PLoS Pathog. Molecular Epidemiology of A/H3N2 and A/H1N1 Influenza Virus during a Single Epidemic Season in the United States

[mixin]

This is a long study with numerous charts.
--------------------------------------------

http://www.plospathogens.org/article...268C40D44595FD

Abstract
To determine the spatial and temporal dynamics of influenza A virus during a single epidemic, we examined whole-genome sequences of 284 A/H1N1 and 69 A/H3N2 viruses collected across the continental United States during the 2006–2007 influenza season, representing the largest study of its kind undertaken to date. A phylogenetic analysis revealed that multiple clades of both A/H1N1 and A/H3N2 entered and co-circulated in the United States during this season, even in localities that are distant from major metropolitan areas, and with no clear pattern of spatial spread. In addition, co-circulating clades of the same subtype exchanged genome segments through reassortment, producing both a minor clade of A/H3N2 viruses that appears to have re-acquired sensitivity to the adamantane class of antiviral drugs, as well as a likely antigenically distinct A/H1N1 clade that became globally dominant following this season. Overall, the co-circulation of multiple viral clades during the 2006–2007 epidemic season revealed patterns of spatial spread that are far more complex than observed previously, and suggests a major role for both migration and reassortment in shaping the epidemiological dynamics of human influenza A virus.

Author Summary
This study is the first of its kind to reconstruct the spread of an epidemic of influenza A virus across a single country, in this case the United States. In contrast to a single viral lineage spreading across this country, a phylogenetic analysis of the whole-genome sequences of more than 300 influenza A viruses of the A/H1N1 and A/H3N2 subtypes sampled from the 2006–2007 epidemic season reveals that multiple phenotypically and antigenically distinct viral lineages of entered and co-circulated in the US during this time. Furthermore, the widespread co-circulation of multiple lineages, even in geographically remote localities, allowed for frequent reassortment between influenza A viruses of the same subtype. Through reassortment, a minor lineage of A/H3N2 viruses surprisingly re-acquired sensitivity to the adamantane class of antiviral drugs, and a new A/H1N1 antigenic variant emerged that later became globally dominant. In sum, these results highlight the complexity of the spread of influenza A virus in time and space, and highlight the need for intensified global surveillance involving whole-genome sequence data.

[gsgs]

As for H1N1

I had also distinguished 3 main clades with 179+96+16 viruses:
http://www.setbb.com/fluwiki2/viewto...forum=fluwiki2

from the picture
http://magictour.free.fr/panflu/h1n1u.GIF

I would subdivide them into 4+3+5 subclades, 12 in total.

Of course, you can continue with sub-sub-clades and maybe even sub-sub-sub clades,
but probably not more.

Each of the 12 subclades is characterized by about 5-20 markers in the genome
(maybe I can count it more exactly later...)
One virus introduced at Christmas and then mutation until end of February with only 2 of its progenies
surviving as descendants from different children (so the Christmas virus would be the
most recent common anchestor of the two) would produce about 12 diferences in the genome,
which would produce about 3 recognizable markers in each of the 2 strains, were there
multiple viruses in the clades. But this assumes continuous acquisition of mutations
while often multiple mutations may occur in even one host , so the mutations do cluster a bit.

However, I think these 12 sub-clades are distinguished by enough markers so we can
conclude that they were independent introductions before Christmas,Thanksgiving.
This should also hold for most of the sub-sub-clades.
Just counting for the big group of >170 H1N1-viruses, I'd estimate by looking at the picture
roughly 10 different introductions before Christmas , maybe 20-30 in total for all 3 groups.
And that's just for H1N1.
Given that about 10 million US-people were infected, that's about 500000 infected people
per introduction in average...


assuming 36 mutations per year in the genome of 8 segments, ~13000 nucleotides,
~80% of mutations at 3rd positions



Now, hopefully we get lots of H1N1 genomes from season 2007/8
too, to show whether (progenies of) some of the viruses
from 2006/7 did survive. It is assumed that the US-viruses
die out and the next season's viruses come from SE-Asia
where influenza is the whole year.

So when we want to study the evolution, this project
should be done in e.g. Guangdong with ~1000 genomes
from the whole year. As sequencing becomes cheap,
this might be realized in the next years

-----edit1------
I think it's better to classify those viruses, to form and distinguish those groups
by sets of common polymorphisms ("markers") rather than by neighborhood in phylo-trees.

-------edit2---------

reassortments in H1N1,USA 2006/7

--------------------------------------
004 >A/Kentucky/UR06-0476/2007(H1N1)
005 >A/Mississippi/UR06-0378/2007(H1N1)
006 >A/Tennessee/UR06-0045/2007(H1N1)
007 >A/Texas/UR06-0217/2007(H1N1)
008 >A/California/UR06-0479/2007(H1N1)
009 >A/California/UR06-0393/2007(H1N1)
have reassortment segments 1346-2578
--------------------------------------
010 >A/Tennessee/UR06-0055/2007(H1N1)
has reassortment 34-125678 with the above group
---------------------------------------
112 >A/Ohio/UR06-0100/2007(H1N1)
has reassortment 35-124678
---------------------------------------
243 >A/Virginia/UR06-0562/2007(H1N1)
has probable reassortment 6-1234578
---------------------------------------

for the vaccine strains Solomon,Brisbane only a few segments are available.
In the other segments they are probably close to:
A/Solomon Islands/3/2006(H1N1) - A/New York/UR06-0199/2007(H1N1)
A/Brisbane/59/2007(H1N1) - A/Kentucky/UR06-0476/2007(H1N1)

Brisbane is probably a 1346 reassortant

[HenryN]

Although A/Solomon Islands/3/2006-like viruses and A/Brisbane/59/2007-like A/H1N1 viruses were represented only by minor clades during the 2006–2007 season (H and F, respectively), Solomon Islands-like viruses achieved global A/H1N1 dominance by the start of the 2007–2008 season, and the reassortant clade of Brisbane-like viruses rose to dominance later during the 2007–2008 season [39].

The above quote references the CDC MMWR and perpetuates the myth that there were Solomon Islands-like viruses in circulation at the start of the 2007/2008 season. In 2007/2008, the the H1N1 sub-clades in circulation were Brisbane (clade 2B) and Hong Kong (clade 2C). Solomon Island (clade 2A) and New Caledonia (clade 1) ended in the 2006/2007 season.

[gsgs]

the confusion may arise since sometimes they look at amino-acid
sequences and compare with vaccine-strains and then they
look at nucleotide-sequences.

Brisbane is not vaccine-strain yet and e.g. the Europeans subsume
it under Solomon while CDC considers sequencing-differences
as well as ferret-sera tests

[HenryN]

Originally Posted by gsgs

the confusion may arise since sometimes they look at amino-acid
sequences and compare with vaccine-strains and then they
look at nucleotide-sequences.

Brisbane is not vaccine-strain yet and e.g. the Europeans subsume
it under Solomon while CDC considers sequencing-differences
as well as ferret-sera tests

The confusion is from poor ferret anti-sera and test targets. The phylogenetic data are clear, regardless of whether nucleotide or protein sequences are used.

[gsgs]

EISS gives 3 numbers per strain:
http://www.eiss.org/cgi-files/figure...rope&type=char

Caledonia (4,4,0)
Solomon(2228,1897,658)

total influenza(4029,3316,1298)

first number: antigenic and/or genetic
second number: antigenic
third number: genetic

> sentinal and non-sentinal combined

whatever that means. (?)

[HenryN]

Originally Posted by gsgs

EISS gives 3 numbers per strain:
http://www.eiss.org/cgi-files/figure...rope&type=char

Caledonia (4,4,0)
Solomon(2228,1897,658)

total influenza(4029,3316,1298)

first number: antigenic and/or genetic
second number: antigenic
third number: genetic

> sentinal and non-sentinal combined

whatever that means. (?)

The antigenic data are wrong because the targets and sera are poor.

[HenryN]

Commentary

http://www.recombinomics.com/News/08...ch_Spread.html

[gsgs]

the most amazing virus is
A/Tennessee/UR06-0055,3m,Dyersburg/22-Jan-2007(H1N1)

http://www.ncbi.nlm.nih.gov/entrez/v...i?val=CY028207
It's not included in the paper. Why ?

It seems to be a 1678-2345 reassortant of
A/Tennessee/UR06-0045,2f,Dyersburg/18-Jan-2007(H1N1) [clade F,Brisbane]
and a virus similar to A/Tennessee/UR06-0238,4m,Knoxville/12-Feb-2007 [clade A,major clade]

(Knoxville is ~300km from Dyersburg)
the samples of the 3m and 2f are 4 days apart, maybe same family ?

Apparantly the reassortant virus wasn't found elsewhere and hopefully
didn't create a new strain, which usually appear in SE-Asia, not USA.

[AlaskaDenise]

Originally Posted by niman

Commentary

http://www.recombinomics.com/News/08...ch_Spread.html

Commentary

Vaccine Mismatch Drives Spread of H1N1 Tamiflu Resistance
Recombinomics Commentary 19:51
August 25, 2008

Although A/Solomon Islands/3/2006-like viruses and A/Brisbane/59/2007-like A/H1N1 viruses were represented only by minor clades during the 2006–2007 season (H and F, respectively), Solomon Islands-like viruses achieved global A/H1N1 dominance by the start of the 2007–2008 season, and the reassortant clade of Brisbane-like viruses rose to dominance later during the 2007–2008 season [39].

The above comments from today’s PLOS paper on H1N1 and H3N2 circulation in the United States during the 2006/2007 season is based on the MMWR characterization of H1N1 in the 2007/2008 season, which is misleading and adds to the confusion regarding the emergence of oseltamivir resistance in H1N1.

The emergence is readily followed through phylogenetic analysis which distinguishes four different sub-clades, New Caledonia/20 (clade 1), Solomon Island/3 (clade 2A), Brisbane/59 (clade 2B), and Hong Kong/2652 (clade 2C). In the United States in 2006/2007, clade 1 was dominant, and there were small numbers of clade 2A and clade 2B in circulation. However, clade 1 and clade 2A were replaced by clade 2B and clade 2C in 2007/2008, but these isolates were initially called Solomon Island–like because of cross reactivity of ferret anti-sera with isolates grown in chicken eggs. The differences between the titers from Solomon Island/3 and Brisbane/59 was only a factor of two, so all isolate were initially classified as Solomon Island/3–like and a match for the new vaccine, which used Solomon Island/3 as the target.

However, when Brisbane/59 grown in mammalian MDCK cells was used as a target, the dramatic differences in antigenicity were clear. The titer for Brisbane/59 (clade 2B) was 320, but the level dropped to 40 for the anti-sera against Hong Kong/2652 (clade 2C), and was below the limits of detection (40) for the anti-sera against Solomon Island/3 (clade 2A) or New Caledonia/20 (clade 1).

Thus, the differences between the sub-clades were significantly different by both phylogenetic analysis and serology, but the poor serological data of egg grown targets led to an initial grouping of all three clade 2 sub-clades into the Solomon Island/3–like group. However, though there was no reported Solomon Island/3–like H1N1 in circulation in the 2007/2008 season. The Solomon Island/3 vaccine target was a mismatch, but the confusion generated by the earlier MMWR still persists in peer reviewed publications as well as this month’s European surveillance report.

In the upcoming flu season in the northern hemisphere, the Solomon Island/3 target is being replaced by Brisbane/59, but recent sequence data from South Africa raises concerns that the Brisbane/59 vaccine will have limited utility in the fall, because the dominant H1N1 strain in South Africa is oseltamivir resistance and already has acquired a cluster of non-synonymous changes flanking the receptor bind domain at position 190 (H3 numbering). Initially, South Africa reported that the first 23 isolates that were sequenced all had H274Y. More recently, the 100% resistance was extended to the first 107 isolates. Similarly, the first 10 H1N1 isolates from Australia this season have H274Y.

Although the isolates in South Africa can be divide into two groups, all isolates link back to the clade 2B linear in circulation in the northern hemisphere. Thus, the emergence and spread of H274Y can be easily followed via phylogenetic analysis, which applies to the three gene segments which had been recently sequenced, HA, NA, and MP, although there is more genetic diversity in the HA and NA genes and there fore easier to see independent introductions.

H274Y was first reported in clade 2C in China in the 2005/2006 season, which was followed by acquisition of H274Y by clade 1 in the 2006/2007 season in United States. In October, 2007, the first report of H294Y in the clade 2B was reported in two isolates in Hawaii. All of the above isolates had identical sequences downstream from H274Y. The polymorphisms was subsequently acquired in a related clade 2B sequence which then became dominant and was a precursor for the dominant sequence in South Africa.

Thus, the H1N1 mismatch last year may have contributed to the dominance of the clade 2B sequence, which has subsequently led to increases in oseltamivir resistance to 100% of H1N1 isolates in South Africa and Australia.


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