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niman
 Post subject: Re: Australia Sequence Links Three D225G/N Sub-clades
PostPosted: Sun Jan 31, 2010 6:29 pm 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 6528
Location: Pittsburgh, PA USA
A308G (codes for D89G)
Sequences with D225G/N in bold

A/SYDNEY/2503/2009
A/SYDNEY/2501/2009
A/VICTORIA/2125/2009
gb|CY055075.1| Influenza A virus (A/Australia/6/2009(H1N1)) s... 32.2 12
gb|CY055067.1| Influenza A virus (A/Australia/4/2009(H1N1)) s... 32.2 12
gb|GU332630.1| Influenza A virus (A/cat/IA/26991/2009(H1N1)) ... 32.2 12
gb|CY052005.1| Influenza A virus (A/Norway/3433/2009(H1N1)) s... 32.2 12
gb|CY049691.1| Influenza A virus (A/Singapore/GP2711/2009(H1N... 32.2 12
gb|CY047150.1| Influenza A virus (A/Catalonia/S1138/2009(H1N1... 32.2 12
gb|GU014748.1| Influenza A virus (A/Gifu-C/67/2009(H1N1)) seg... 32.2 12
gb|GQ377064.1| Influenza A virus (A/Virginia/05/2009(H1N1)) s... 32.2 12
gb|GQ232009.1| Influenza A virus (A/Kentucky/05/2009(H1N1)) s... 32.2 12

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Last edited by niman on Sun Jan 31, 2010 6:43 pm, edited 2 times in total.

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niman
 Post subject: Re: Australia Sequence Links Three D225G/N Sub-clades
PostPosted: Sun Jan 31, 2010 6:30 pm 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 6528
Location: Pittsburgh, PA USA
T519C

A/SYDNEY/2503/2009
A/SYDNEY/2501/2009
A/VICTORIA/2125/2009
gb|CY055075.1| Influenza A virus (A/Australia/6/2009(H1N1)) s... 32.2 12
gb|CY055067.1| Influenza A virus (A/Australia/4/2009(H1N1)) s... 32.2 12
gb|GU371256.1| Influenza A virus (A/Orenburg/IIV2974/2009(H1N... 32.2 12
gb|GU332630.1| Influenza A virus (A/cat/IA/26991/2009(H1N1)) ... 32.2 12
gb|CY052005.1| Influenza A virus (A/Norway/3433/2009(H1N1)) s... 32.2 12
gb|CY049691.1| Influenza A virus (A/Singapore/GP2711/2009(H1N... 32.2 12
gb|GU014748.1| Influenza A virus (A/Gifu-C/67/2009(H1N1)) seg... 32.2 12

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Last edited by niman on Sun Jan 31, 2010 6:42 pm, edited 2 times in total.

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niman
 Post subject: Re: Australia Sequence Links Three D225G/N Sub-clades
PostPosted: Sun Jan 31, 2010 6:37 pm 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 6528
Location: Pittsburgh, PA USA
T739C (codes for Y233H)

A/North Carolina/39/2009
A/North Carolina/40/2009
A/North Carolina/41/2009
A/North Carolina/42/2009
A/North Carolina/49/2009
gb|CY055075.1| Influenza A virus (A/Australia/6/2009(H1N1)) s... 30.2 48
gb|GU369673.1| Influenza A virus (A/Ankara/29/2009(H1N1)) seg... 30.2 48
gb|GU052197.1| Influenza A virus (A/quail/Italy/39403/1965(H1... 30.2 48
gb|GU052184.1| Influenza A virus (A/mallard/Netherlands/02/20... 30.2 48
gb|CY044171.1| Influenza A virus (A/Bethesda/SP506/2009(H1N1)... 30.2 48
gb|CY043872.1| Influenza A virus (A/mallard/Sweden/4/2005(H10... 30.2 48
gb|CY043118.1| Influenza A virus (A/Bethesda/SP508/2009(H1N1)... 30.2 48
gb|GQ325650.1| Influenza A virus (A/environment/Dongting Lake... 30.2 48
gb|GQ325642.1| Influenza A virus (A/environment/Dongting Lake... 30.2 48
gb|GQ325634.1| Influenza A virus (A/environment/Dongting Lake... 30.2 48
gb|GQ247860.1| Influenza A virus (A/ostrich/SouthAfrica/2001(... 30.2 48
gb|EU599312.1| Influenza A virus (A/teal/Egypt/912908/2005(H1... 30.2 48
gb|EU599308.1| Influenza A virus (A/teal/Egypt/912823/2005(H1... 30.2 48
gb|EU599282.1| Influenza A virus (A/shoveler/Egypt/900845/200... 30.2 48
gb|EU599276.1| Influenza A virus (A/shoveler/Egypt/900600/200... 30.2 48
gb|FJ183474.1| Influenza A virus (A/mallard/Bavaria/3/2006(H1... 30.2 48
dbj|AB450456.1| Influenza A virus (A/duck/Mongolia/149/03(H10... 30.2 48
dbj|AB450443.1| Influenza A virus (A/duck/Hokkaido/W87/2007(H... 30.2 48
gb|EU249366.1| Influenza A virus (A/shorebird/Korea/S331/2006... 30.2 48
gb|EU249364.1| Influenza A virus (A/shorebird/Korea/S285/2006... 30.2 48
dbj|AB296078.1| Influenza A virus (A/duck/Shimane/45/1997(H10... 30.2 48
dbj|AB292781.1| Influenza A virus (A/duck/Hong Kong/562/1979(... 30.2 48
dbj|AB292666.1| Influenza A virus (A/chicken/Germany/N/1949(H... 30.2 48
dbj|AB292412.1| Influenza A virus (A/duck/Hong Kong/786/1979(... 30.2 48
dbj|AB289339.1| Influenza A virus (A/swan/Shimane/1331/1981(H... 30.2 48
gb|CY014671.1| Influenza A virus (A/chicken/Germany/n/1949(H1... 30.2 48
gb|CY014644.1| Influenza A virus (A/quail/Italy/1117/1965(H10... 30.2 48
gb|CY014619.1| Influenza A virus (A/duck/Hong Kong/562/1979(H... 30.2 48
dbj|AB274041.1| Influenza A virus (A/duck/Hokkaido/18/00(H10N... 30.2 48
emb|AM087216.1| Influenza A virus (A/mallard/Iran/V15/04(H10N... 30.2 48
emb|AM087215.1| Influenza A virus (A/mallard/Iran/V40/04(H10N... 30.2 48
gb|AF311750.1| Influenza A virus (A/shorebird/Taiwan/31/99(H1... 30.2 48

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Last edited by niman on Sun Jan 31, 2010 6:41 pm, edited 2 times in total.

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niman
 Post subject: Re: Australia Sequence Links Three D225G/N Sub-clades
PostPosted: Sun Jan 31, 2010 6:39 pm 
Online

Joined: Wed Aug 19, 2009 10:42 am
Posts: 6528
Location: Pittsburgh, PA USA
T933C

gb|CY055075.1| Influenza A virus (A/Australia/6/2009(H1N1)) s... 38.2 0.19
gb|GU326329.1| Influenza A virus (A/Shandong/SWL4116/2009(H1N... 38.2 0.19
gb|CY052282.1| Influenza A virus (A/Texas/43292238/2009(H1N1)... 38.2 0.19
dbj|AB536768.1| Influenza A virus (A/Nagasaki/HA-57/2009(H1N1... 38.2 0.19
dbj|AB535748.1| Influenza A virus (A/Nagasaki/HA-63/2009(H1N1... 38.2 0.19
gb|CY051823.1| Influenza A virus (A/Texas/43242018/2009(H1N1)... 38.2 0.19
gb|GU189649.1| Influenza A virus (A/Zhejiang/DTID-ZJU03/2009(... 38.2 0.19
gb|GU112090.1| Influenza A virus (A/Zhejiang/DTID-ZJU02/2009(... 38.2 0.19
gb|GU108486.1| Influenza A virus (A/Zhejiang-Yiwu/11/2009(H1N... 38.2 0.19
gb|CY047712.1| Influenza A virus (A/Hangzhou/1/2009(H1N1)) se... 38.2 0.19
dbj|AB434336.1| Influenza A virus (A/swine/Saraburi/NIAH13021... 38.2 0.19
gb|EU296607.1| Influenza A virus (A/swine/Saraburi/NIAH13021/... 38.2 0.19
gb|AY060052.1| Influenza A virus (A/SW/MN/17138/01(H1N2)) hem... 38.2 0.19

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niman
 Post subject: Re: Australia Sequence Links Three D225G/N Sub-clades
PostPosted: Sun Jan 31, 2010 9:29 pm 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 6528
Location: Pittsburgh, PA USA
Commentary

http://www.recombinomics.com/News/01311 ... China.html

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niman
 Post subject: Re: Australia Sequence Links Three D225G/N Sub-clades
PostPosted: Sun Jan 31, 2010 9:46 pm 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 6528
Location: Pittsburgh, PA USA
The commentary gives more detail on the linkage and recombination. Having the same set of polymorphisms aggregated onto one sequence in Australia demonatrates how these gene pieces (polymorphisms) jump from one genetic sequence to the next and one continent to the next. Australia has markers from Australia, Asia, and North America which are key markers in sub-clades which have D225G, D225N, or both.

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Gator Flu Watcher
 Post subject: Re: Australia Sequence Links Three D225G/N Sub-clades
PostPosted: Sun Jan 31, 2010 10:34 pm 
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Joined: Sun Oct 11, 2009 4:44 pm
Posts: 446
What is the information on whether they were fatal cases or not in these sequences?
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niman
 Post subject: Re: Australia Sequence Links Three D225G/N Sub-clades
PostPosted: Sun Jan 31, 2010 10:45 pm 
Online

Joined: Wed Aug 19, 2009 10:42 am
Posts: 6528
Location: Pittsburgh, PA USA
Gator Flu Watcher wrote:
What is the information on whether they were fatal cases or not in these sequences?

There were at least 3 fatalities in the North Carolina cluster, so it is likely that the three sequences with D225G or D225N came from those patients. The first isolates from Zhejiang was from a severe case. She was hospitalized over a month and likely recovered, but was characterized as the first severe H1N1 case in Zhejiang Province. The status of the Australian patients is unclear. Virtually all Ukraine or Russian sequences with D225G/N were from fatal cases.

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niman
 Post subject: Re: Australia Sequence Links Three D225G/N Sub-clades
PostPosted: Wed Mar 03, 2010 6:05 am 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 6528
Location: Pittsburgh, PA USA
New sequences from Austrailia (at Genbank), provide compelling evidence for recombination in Austrailia. The travel logs above will be updated with the newly released sequences.

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niman
 Post subject: Re: Australia Sequence Links Three D225G/N Sub-clades
PostPosted: Wed Mar 03, 2010 6:17 am 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 6528
Location: Pittsburgh, PA USA
niman wrote:
A308G (codes for D89G)
Sequences with D225G/N in bold

A/SYDNEY/2503/2009
A/SYDNEY/2501/2009
A/VICTORIA/2125/2009
gb|CY055075.1| Influenza A virus (A/Australia/6/2009(H1N1)) s... 32.2 12
gb|CY055067.1| Influenza A virus (A/Australia/4/2009(H1N1)) s... 32.2 12
gb|GU332630.1| Influenza A virus (A/cat/IA/26991/2009(H1N1)) ... 32.2 12
gb|CY052005.1| Influenza A virus (A/Norway/3433/2009(H1N1)) s... 32.2 12
gb|CY049691.1| Influenza A virus (A/Singapore/GP2711/2009(H1N... 32.2 12
gb|CY047150.1| Influenza A virus (A/Catalonia/S1138/2009(H1N1... 32.2 12
gb|GU014748.1| Influenza A virus (A/Gifu-C/67/2009(H1N1)) seg... 32.2 12
gb|GQ377064.1| Influenza A virus (A/Virginia/05/2009(H1N1)) s... 32.2 12
gb|GQ232009.1| Influenza A virus (A/Kentucky/05/2009(H1N1)) s... 32.2 12

gb|CY056164.1| Influenza A virus (A/Pensacola/INS40/2009(H1N1... 32.2 12
gb|CY055940.1| Influenza A virus (A/Australia/82/2009(H1N1)) ... 32.2 12
gb|CY055932.1| Influenza A virus (A/Australia/81/2009(H1N1)) ... 32.2 12
gb|CY055924.1| Influenza A virus (A/Australia/80/2009(H1N1)) ... 32.2 12
gb|CY055908.1| Influenza A virus (A/Australia/73/2009(H1N1)) ... 32.2 12
gb|CY055900.1| Influenza A virus (A/Australia/72/2009(H1N1)) ... 32.2 12
gb|CY055892.1| Influenza A virus (A/Australia/70/2009(H1N1)) ... 32.2 12
gb|CY055884.1| Influenza A virus (A/Australia/69/2009(H1N1)) ... 32.2 12
gb|CY055876.1| Influenza A virus (A/Australia/66/2009(H1N1)) ... 32.2 12
gb|CY055868.1| Influenza A virus (A/Australia/65/2009(H1N1)) ... 32.2 12
gb|CY055860.1| Influenza A virus (A/Australia/64/2009(H1N1)) ... 32.2 12
gb|CY055836.1| Influenza A virus (A/Australia/60/2009(H1N1)) ... 32.2 12
gb|CY055828.1| Influenza A virus (A/Australia/59/2009(H1N1)) ... 32.2 12
gb|CY055812.1| Influenza A virus (A/Australia/57/2009(H1N1)) ... 32.2 12
gb|CY055796.1| Influenza A virus (A/Australia/54/2009(H1N1)) ... 32.2 12
gb|CY055788.1| Influenza A virus (A/Australia/53/2009(H1N1)) ... 32.2 12
gb|CY055780.1| Influenza A virus (A/Australia/51/2009(H1N1)) ... 32.2 12
gb|CY055756.1| Influenza A virus (A/Australia/45/2009(H1N1)) ... 32.2 12
gb|CY055740.1| Influenza A virus (A/Australia/43/2009(H1N1)) ... 32.2 12
gb|CY055732.1| Influenza A virus (A/Australia/42/2009(H1N1)) ... 32.2 12
gb|CY055724.1| Influenza A virus (A/Australia/40/2009(H1N1)) ... 32.2 12
gb|CY055716.1| Influenza A virus (A/Australia/39/2009(H1N1)) ... 32.2 12
gb|CY055708.1| Influenza A virus (A/Australia/37/2009(H1N1)) ... 32.2 12
gb|CY055700.1| Influenza A virus (A/Australia/36/2009(H1N1)) ... 32.2 12
gb|CY055692.1| Influenza A virus (A/Australia/35/2009(H1N1)) ... 32.2 12
gb|CY055676.1| Influenza A virus (A/Australia/31/2009(H1N1)) ... 32.2 12
gb|CY055668.1| Influenza A virus (A/Australia/29/2009(H1N1)) ... 32.2 12
gb|CY055653.1| Influenza A virus (A/Australia/27/2009(H1N1)) ... 32.2 12
gb|CY055637.1| Influenza A virus (A/Australia/25/2009(H1N1)) ... 32.2 12
gb|CY055621.1| Influenza A virus (A/Australia/23/2009(H1N1)) ... 32.2 12
gb|CY055613.1| Influenza A virus (A/Australia/21/2009(H1N1)) ... 32.2 12
gb|CY055605.1| Influenza A virus (A/Australia/20/2009(H1N1)) ... 32.2 12
gb|CY055581.1| Influenza A virus (A/Australia/14/2009(H1N1)) ... 32.2 12
gb|CY055550.1| Influenza A virus (A/Australia/10/2009(H1N1)) ... 32.2 12
gb|CY055542.1| Influenza A virus (A/Australia/9/2009(H1N1)) s... 32.2 12
gb|CY055534.1| Influenza A virus (A/Australia/7/2009(H1N1)) s... 32.2 12
gb|CY055526.1| Influenza A virus (A/Australia/1/2009(H1N1)) s... 32.2 12
gb|GU459110.1| Influenza A virus (A/Pavia/8/2009(H1N1)) segme... 32.2 12
gb|CY055075.1| Influenza A virus (A/Australia/6/2009(H1N1)) s... 32.2 12
gb|CY055067.1| Influenza A virus (A/Australia/4/2009(H1N1)) s... 32.2 12
gb|GU332630.1| Influenza A virus (A/cat/IA/26991/2009(H1N1)) ... 32.2 12
gb|CY052005.1| Influenza A virus (A/Norway/3433/2009(H1N1)) s... 32.2 12
gb|CY049691.1| Influenza A virus (A/Singapore/GP2711/2009(H1N... 32.2 12
gb|CY047150.1| Influenza A virus (A/Catalonia/S1138/2009(H1N1... 32.2 12
gb|GU014748.1| Influenza A virus (A/Gifu-C/67/2009(H1N1)) seg... 32.2 12
gb|GQ377064.1| Influenza A virus (A/Virginia/05/2009(H1N1)) s... 32.2 12
gb|GQ232009.1| Influenza A virus (A/Kentucky/05/2009(H1N1)) s... 32.2 12

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