S.I...K....SM......-----
>KC535047,A/Quebec/024/2012(H3N2) ...R.NI...........AGS...S.I...K....SM......-----
>KC535048,A/Quebec/025/2012(H3N2) ...R.NI...........AGS...S.I...K....SM......-----
>KC535054,A/Quebec/033/2012(H3N2) ...R.NI...........AGS...S.I...K....SM......-----
>KC535058,A/Quebec/037/2012(H3N2) ...R.NI...........AGS...S.I...K....SM......-----
>KC526205,A/Ontario/031/2012(H3N2) ...R.NI..........RAGS...S.I...K....SM...........
>KC526206,A/Ontario/032/2012(H3N2) ...R.NI..........RAGS...S.I...K....SM...........
>KC535034,A/Quebec/011/2012(H3N2) ...R.NI...........AGS...S.I..VK....SM......-----
>KC535050,A/Quebec/028/2012(H3N2) ...R.NI...........AGS..VS.I...K....SM......-----
>KC535059,A/Quebec/038/2012(H3N2) ...R.NI...........AGS..VS.I...K....SM......-----
>KC535051,A/Quebec/029/2012(H3N2) ...R.NI...........AGS...S.I...K....SML.....-----
>KC535053,A/Quebec/031/2012(H3N2) ...R.NI...........AGS...S.I...K....SM......-----
>KC535064,A/Manitoba/004/2012(H3N2) ...R.NI...........AGS...S.I...K....SM.....R-----
>KC535056,A/Quebec/035/2012(H3N2) ...R.NI...........AGS...S.I.K.K....SM.....------
>KC535021,A/British Columbia/022/2012(H3N2) ...R.NI...........AGS...S.I...K....S.......-----
>KC535028,A/British Columbia/003/2013(H3N2) ...R.NI...........AGS...S.I...K....S.......-----
>KC535032,A/British Columbia/007/2013(H3N2) ...R.NI...........AGS...S.I...K....S..----------
>KC535033,A/British Columbia/008/2013(H3N2) ...R.NI...........AGS...S.I...K....S.......-----
>KC535020,A/British Columbia/021/2012(H3N2) ...R.NI...........AGS...S.I...K....S...E...-----
>KC535029,A/British Columbia/004/2013(H3N2) ...R.NI...........AGS...S.I...K....S....R..-----
>KC535019,A/British Columbia/020/2012(H3N2) ...RINI...........AGS...S.I...K....S...........-
>KC535023,A/British Columbia/024/2012(H3N2) ...R.NI...........AGS...S.I...K....S.......-----
>KC535024,A/British Columbia/025/2012(H3N2) ...R.NI...........AGS...S.I.K.K....S......------
>KC535031,A/British Columbia/006/2013(H3N2) .....NI...........AGS...S.I...K....S..F....-----
>KC535057,A/Quebec/036/2012(H3N2) ...R.NI...........AGS...S.I...K....S.......-----
000000000000000000000000000000000000000000000000
000000000000011111111112222222223333333334445555
124456666777800134456780113488990122677890290236
963991469038348070481378459658468708324452745681
------------------------------------------------
LTKQVSTEDSQEIVKYNSTRNLNIASVIRANEKTANVQSKGGKIDGIR
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February 9th, 2013, 03:00 AM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,950
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Re: H3n2
H3 in Denmark had seven mutations at key antigenic sites
http://www.cidrap.umn.edu/cidrap/con...13fluscan.html
http://www.eurosurveillance.org/View...rticleId=20397
Based on HA amino acid sequence analysis, the Danish A(H3N2) viruses formed two main clades,
A and B (Figure 2).
Clade B is within the defined 3C A(H3) phylogenetic clade, where the 2012/13 A(H3N2)
vaccine component (A/Victoria/361/2011) is assigned,
but the Danish clade A should probably be assigned a new A(H3) clade. Five of the 22
Danish HA sequences included in the phylogenetic analysis, collected from week 46
(11 December 2012) to week 1 (2 January 2013), were from patients who had been
vaccinated before week 47: all five were located in clade A (Figure 2).
Altogether, seven amino acid substitutions in the HA defined the Danish clade A,
compared with egg-grown/tissue grown A/Victoria/361/2011 –
T128A, R/Q156H,V186G;R142G,N145S;N278K;S/Y219S.
Additional substitutions were Q33R, E/D190D and V347M.
The clade B viruses did not possess the substitutions at positions 128, 142 and 347.
The clade A viruses have lost the 126 N-linked glycosylation seen in A/Victoria/361/2011
and clade B (predicted by NetNGlyc 1.0 server [7]. For comparison, we included reference
HA sequences from influenza A(H3) viruses, obtained from the EpiFlu database of the
Global Initiative on Sharing Avian Influenza Data (GISAID) (Table 3).
=================================================0
DK-A = Quebec (Q49R,S61N,T64I,T144A,R158G,N161S,A214S,V239I,N294 K,N328S,V363M)
DK-B = Alberta (Q49R,S61N,T64I,N161S,A214S,V239I,N294K,N328S)
[as compared to Egypt/Iowa/2009]
while the vax-strain A/Victoria/361/2011 seems to have the additional mutations
H172RorQ,G202V,S235SorY,D190EorD
---------------------------------------------------------
6 H3-HAs from USA today at genbank
5 (3CA+2IL) are DK-B=ALB
1 (CA) is DK-A = Quebec
---------------------------------------------------------------
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February 27th, 2013, 06:28 AM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,950
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Re: H3n2
lots of new sequences today at genbank
here are all human H3N2s since Sept.2012
you can immediately spot one reassortment at the 2 black bars on the right,
where the sequences are similar in HA but different in MP,PB2,PA
--------well, that's the old reassortment from 2011, both are still there and evolved in the meantime.
53 full genomes from Texas ("JMM") , 4 groups and 2-3 minor overlaps by exchanging(reassorting) segments
1.) 28 of them are similar to the Czech/121 virus from last season
4.) 8 of them are the 2011-reassorted virus
3.) 12 of them are a strain, that I don't know yet where it comes from, different from the other
3 strains circulating in Texas, but probably still a descendent from Egypt/Iowa/2009
2.) 4 are reassorted, getting segments 24568 from group 1.) and 137 from an ancester of group 3.)
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February 28th, 2013, 02:02 AM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,950
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Re: H3n2
so, do the sequences give us hints, why this season was so bad in USA ?
Not really. I'm not sure.
And we have a severe season in Europe too, but with other strains.
-----------------------------------------------------------------------------------------------
the first appearance of the Czech/121 strain "1.)" , 28 out of 53 in Texas
and 75 out of 82 in Canada, was in many Singapore isolates from mid 2011
first: A/Singapore/TT430/2011/07/29
--------------------------------------------------------------------------------------------------------
the first appearance of the additional HA-mutations that are in the new reassorted
strain "2.)", in 4 out of 53 recent Texas genomes
- -not seen before
---------------------------------------------------------------------------------------------------------------
the first appearance of the new 3.) strain ,12 out of 53 in Texas, was in
A/Pavia/131/2012/02/21
A/St.Petersburg/RII25/2012/02/23
A/Ekaterinburg/RII3/2012/02/29
------------------------------------------------------------------------------------------------------------------
the first appearance of that "reassorted-2011" strain, "2.)", now seen in 8 out of 53 of the
Texas-JMM-genomes and in 7 out of 82 recent HAs from Canada
was in A/Pennsylvania/02/2010/02/21 , which is now public.
http://www.ncbi.nlm.nih.gov/nuccore/KC535475
It was passaged 2010/02/21, but colleced 2010/01/07.
H3N2 was very rare in 2009/2010, but indeed there was
one H3 from week 2 in region 3:
http://www.cdc.gov/flu/weekly/region...a/whoreg3t.htm
And this sequence had been mentioned on the web already in Sept.2010.
2010 is surprisingly early for that new strain, which was one of the dominating H3 strains
the season later, and surprising is also that it first appeared in USA.
It would be interesting to see the travel history of that 74 year old male
from Pennsylvania. Was he in Asia over Christmas ? Maybe that was the reason why he
was sampled in the first place.
The next appearance was in Netherlands,April,2010.
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March 15th, 2013, 02:44 PM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,950
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Re: H3n2
HA and NA from Japan,Hokkaido,2013 have been published.
It is very similar to the Texas genomes from Nov.
e.g. JMM_22
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May 17th, 2013, 08:28 AM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,950
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Re: H3n2
H3N2 in USA season 2011/2012
---------------------------------------
there are 3 sorts of human H3N2-HAs since July 2012 :
~75% is the Czech/121 strain , ~20 the reassorted/2011 strain, ~5% the new Texas strain
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