H5N1 Assam 2008 (November)

HenryN · #1 March 26th, 2009, 10:29 AM

12: FJ839923	Reports	Links
Influenza A virus (A/chicken/Assam/140203/2008(H5N1)) segment 6 neuraminidase (NA) gene, partial cds gi\|225422944\|gb\|FJ839923.1\|[225422944]

13: FJ839922
Reports
Links
Influenza A virus (A/chicken/Assam/140203/2008(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds
gi|225422942|gb|FJ839922.1|[225422942]

14: FJ839921
Reports
Links
Influenza A virus (A/chicken/Assam/140187/2008(H5N1)) segment 6 neuraminidase (NA) gene, partial cds
gi|225422940|gb|FJ839921.1|[225422940]

15: FJ839920	Reports	Links
Influenza A virus (A/chicken/Assam/140187/2008(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds gi\|225422938\|gb\|FJ839920.1\|[225422938]

HenryN · #2 March 26th, 2009, 10:32 AM

Both isolates are clade 2.2.3 (Uvs Lake version)

HenryN · #3 March 26th, 2009, 11:14 AM

NA does NOT have G743A

HenryN · #4 March 31st, 2009, 09:36 AM

Top 100 HA matches

gb|FJ839922.1| Influenza A virus (A/chicken/Assam/140203/2008... 3079 0.0
gb|FJ839920.1| Influenza A virus (A/chicken/Assam/140187/2008... 3079 0.0
gb|EU700511.1| Influenza A virus (A/saker falcon/Kuwait/0286/... 2966 0.0
gb|CY029988.1| Influenza A virus (A/chicken/Kuwait/KISR8/2007... 2966 0.0
gb|CY029980.1| Influenza A virus (A/chicken/Kuwait/KISR7/2007... 2966 0.0
gb|CY029972.1| Influenza A virus (A/chicken/Kuwait/KISR6/2007... 2966 0.0
gb|EU391537.1| Influenza A virus (A/falcon/Kuwait/1019-7/2007... 2962 0.0
gb|CY029964.1| Influenza A virus (A/chicken/Kuwait/KISR5/2007... 2962 0.0
gb|CY029996.1| Influenza A virus (A/chicken/Kuwait/KISR9/2007... 2957 0.0
gb|CY029956.1| Influenza A virus (A/chicken/Kuwait/KISR3/2007... 2957 0.0
gb|EU424135.1| Influenza A virus (A/houbara bustard/Saudi Ara... 2957 0.0
dbj|AB284324.1| Influenza A virus (A/common goldeneye/Mongoli... 2957 0.0
dbj|AB263752.1| Influenza A virus (A/whooper swan/Mongolia/2/... 2957 0.0
gb|CY029948.1| Influenza A virus (A/chicken/Kuwait/KISR2/2007... 2953 0.0
gb|EU233691.1| Influenza A virus (A/chicken/Korea/CA7/2006(H5... 2953 0.0
gb|DQ914808.1| Influenza A virus (A/grebe/Tyva/Tyv06-1/2006(H... 2953 0.0
emb|AM914026.1| Influenza A virus (A/domestic duck/Germany/R2... 2947 0.0
emb|AM914004.1| Influenza A virus (A/domestic goose/Germany/R... 2947 0.0
emb|FM177119.1| Influenza A virus (A/chicken/Germany/R3234/20... 2947 0.0
emb|FM177127.1| Influenza A virus (A/chicken/Germany/R3272/20... 2947 0.0
gb|EU871936.1| Influenza A virus (A/common gull/Chany/P/2006(... 2947 0.0
gb|EU233707.1| Influenza A virus (A/duck/Korea/Asan5/2006(H5N... 2947 0.0
gb|EU233715.1| Influenza A virus (A/duck/Korea/Asan6/2006(H5N... 2947 0.0
gb|EU233731.1| Influenza A virus (A/environment/Korea/W149/20... 2947 0.0
emb|AM914012.1| Influenza A virus (A/great crested grebe/Germ... 2944 0.0
emb|FM177135.1| Influenza A virus (A/chicken/Germany/R3294/20... 2944 0.0
emb|FM165530.1| Influenza A virus (A/Peking duck/Germany/R195... 2944 0.0
gb|CY034733.1| Influenza A virus (A/chicken/Manshera/NARC1033... 2944 0.0
gb|EU401795.1| Influenza A virus (A/goose/Lahore-Pakistan/NAR... 2944 0.0
emb|AM773724.1| Influenza A virus (A/black-necked grebe/Germa... 2944 0.0
gb|CY021373.1| Influenza A virus (A/chicken/Afghanistan/1573-... 2944 0.0
gb|CY020621.1| Influenza A virus (A/chicken/Afghanistan/1573-... 2944 0.0
gb|CY037770.1| Influenza A virus (A/chicken/Sihala/NARC3303.4... 2938 0.0
gb|CY037762.1| Influenza A virus (A/chicken/Rawalakot/NARC244... 2938 0.0
gb|EU443555.1| Influenza A virus (A/Cygnus olor/Czech Republi... 2938 0.0
gb|EU443554.1| Influenza A virus (A/turkey/Czech Republic/103... 2938 0.0
gb|EU443553.1| Influenza A virus (A/chicken/Czech Republic/11... 2938 0.0
gb|CY020637.1| Influenza A virus (A/chicken/Afghanistan/1573-... 2938 0.0
gb|DQ861291.1| Influenza A virus (A/duck/Tuva/01/2006(H5N1)) ... 2938 0.0
emb|AM914014.1| Influenza A virus (A/domestic duck/Germany/R1... 2935 0.0
gb|CY020629.1| Influenza A virus (A/chicken/Afghanistan/1573-... 2935 0.0
gb|FJ390028.1| Influenza A virus (A/chicken/Astana/6/2005(H5N... 2931 0.0
emb|AM914021.1| Influenza A virus (A/domestic duck/Germany/R1... 2929 0.0
gb|CY034725.1| Influenza A virus (A/goose/Islamabad/NARC7757/... 2929 0.0
gb|EU233675.1| Influenza A virus (A/chicken/Korea/IS/2006(H5N... 2929 0.0
gb|EU233683.1| Influenza A virus (A/chicken/Korea/IS2/2006(H5... 2929 0.0
emb|AM749443.1| Influenza A virus (A/mute swan/Germany/R1359/... 2929 0.0
gb|DQ863503.1| Influenza A virus (A/Grebe/Tyva/Tyv06-8/2006(H... 2929 0.0
gb|DQ852600.1| Influenza A virus (A/grebe/Tyva/Tyv06-2/06(H5N... 2929 0.0
emb|AM914016.1| Influenza A virus (A/domestic duck/Germany/R1... 2926 0.0
gb|EU401794.1| Influenza A virus (A/turkey/Islamabad-Pakistan... 2926 0.0
gb|EU233739.1| Influenza A virus (A/environment/Korea/W150/20... 2926 0.0
gb|EU257631.1| Influenza A virus (A/Cygnus cygnus/Krasnodar/3... 2926 0.0
gb|EU163431.1| Influenza A virus (A/chicken/Krasnodar/300/07(... 2926 0.0
gb|CY016787.1| Influenza A virus (A/chicken/Afghanistan/1207/... 2926 0.0
emb|FM165522.1| Influenza A virus (A/Cygnus olor/Germany/R137... 2920 0.0
gb|FJ183472.1| Influenza A virus (A/mallard/Bavaria/10/2007(H... 2920 0.0
gb|EF362426.1| Influenza A virus (A/chicken/India/NIV33491/06... 2920 0.0
gb|EF362418.1| Influenza A virus (A/chicken/India/NIV33487/06... 2920 0.0
emb|AM749442.1| Influenza A virus (A/mute swan/Germany/R1349/... 2920 0.0
gb|EU401796.1| Influenza A virus (A/peacock/Mansehra-Pakistan... 2919 0.0
emb|FM163448.1| Influenza A virus (A/turkey/Poland/R3249/2007... 2917 0.0
emb|FM163440.1| Influenza A virus (A/chicken/Poland/R3248/200... 2917 0.0
gb|FJ602811.1| Influenza A virus (A/common cormorant/Qinghai/... 2917 0.0
gb|CY034729.1| Influenza A virus (A/crow/Peshawer/NARC7914/20... 2917 0.0
gb|CY034727.1| Influenza A virus (A/turkey/Islamabad/NARC7873... 2917 0.0
gb|DQ864715.1| Influenza A virus (A/chicken/Adygea/203/06(H5N... 2917 0.0
gb|EU233723.1| Influenza A virus (A/quail/Korea/KJ4/2006(H5N1... 2913 0.0
gb|FJ602813.1| Influenza A virus (A/bar-headedgoose/Qinghai/1... 2911 0.0
gb|FJ602810.1| Influenza A virus (A/great black-headed gull/Q... 2911 0.0
gb|FJ476174.1| Influenza A virus (A/swan/England/26-70/2008(H... 2911 0.0
gb|CY016779.1| Influenza A virus (A/cygnus cygnus/Iran/754/20... 2911 0.0
gb|FJ602867.1| Influenza A virus (A/brown-headed gull/Qinghai... 2908 0.0
gb|FJ602866.1| Influenza A virus (A/bar-headed goose/Qinghai/... 2908 0.0
gb|FJ602815.1| Influenza A virus (A/bar-headed goose/Qinghai/... 2908 0.0
gb|FJ602812.1| Influenza A virus (A/common cormorant/Qinghai/... 2908 0.0
gb|FJ602807.1| Influenza A virus (A/brown-headed gull/Qinghai... 2908 0.0
gb|FJ602806.1| Influenza A virus (A/brown-headed gull/Qinghai... 2908 0.0
gb|FJ602805.1| Influenza A virus (A/bar-headed goose/Qinghai/... 2908 0.0
gb|CY034731.1| Influenza A virus (A/peacock/Chakshahzad/NARC9... 2908 0.0
gb|EF605603.1| Influenza A virus (A/chicken/Russia_Krasnodar/... 2904 0.0
gb|DQ864720.1| Influenza A virus (A/cat/Dagestan/87/06(H5N1))... 2904 0.0
gb|DQ864717.1| Influenza A virus (A/goose/Crimea/615/05(H5N1)... 2904 0.0
gb|FJ602814.1| Influenza A virus (A/great black-headed gull/Q... 2902 0.0
gb|FJ602809.1| Influenza A virus (A/bar-headed goose/Qinghai/... 2902 0.0
gb|FJ602808.1| Influenza A virus (A/bar-headed goose/Qinghai/... 2902 0.0
gb|EU650486.1| Influenza A virus (A/falcon/Saudi Arabia/6732-... 2902 0.0
gb|EF205159.1| Influenza A virus (A/chicken/Krasnodar/123/06(... 2902 0.0
gb|EU233699.1| Influenza A virus (A/chicken/Korea/IS3/2006(H5... 2899 0.0
gb|DQ887061.1| Influenza A virus (A/chicken/Navapur/7972/2006... 2899 0.0
gb|EF205155.1| Influenza A virus (A/chicken/Omsk/14/05(H5N1))... 2899 0.0
gb|DQ864711.1| Influenza A virus (A/duck/Novosibirsk/02/05(H5... 2899 0.0
gb|DQ095617.2| Influenza A virus (A/Bar-headed Goose/Qinghai/... 2895 0.0
gb|DQ095613.2| Influenza A virus (A/Bar-headed Goose/Qinghai/... 2895 0.0
gb|DQ095612.2| Influenza A virus (A/Bar-headed Goose/Qinghai/... 2895 0.0
gb|DQ095620.1| Influenza A virus (A/Bar-headed Goose/Qinghai/... 2895 0.0
gb|EU190482.1| Influenza A virus (A/domestic goose/Pavlodar/1... 2893 0.0
gb|CY016819.1| Influenza A virus (A/cygnus olor/Croatia/1/200... 2893 0.0
gb|DQ650663.1| Influenza A virus (A/chicken/Crimea/08/2005(H5... 2893 0.0
gb|DQ676834.1| Influenza A virus (A/chicken/Krasnodar/01/2006... 2893 0.0

HenryN · #5 March 31st, 2009, 10:00 AM

S. Nagarajan, H. V. Murugkar, C. Tosh, P. Behera, R. Jain, S. Tripathi, R. Khandia, V. Gupta, D. D. Kulkarni, and S. C. Dubey Avian influenza virus (H5N1) in chickens in India
Vet Rec. 2009 164: 128.

: [Full Text] [PDF]

HenryN · #6 March 31st, 2009, 05:22 PM

Commentary

http://www.recombinomics.com/News/03...ake_Assam.html

AlaskaDenise · #7 April 1st, 2009, 03:30 PM

Quote:

Originally Posted by niman

Commentary

http://www.recombinomics.com/News/03...ake_Assam.html

Commentary

Uvs Lake H5N1 Flies Into Assam India

Recombinomics Commentary 21:39
March 31, 2009

HA and NA sequences from the H5N1 outbreak in Assam, India were released at Genbank. The two HA sequences, A/chicken/Assam/140187/2008 and A/chicken/Assam/140203/2008 were identical and clade 2.2.3, as seen previously in isolates from south Asia (India, Pakistan, Afghanistan). However, the current sequences are the Uvs Lake strain that was initially isolated from a massive wild bird outbreak at Uvs Lake in Mongolia and the adjacent region in Siberia (Tyva) in the summer of 2006. These sequences were subsequently found in outbreaks in South Korea and Japan at the end of 2006 / beginning of 2007. However, another set of sequences was found in early 2007, and these sequences had acquired G743A, which was also acquired by distinct clade 2.2 isolates in Egypt, Russia, Ghana, and Nigeria in early 2007.

However, the Assam sequences do not have G743A, suggesting they originated from sequences that did not fly west to the Middle East and Europe (the sequences in Kuwait, including G743A, were subsequently reported throughout Europe, beginning in the summer of 2007). Phylogenetic analysis also shows that the Assam sequences are on a lower branch that is distinct from the isolates with G743A. Moreover, the newly acquired polymorphisms in the Assam sequences were not clade 2.2 sequences, but were largely polymorphisms found in other H5N1 clades circulating in Asia.

These data support migration of the H5N1 sequences from Mongolia or Russia to India via the south Asia flyway, which connects those countries. This connection was expected, because all prior outbreaks in the region were clade 2.2, which was initially reported in countries to the north of India that were in this flyway.

However, the linkage with Uvs Lake sequences, populated with Asian polymorphisms further supports the migration of H5N1 into India via migratory birds.

.