225G Worldwide Tracking & Evaluation

[sharon sanders]

Re: 225G Preliminary Worldwide Tracking & Evaluation

Please listen to:

http://www.twiv.tv/2009/12/13/twiv-62-persistence-of-west-nile-virus/

[gsgs]

Re: 225G Preliminary Worldwide Tracking & Evaluation

why ?

isn't there some speech recognition software to convert it into
text, searchable,splittable ?

isn't there someone who posts the direct entry-points of the subjects
so you needn't listen to the whole thing ?

[sharon sanders]

Re: 225G Preliminary Worldwide Tracking & Evaluation

Interesting listen. Apparently D225G will not lead to vaccine failure. Peter Palese is also referred to in this show as supportive of this idea. In fact, there seems to be consensus that D225G is not proven to cause increased virulence in H1N1 illnesses.

[gsgs]

Re: 225G Preliminary Worldwide Tracking & Evaluation

biology is not a science of proof but of evidence

9 of 50 new samples from England have D225E(H3)

D225E apparantly did spread in Texas

does D225E spread

[gsgs]

Re: 225G Preliminary Worldwide Tracking & Evaluation

vaccine escape is not the main issue
increased virulence and possible spread thereof is the issue

[mixin]

Re: 225G Preliminary Worldwide Tracking & Evaluation

Are these 716E and 717G? And is 718 where we would find "N"?

C:\gs>travel1 mxha5 716
>A/California/07/2009/04/09
>A/California/13/2009/04/21
>A/Catalonia/NS1706/2009/07/29
>A/Catalonia/NS2001/2009/08/03
>A/Catalonia/NS2008/2009/08/03
>A/Georgia/01/2009/04/27
>A/Hiroshima/201/2009/06/17
>A/Mexico/3955/2009/04/02
>A/Mexico/InDRE4114/2009
>A/Mexico/InDRE4114/2009
>A/Monterrey/3/2009
>A/Nebraska/02/2009/04
>A/New York/04/2009/04
>A/New York/11/2009/04/25
>A/New York/31/2009/04/24
>A/Norway/2924/2009/08/10
>A/Norway/3206-3/2009/09/01
>A/Sao Paulo/53206/2009/07/19
>A/Sao Paulo/53225/2009/08/01
>A/Singapore/GP2312/2009/07/31
>A/Singapore/GP2641/2009/08/05
>A/Singapore/GP2651/2009/08/05
>A/Texas/04/2009/04/14
>A/Texas/05/2009/04/15
>A/Texas/10/2009/04/23
>A/Texas/11/2009/04/23
>A/Vladivostok/01/2009
>A/Zhejiang-Yiwu/11/2009/09/06
>A/Zhejiang/DTID-ZJU02/2009/09/07
>A/Zhejiang/DTID-ZJU03/2009/09/07
>A/swine/Alberta/OTH-33-3/2009/05/03
31

C:\gs>travel1 mxha5 717
>A/Almati/01/2009
>A/Ancona/05/2009/07/12
>A/Athens/893/2009/06/09
>A/California/25/2009/06/15
>A/Catalonia/378/2009/06/23
>A/Catalonia/387/2009/06/26
>A/Catalonia/NS2001/2009/08/03
>A/Catalonia/NS2008/2009/08/03
>A/Catalonia/NS5408/2009/11/04
>A/Catalonia/S1120/2009/07/20
>A/Catalonia/S1161/2009/07/28
>A/Catalonia/S1165/2009/07/30
>A/Catalonia/S1182/2009/07/29
>A/Catalonia/S1183/2009/07/28
>A/Catalonia/S1187/2009/07/30
>A/Catalonia/S1199/2009/08/06
>A/Catalonia/S1205/2009/08/05
>A/Catalonia/S1209/2009/08/05
>A/Catalonia/S1215/2009/08/12
>A/Catalonia/S1222/2009/08/10
>A/Catalonia/S1227/2009/08/10
>A/Catalonia/S1236/2009/08/13
>A/Catalonia/S1237/2009/08/13
>A/Catalonia/S1248/2009/08/18
>A/Catalonia/S1249/2009/08/18
>A/Catalonia/S1254/2009/08/19
>A/Catalonia/S1260/2009/08/19
>A/Catalonia/S1265/2009/08/24
>A/Catalonia/S1269/2009/08/24
>A/Catalonia/S1272/2009/08/25
>A/Catalonia/S1273/2009/08/25
>A/Catalonia/S1286/2009/08/25
>A/Catalonia/S1300/2009/08/28
>A/Catalonia/S1304/2009/08/28
>A/Catalonia/S1331/2009/09/03
>A/Catalonia/S1333/2009/09/01
>A/Catalonia/S1350/2009/09/09
>A/Catalonia/S1369/2009/09/15
>A/Catalonia/S1379/2009/09/16
>A/Catalonia/S1436/2009/09/28
>A/Catalonia/S1453/2009/09/30
>A/Catalonia/S1478/2009/10/05
>A/Catalonia/S1479/2009/10/05
>A/Catalonia/S1490/2009/10/07
>A/Catalonia/S1545/2009/10/19
>A/Catalonia/S1587/2009/10/22
>A/Catalonia/S1592/2009/10/21
>A/Catalonia/S1604/2009/10/26
>A/Catalonia/S1605/2009/10/26
>A/Catalonia/S1606/2009/10/26
>A/Catalonia/S1632/2009/10/28
>A/Catalonia/S1637/2009/10/28
>A/Catalonia/S1641/2009/10/28
>A/Catalonia/S1672/2009/11/02
>A/Catalonia/S1674/2009/11/02
>A/Catalonia/S1698/2009/11/02
>A/Catalonia/S1748/2009/11/09
>A/Catalonia/S1758/2009/11/09
>A/Catalonia/S1761/2009/11/09
>A/Catalonia/S1828/2009/11/12
>A/Catalonia/S1829/2009/11/13
>A/Catalonia/S1830/2009/11/13
>A/Catalonia/S1834/2009/11/16
>A/Catalonia/S1835/2009/11/16
>A/Changsha/78/2009/06/29
>A/Hong Kong/2369/2009/06/11
>A/Italy/172/2009
>A/Milan/80/2009/07/08
>A/Milan/83/2009/07/15
>A/Nagasaki/HA-44/2009/08/20
>A/New Jersey/01/2009/04
>A/New York/4780/2009/08/18
>A/New York/4787/2009/08/21
>A/New York/4789/2009/08/20
>A/New York/4790/2009/08/21
>A/New York/4791/2009/08/24
>A/New York/4810/2009/08/21
>A/Norway/2674/2009/07/27
>A/Norway/2690/2009/07/29
>A/Norway/3059/2009/08/11
>A/Norway/3206-3/2009/09/01
>A/Norway/3478/2009/09/07
>A/Norway/4023/2009/10/14
>A/Paris/2591/2009/05/01
>A/Sapporo/1/2009/06/11
>A/Serbia/3547/2009
>A/Singapore/GP2651/2009/08/05
>A/Singapore/ON1187/2009/07/15
88

[gsgs]

Re: 225G Preliminary Worldwide Tracking & Evaluation

715,716,717 --> 239(h1)=225(h3)

[mixin]

Re: 225G Preliminary Worldwide Tracking & Evaluation

D: GAT, GAC
N: AAT, AAC
G: GGT, GGC, GGA, GGG
E: GAA,GAG

So is this right?

"A" at 715 = 225N
"G" at 716 = 225G
"A" or "G" at 717 = 225E
----------------------------------

(From Gs
yes.

once it goes to N it can only easily go back to D
once it goes to G , it can easily go to E (if encoded GGA,GGG)
once it goes to E, it can eaily go to G

GAT(D)-GGT(G)-GGA(G)-GAA(E)-GAT(D)

did GGA or GGG occur already ? (mutation at both, 716 and 717)

also AGT(S)

[mixin]

Re: 225G Preliminary Worldwide Tracking & Evaluation

From checking both lists, then running with your program, these 4 have mutations at both positions. Singapore is strange; it has "n"s in the nucleotide portion and I had a poor result with mutatm.

>A/Catalonia/NS2001/2009/08/03
T658A(4),A716G(4),T717A(4),G900A(4),A934G(4),C1408 T(4),

>A/Catalonia/NS2008/2009/08/03
T658A(4),A716G(4),T717A(4),G900A(4),A934G(4),C1408 T(4),

>A/Norway/3206-3/2009/09/01 Y ~
C460T(4),T658A(4),A716G(4),T717A(4),C1408T(4),

>A/Singapore/GP2651/2009/08/05

[Gert van der Hoek]

Re: 225G Preliminary Worldwide Tracking & Evaluation

Journal of Virology, September 2000, p. 8502-8512, Vol. 74, No. 18
0022-538X/00/$04.00+0


Early Alterations of the Receptor-Binding Properties of H1, H2, and H3 Avian Influenza Virus Hemagglutinins after Their Introduction into Mammals

Mikhail Matrosovich,1,2,* Alexander Tuzikov,3 Nikolai Bovin,3 Alexandra Gambaryan,2 Alexander Klimov,4 Maria R. Castrucci,5 Isabella Donatelli,5 and Yoshihiro Kawaoka1,6,7
Department of Virology and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 381051; M. P. Chumakov Institute of Poliomyelitis and Viral Encephalitides, 142 782 Moscow,2 and Shemyakin Institute of Bioorganic Chemistry, 117871 Moscow,3 Russia; Influenza Branch, Centers for Disease Control and Prevention, Atlanta, Georgia 303334; Department of Virology and WHO National Influenza Centre, Instituto Superiore di Sanita, Rome 00161, Italy5; Department of Pathology, University of Tennessee at Memphis, Memphis, Tennessee 381636; and Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin 537067

Received 24 February 2000/Accepted 20 June 2000

Interspecies transmission of influenza A viruses circulating in wild aquatic birds occasionally results in influenza outbreaks in mammals, including humans.

To identify early changes in the receptor binding properties of the avian virus hemagglutinin (HA) after interspecies transmission and to determine the amino acid substitutions responsible for these alterations, we studied the HAs of the initial isolates from the human pandemics of 1957 (H2N2) and 1968 (H3N2), the European swine epizootic of 1979 (H1N1), and the seal epizootic of 1992 (H3N3), all of which were caused by the introduction of avian virus HAs into these species.

The viruses were assayed for their ability to bind the synthetic sialylglycopolymers 3'SL-PAA and 6'SLN-PAA, which contained, respectively, 3'-sialyllactose (the receptor determinant preferentially recognized by avian influenza viruses) and 6'-sialyl(N-acetyllactosamine) (the receptor determinant for human viruses).

Avian and seal viruses bound 6'SLN-PAA very weakly, whereas the earliest available human and swine epidemic viruses bound this polymer with a higher affinity.

For the H2 and H3 strains, a single mutation, 226QL, increased binding to 6'SLN-PAA, while among H1 swine viruses, the 190ED and 225GE mutations in the HA appeared important for the increased affinity of the viruses for 6'SLN-PAA.

Amino acid substitutions at positions 190 and 225 with respect to the avian virus consensus sequence are also present in H1 human viruses, including those that circulated in 1918, suggesting that substitutions at these positions are important for the generation of H1 human pandemic strains.

These results show that the receptor-binding specificity of the HA is altered early after the transmission of an avian virus to humans and pigs and, therefore, may be a prerequisite for the highly effective replication and spread which characterize epidemic strains.

* Corresponding author. Mailing address: Department of Virology and Molecular Biology, St. Jude Children's Research Hospital, 332 North Lauderdale, Memphis, TN 38105-2794. Phone: (901) 495-3412. Fax: (901) 523-2622. E-mail: Mikhail.Matrosovich@stjude.org.

Journal of Virology, September 2000, p. 8502-8512, Vol. 74, No. 18
0022-538X/00/$04.00+0

http://jvi.asm.org/cgi/content/abstract/74/18/8502

[mixin]

Re: 225G Preliminary Worldwide Tracking & Evaluation

Some new sequences from Sweden were submitted to GISAID.

One is from a deceased 53yo Male.

Using gs's program, I'm seeing "T717A" in the HA segment. I haven't run any of the others yet.

Edited to add: that was the only one out of 7 that has a mutation at that position.

[Treyfish]

Re: Hong Kong: A total of Five patients have been infected with D222G containing mutation H1N1 2009 so far (12/3/09)

total of 8 norway varient patients

Hong Kong's re-discovery of new variants of influenza virus
2009-12-18 20:31:00
Center for Health Protection, the Center has found three variants of influenza A H1N1 influenza virus, the variant gene and the same as found in Norway.

The variant virus is Center for Health Protection Public Health Laboratory Service has its conventional virus isolation monitoring system was found. Hong Kong, bringing the total number of cases found in eight variants.

The spokesman said: "In so far been detected in 351 cases of virus isolation, the CHP total of eight influenza A H1N1 influenza gene sequences and Norway the same year, data released in November."

In eight cases, three patients died, another patient in intensive care and the remaining four patients have already been discharged.

The spokesman said that some strains of oseltamivir (ie, Tamiflu) and zanamivir (ie, Relenza) have no resistance. CHP will continue through the laboratory surveillance system to monitor influenza viruses in Hong Kong; If there are unusual circumstances will be made public.http://news.sina.com.hk/cgi-bin/nw/s...1365637/1.html

[Giuseppe]

Re: Hong Kong: A total of Five patients have been infected with D222G containing mutation H1N1 2009 so far (12/3/09)

Hong Kong: Three more Norwegian-like mutations of human swine influenza virus detected (12/18/09)

The Centre for Health Protection (CHP) of the Department of Health today (December 18) said it had made three more detections of a human swine influenza (HSI) virus strain with mutation similar to the one reported by Norway.

The detections arose from an ongoing surveillance program of virus isolates performed by the Centre's Public Health Laboratory Service Branch.

That brought to eight the total number of such detections so far in Hong Kong.

A CHP spokesman said, "Out of 351 virus isolates so far tested, CHP has detected eight viral gene sequences with the same mutation as the one reported in Norway in November this year."

''Among these eight cases, three of the patients passed away and one is still receiving intensive care treatment.

The other four recovered.

Five of the eight cases have been announced earlier by the CHP.

The spokesman said that the significance of the mutation was being assessed by scientists in the World Health Organisation network of influenza laboratories.

"CHP is closely monitoring influenza viruses worldwide and remains vigilant for changes in the virus that may have public health significance," he said.

"These viruses are still sensitive to antiviral drugs, oseltamivir and zanamivir."

"CHP will continue to monitor influenza viruses in Hong Kong through its laboratory surveillance program and alert the public of any unusual signs," he said.
-

View Original Article

[mixin]

Re: 225G Preliminary Worldwide Tracking & Evaluation

Here is a revised list of the Genbank sequences with D225G or some other change at that position; the passage history is also included. I put them all together in one file at Genbank in case anyone wants to analyze them.

http://www.ncbi.nlm.nih.gov/sites/myncbi/collections/public/1LCwbbJY3ddeUc4JY6G0Ge15P/

Note that some have a "G" and others have an "X". When the sample is grown in eggs or whatever, and the nucleotide has both "G"s and "A"s at 225, it shows up as an "R" in the nucleotide part and it becomes an "X" in the amino acid part.

C:\gs>travel1 mxha5 716

>A/California/07/2009/04/09 has G E2
>A/California/13/2009/04/21 has X E2

>A/Catalonia/NS1706/2009/07/29 G
>A/Catalonia/NS2001/2009/08/03 G
>A/Catalonia/NS2008/2009/08/03 G

>A/Georgia/01/2009/04/27 G C1

>A/Hiroshima/201/2009/06/17 G E1+1

>A/Mexico/3955/2009/04/02 G E2
>A/Mexico/InDRE4114/2009 G
>A/Mexico/InDRE4114/2009 G E2/E1
>A/Monterrey/3/2009 (No amino acid shown)

>A/Nebraska/02/2009/04 X E2
>A/New York/04/2009/04 G E2
>A/New York/11/2009/04/25 X E2
>A/New York/31/2009/04/24 X E2
>A/Utah/42/2009/07/24 G
>A/Utah/42/2009/07/24 R

>A/Norway/2924/2009/08/10 X MDCK1
>A/Norway/3206-3/2009/09/01 G MDCK2
>A/Finland/614/2009/07/24 R

>A/Sao Paulo/53206/2009/07/19 G Necropsy Lung
>A/Sao Paulo/53225/2009/08/01 G Necropsy Lung

>A/Singapore/GP2312/2009/07/31 PKVRXXXXRMNYY p1
>A/Singapore/GP2641/2009/08/05 PKXXXQXXRMNYY p1
>A/Singapore/GP2651/2009/08/05 PKXXXQXXRMNYY p1

>A/Texas/04/2009/04/14 X X/E2
>A/Texas/05/2009/04/15 G X/E2
>A/Texas/10/2009/04/23 X E2
>A/Texas/11/2009/04/23 G E2
>A/Texas/42291877/2009 R

>A/Vladivostok/01/2009 G

>A/Zhejiang-Yiwu/11/2009/09/06 G
>A/Zhejiang/DTID-ZJU02/2009/09/07 G
>A/Zhejiang/DTID-ZJU03/2009/09/07 G

>A/swine/Alberta/OTH-33-3/2009/05/03 T

[gsgs]

Re: 225G Preliminary Worldwide Tracking & Evaluation

AUTHORS Ramirez-Gonzalez,J.E., Gonzalez-Duran,E., Wong-Arambula,C.E.,
Alcantara-Perez,P., Olivera-Diaz,H., Cortes-Ortiz,I.,
Lopez-Martinez,I., Barrera-Badillo,G., Diaz-Quinonez,J.A. and
Alpuche-Aranda,C.
TITLE Identification of pandemic flu D222N and D222G mutation in Mexican
isolates
JOURNAL Unpublished



Influenza A virus
(A/Mexico/InDRE36529/2009(H1N1)) CY053632
Influenza A virus
(A/Mexico/InDRE39951/2009(H1N1)) CY053633
Influenza A virus
(A/Mexico/InDRE40791/2009(H1N1)) CY053634
Influenza A virus
(A/Mexico/InDRE41427/2009(H1N1)) CY053635
Influenza A virus
(A/Mexico/InDRE41741/2009(H1N1)) CY053636
Influenza A virus
(A/Mexico/InDRE42372/2009(H1N1)) CY053637
Influenza A virus
(A/Mexico/InDRE43149/2009(H1N1)) CY053638
Influenza A virus
(A/Mexico/InDRE43950/2009(H1N1)) CY053639
Influenza A virus
(A/Mexico/InDRE50617/2009(H1N1)) CY053640
Influenza A virus
(A/Mexico/InDRE50625/2009(H1N1))