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PostPosted: Wed Mar 03, 2010 6:05 am 
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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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PostPosted: Wed Mar 03, 2010 6:17 am 
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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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PostPosted: Wed Mar 03, 2010 6:19 am 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
niman wrote:
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

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|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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PostPosted: Wed Mar 03, 2010 6:22 am 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
niman wrote:
T933C
A/SYDNEY/2501/2009
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

A/SYDNEY/2501/2009
gb|CY055924.1| Influenza A virus (A/Australia/80/2009(H1N1)) ... 38.2 0.20
gb|CY055876.1| Influenza A virus (A/Australia/66/2009(H1N1)) ... 38.2 0.20
gb|CY055788.1| Influenza A virus (A/Australia/53/2009(H1N1)) ... 38.2 0.20
gb|CY055732.1| Influenza A virus (A/Australia/42/2009(H1N1)) ... 38.2 0.20
gb|CY055716.1| Influenza A virus (A/Australia/39/2009(H1N1)) ... 38.2 0.20
gb|CY055637.1| Influenza A virus (A/Australia/25/2009(H1N1)) ... 38.2 0.20
gb|FJ752522.1| Influenza A virus (A/swine/Pingtung/64-26/2007... 38.2 0.20
gb|GU459110.1| Influenza A virus (A/Pavia/8/2009(H1N1)) segme... 38.2 0.20
gb|CY055075.1| Influenza A virus (A/Australia/6/2009(H1N1)) s... 38.2 0.20
gb|GU326329.1| Influenza A virus (A/Shandong/SWL4116/2009(H1N... 38.2 0.20
gb|CY052282.1| Influenza A virus (A/Texas/43292238/2009(H1N1)... 38.2 0.20
dbj|AB536768.1| Influenza A virus (A/Nagasaki/HA-57/2009(H1N1... 38.2 0.20
dbj|AB535748.1| Influenza A virus (A/Nagasaki/HA-63/2009(H1N1... 38.2 0.20
gb|CY051823.1| Influenza A virus (A/Texas/43242018/2009(H1N1)... 38.2 0.20
gb|GU189649.1| Influenza A virus (A/Zhejiang/DTID-ZJU03/2009(... 38.2 0.20
gb|GU112090.1| Influenza A virus (A/Zhejiang/DTID-ZJU02/2009(... 38.2 0.20
gb|GU108486.1| Influenza A virus (A/Zhejiang-Yiwu/11/2009(H1N... 38.2 0.20
gb|CY047712.1| Influenza A virus (A/Hangzhou/1/2009(H1N1)) se... 38.2 0.20
dbj|AB434336.1| Influenza A virus (A/swine/Saraburi/NIAH13021... 38.2 0.20
gb|EU296607.1| Influenza A virus (A/swine/Saraburi/NIAH13021/... 38.2 0.20
gb|AY060052.1| Influenza A virus (A/SW/MN/17138/01(H1N2)) hem... 38.2 0.20

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PostPosted: Wed Mar 03, 2010 7:39 am 
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Joined: Sat Jan 30, 2010 2:44 am
Posts: 926
Dr Niman,

Is there a simple way to explain these travel logs? I don't know what they mean.

The last mean H3N2 viruses had Perth and Brisbane names - will Sydney/A be the killer this time around? Pity, I live there.....


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PostPosted: Wed Mar 03, 2010 7:53 am 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
Dingo wrote:
Dr Niman,

Is there a simple way to explain these travel logs? I don't know what they mean.

The last mean H3N2 viruses had Perth and Brisbane names - will Sydney/A be the killer this time around? Pity, I live there.....

Each travel log shows a series of isolates with the same change. The location of the isolates are in the name. I had written a commentray about a montn ago showing that an Australian isolate had markers from each of the three clades with D225G/N that were not the Ukraine clade. A new series of Austrailian sequneces (largely from last summer) which furtehr supported the recombunation (because they had the same polymorphism shared by the Austraian sequence and the sequneces from China with D225G/N). However, the Australian D225G/N sequences were relatively recent and could be signaling more such sequences in upcoming moths in Australian and the southern hemisphere.

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PostPosted: Wed Mar 03, 2010 9:46 am 
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Posts: 926
niman wrote:
Dingo wrote:
Dr Niman,

Is there a simple way to explain these travel logs? I don't know what they mean.

The last mean H3N2 viruses had Perth and Brisbane names - will Sydney/A be the killer this time around? Pity, I live there.....


Each travel log shows a series of isolates with the same change. The location of the isolates are in the name. I had written a commentray about a montn ago showing that an Australian isolate had markers from each of the three clades with D225G/N that were not the Ukraine clade. A new series of Austrailian sequneces (largely from last summer) which furtehr supported the recombunation (because they had the same polymorphism shared by the Austraian sequence and the sequneces from China with D225G/N). However, the Australian D225G/N sequences were relatively recent and could be signaling more such sequences in upcoming moths in Australian and the southern hemisphere.


Thanks. How recent is "relatively recent"?

As I read about your northern hemisphere last wave, Ukraine and various mutations found, I began to get a very uneasy feeling that this thing was kind of re-arming and getting ready for the Southern hemisphere second wave, which I suspect will come earlier than most here think.


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PostPosted: Wed Mar 03, 2010 10:01 am 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
Dingo wrote:
niman wrote:
Dingo wrote:
Dr Niman,

Is there a simple way to explain these travel logs? I don't know what they mean.

The last mean H3N2 viruses had Perth and Brisbane names - will Sydney/A be the killer this time around? Pity, I live there.....


Each travel log shows a series of isolates with the same change. The location of the isolates are in the name. I had written a commentray about a montn ago showing that an Australian isolate had markers from each of the three clades with D225G/N that were not the Ukraine clade. A new series of Austrailian sequneces (largely from last summer) which furtehr supported the recombunation (because they had the same polymorphism shared by the Austraian sequence and the sequneces from China with D225G/N). However, the Australian D225G/N sequences were relatively recent and could be signaling more such sequences in upcoming moths in Australian and the southern hemisphere.


Thanks. How recent is "relatively recent"?

As I read about your northern hemisphere last wave, Ukraine and various mutations found, I began to get a very uneasy feeling that this thing was kind of re-arming and getting ready for the Southern hemisphere second wave, which I suspect will come earlier than most here think.

The latest example was November, but a couple were also from July.

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PostPosted: Wed Mar 03, 2010 10:07 am 
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Posts: 926
niman wrote:
Dingo wrote:

Thanks. How recent is "relatively recent"?

As I read about your northern hemisphere last wave, Ukraine and various mutations found, I began to get a very uneasy feeling that this thing was kind of re-arming and getting ready for the Southern hemisphere second wave, which I suspect will come earlier than most here think.


The latest example was November, but a couple were also from July.


Thanks. We're just enjoying the tail end of our summer and the beaches are still crowded. Looks like autumn will be interesting.

From memory, you guys had a bit of summer spike and then we copped infections in Victoria in the south from travellers returning from the US and it took off in our mild winter. I wonder if we'll cop our next wave before you this time, or vice versa?


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PostPosted: Wed Mar 03, 2010 10:38 am 
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Posts: 56044
Location: Pittsburgh, PA USA
Dingo wrote:
niman wrote:
Dingo wrote:

Thanks. How recent is "relatively recent"?

As I read about your northern hemisphere last wave, Ukraine and various mutations found, I began to get a very uneasy feeling that this thing was kind of re-arming and getting ready for the Southern hemisphere second wave, which I suspect will come earlier than most here think.


The latest example was November, but a couple were also from July.


Thanks. We're just enjoying the tail end of our summer and the beaches are still crowded. Looks like autumn will be interesting.

From memory, you guys had a bit of summer spike and then we copped infections in Victoria in the south from travellers returning from the US and it took off in our mild winter. I wonder if we'll cop our next wave before you this time, or vice versa?

The virus does move around, but there are regional differences. Last summer D225E was widespread in western Europe (30-50% of samples in countries like UK, Spain, Italy), however, out of all of the sequences just released (primarily from US and Australia), none had D225E.

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