7.5.09

Genetic Sequence of H1N1, aka #Swineflu, Up Close and Personal

GenBank sequences from 2009 H1N1 influenza outbreak
All submitted influenza sequences are available in GenBank as soon as they are processed. The 2009 H1N1 influenza virus sequences are listed on this page and are available for BLAST searching here, and are also available in the NCBI Influenza Virus Sequence Database, and can be retrieved with sequences from other influenza viruses for further analyses using tools integrated to the database.

The following 2009 H1N1 influenza virus sequences were submitted to NCBI and are available in GenBank:

May 06, 2009, 102 submitted by CDC:

PB2 PB1 PA HA NP NA MP NS
Influenza A virus
(A/Arizona/01/2009(H1N1))		 GQ117067 GQ117063 GQ117064 GQ117066 GQ117065
Influenza A virus
(A/Arizona/02/2009(H1N1))		 GQ117076 GQ117075 GQ117079 GQ117074 GQ117077 GQ117078
Influenza A virus
(A/California/04/2009(H1N1))		 GQ117044
Influenza A virus
(A/California/14/2009(H1N1))		 GQ117035 GQ117034 GQ117037 GQ117040 GQ117033 GQ117036 GQ117039 GQ117038
Influenza A virus
(A/Colorado/03/2009(H1N1))		 GQ117119 GQ117117 GQ117118
Influenza A virus
(A/Indiana/09/2009(H1N1))		 GQ117093 GQ117095 GQ117097 GQ117092 GQ117094 GQ117096
Influenza A virus
(A/Kansas/02/2009(H1N1))		 GQ117059 GQ117057 GQ117058
Influenza A virus
(A/Kansas/03/2009(H1N1))		 GQ117062 GQ117060 GQ117061
Influenza A virus
(A/Massachusetts/06/2009(H1N1))		 GQ117043 GQ117041 GQ117042
Influenza A virus
(A/Massachusetts/07/2009(H1N1))		 GQ117103 GQ117101 GQ117102
Influenza A virus
(A/Michigan/02/2009(H1N1))		 GQ117109 GQ117112 GQ117107 GQ117108 GQ117111 GQ117110
Influenza A virus
(A/Minnesota/02/2009(H1N1))		 GQ117070 GQ117069 GQ117068 GQ117071 GQ117073 GQ117072
Influenza A virus
(A/Nebraska/02/2009(H1N1))		 GQ117104 GQ117105 GQ117106
Influenza A virus
(A/New York/09/2009(H1N1))		 GQ117120
Influenza A virus
(A/New York/13/2009(H1N1))		 GQ117115 GQ117116 GQ117113 GQ117114
Influenza A virus
(A/New York/20/2009(H1N1))		 GQ117082
GQ117086		 GQ117080
GQ117083		 GQ117081
GQ117084		 GQ117085
Influenza A virus
(A/New York/22/2009(H1N1))		 GQ117021 GQ117020 GQ117024 GQ117019 GQ117022 GQ117023
Influenza A virus
(A/Ohio/07/2009(H1N1))		 GQ117100 GQ117098 GQ117099
Influenza A virus
(A/South Carolina/09/2009(H1N1))		 GQ117056 GQ117052 GQ117053 GQ117055 GQ117054
Influenza A virus
(A/Texas/07/2009(H1N1))		 GQ117089 GQ117088 GQ117091 GQ117087 GQ117090
Influenza A virus
(A/Texas/08/2009(H1N1))		 GQ117047 GQ117046 GQ117049 GQ117051 GQ117045 GQ117048 GQ117050
Influenza A virus
(A/Texas/09/2009(H1N1))		 GQ117027 GQ117026 GQ117029 GQ117032 GQ117025 GQ117028 GQ117031 GQ117030

May 05, 2009, 20 submitted by Instituto de Salud Carlos III, Spain; 3 by National Institute for Infectious Diseases 'Lazzaro Spallanzani', Italy; 4 by Israel Central Virology Laboratory, 23 by Unknown Pathogen Investigation Collaborative Team (UPICT) and Instituto de Diangnostico y Referencia Epidemiologicos (inDRE), Canada/Mexico:

PB2 PB1 PA HA NP NA MP NS
Influenza A virus
(A/Castilla-La Mancha/GP13/2009(H1N1))		 FJ985753 FJ985751 FJ985754 FJ985750 FJ985752
Influenza A virus
(A/Castilla-La Mancha/GP9/2009(H1N1))		 FJ985768 FJ985766 FJ985769 FJ985765 FJ985767
Influenza A virus
(A/Pais Vasco/GP20/2009(H1N1))		 FJ985763 FJ985761 FJ985764 FJ985760 FJ985762
Influenza A virus
(A/Valencia/GP4/2009(H1N1))		 FJ985758 FJ985756 FJ985759 FJ985755 FJ985757
Influenza A virus
(A/Italy/03/2009(H1N1))		 FJ985804
Influenza A virus
(A/Italy/04/2009(H1N1))		 FJ985805
Influenza A virus
(A/Italy/02/2009(H1N1))		 FJ997636
Influenza A virus
(A/Israel/G-640/2009(H1N1))		 FJ986328
Influenza A virus
(A/Israel/G-645/2009(H1N1))		 FJ986329
Influenza A virus
(A/Israel/MF-119/2009(H1N1))		 FJ986331
Influenza A virus
(A/Israel/MF-70/2009(H1N1))		 FJ986330
Influenza A virus
(A/Canada-NS/RV1535/2009(H1N1))		 FJ998225 FJ998222 FJ998207 FJ998216 FJ998213 FJ998210 FJ998219
Influenza A virus
(A/Canada-ON/RV1527/2009(H1N1))		 FJ998205 FJ998227 FJ998224 FJ998209 FJ998218 FJ998215 FJ998212 FJ998221
Influenza A virus
(A/Mexico/InDRE4487/2009(H1N1))		 FJ998206 FJ998226 FJ998223 FJ998208 FJ998217 FJ998214 FJ998211 FJ998220

May 04, 2009, 4 submitted by Statens Serum Institut, Denmark; 1 by Azienda Ospedaliero-Universitaria Pisana, Italy; 1 by Istituto Superiore di Sanita, Italy; 68 by CDC; 1 by University of Regensburg, Germany:

PB2 PB1 PA HA NP NA MP NS
Influenza A virus
(A/Denmark/513/2009(H1N1))		 FJ982430 FJ982431 FJ982432 FJ982433
Influenza A virus
(A/Italy/01/2009(H1N1))		 FJ982434
Influenza A virus
(A/Italy/02/2009(H1N1))		 FJ984583
Influenza A virus
(A/California/07/2009(H1N1))		 FJ984387 FJ984386
Influenza A virus
(A/California/08/2009(H1N1))		 FJ984365 FJ984367 FJ984368 FJ984366
Influenza A virus
(A/New York/06/2009(H1N1))		 FJ984341 FJ984340 FJ984338 FJ984339
Influenza A virus
(A/New York/10/2009(H1N1))		 FJ984373 FJ984374 FJ984375 FJ984372 FJ984371 FJ984369 FJ984370
Influenza A virus
(A/New York/11/2009(H1N1))		 FJ984346 FJ984347 FJ984345 FJ984344 FJ984342 FJ984343
Influenza A virus
(A/New York/12/2009(H1N1))		 FJ984337 FJ984336 FJ984335 FJ984334
Influenza A virus
(A/New York/15/2009(H1N1))		 FJ984380 FJ984379 FJ984378 FJ984376 FJ984377
Influenza A virus
(A/New York/18/2009(H1N1))		 FJ984351 FJ984353 FJ984354 FJ984355 FJ984352 FJ984350 FJ984348 FJ984349
Influenza A virus
(A/New York/19/2009(H1N1))		 FJ984392 FJ984393 FJ984394 FJ984391 FJ984390 FJ984388 FJ984389
Influenza A virus
(A/New York/23/2009(H1N1))		 FJ984364 FJ984363 FJ984362 FJ984361
Influenza A virus
(A/New York/31/2009(H1N1))		 FJ984359 FJ984360 FJ984358 FJ984357 FJ984356
Influenza A virus
(A/Ohio/07/2009(H1N1))		 FJ984400 FJ984397
FJ984401		 FJ984396 FJ984395
FJ984398		 FJ984399
Influenza A virus
(A/Texas/06/2009(H1N1))		 FJ984385 FJ984384 FJ984383 FJ984381 FJ984382
Influenza A virus
(A/Regensburg/Germany/01/2009(H1N1)) 		FJ984953

May 1, 2009, 13 submitted by CDC; 1 by University of Geneva, Switzerland:

PB2 PB1 PA HA NP NA MP NS
Influenza A virus
(A/California/07/2009(H1N1))		 FJ981613
Influenza A virus
(A/Switzerland/01/2009(H1N1))		 FJ981646
Influenza A virus
(A/Texas/04/2009(H1N1))		 FJ981616 FJ981619 FJ981612
FJ981615		 FJ981618 FJ981614 FJ981617 FJ981620
Influenza A virus
(A/Texas/05/2009(H1N1))		 FJ981610 FJ981609 FJ981608 FJ981611

April 30, 2009, 6 submitted by WHO CC for Reference and Research on Influenza, Australia; 1 by University of Regensburg, Germany; 7 by Ontario Agency for Health Protection and Promotion, Canada; 2 by Erasmus MC Rotterdam, Netherlands:

PB2 PB1 PA HA NP NA MP NS
Influenza A virus
(A/Auckland/3/2009(H1N1)) 		FJ973552 FJ973553
Influenza A virus
(A/Auckland/2/2009(H1N1)) 		FJ973554
Influenza A virus
(A/Auckland/1/2009(H1N1)) 		FJ973557 FJ973555 FJ973556
Influenza A virus
(A/Regensburg/Germany/01/2009(H1N1)) 		FJ974021
Influenza A virus
(A/Toronto/3181/2009(H1N1)) 		FJ974022
Influenza A virus
(A/Toronto/3170/2009(H1N1)) 		FJ974023
Influenza A virus
(A/Toronto/3184/2009(H1N1)) 		FJ974024
Influenza A virus
(A/Toronto/3178/2009(H1N1)) 		FJ974025
Influenza A virus
(A/Toronto/3141/2009(H1N1)) 		FJ974026
Influenza A virus
(A/Toronto/3145/2009(H1N1)) 		FJ974027
Influenza A virus
(A/Toronto/3146/2009(H1N1)) 		FJ974028
Influenza A virus
(A/Netherlands/602/2009(H1N1)) 		CY039527 CY039528

April 29, 2009, 1 submitted by University of Regensburg, Germany; 3 by CDC:

PB2 PB1 PA HA NP NA MP NS
Influenza A virus
(A/Regensburg/Germany/01/2009(H1N1)) 		FJ970928
Influenza A virus
(A/California/06/2009(H1N1))		 FJ971075 FJ971074
Influenza A virus
(A/California/08/2009(H1N1))		 FJ971076

April 28, 2009, 34 submitted by CDC:

PB2 PB1 PA HA NP NA MP NS
Influenza A virus
(A/New York/19/2009(H1N1))		 FJ969509
Influenza A virus
(A/New York/20/2009(H1N1))		 FJ969542 FJ969541
Influenza A virus
(A/Kansas/03/2009(H1N1))		 FJ969523
Influenza A virus
(A/Ohio/07/2009(H1N1))		 FJ969521
FJ969535		 FJ969520
FJ969534
Influenza A virus
(A/California/04/2009(H1N1))		 FJ969516 FJ969515 FJ969512 FJ969517 FJ969513 FJ969514
Influenza A virus
(A/California/07/2009(H1N1))		 FJ969530 FJ969531 FJ969529
FJ969539		 FJ969540 FJ969536 FJ969527
FJ969537		 FJ969528
FJ969538
Influenza A virus
(A/California/08/2009(H1N1))		 FJ969518
FJ969532		 FJ969519
FJ969533
Influenza A virus
(A/California/10/2009(H1N1))		 FJ969511 FJ969510
Influenza A virus
(A/Texas/04/2009(H1N1))		 FJ969525 FJ969526 FJ969524
Influenza A virus
(A/Texas/05/2009(H1N1))		 FJ969522

April 27, 2009, 40 submitted by CDC:

PB2 PB1 PA HA NP NA MP NS
Influenza A virus
(A/California/04/2009(H1N1))		 FJ966079 FJ966080 FJ966081 FJ966082 FJ966083 FJ966084 FJ966085 FJ966086
Influenza A virus
(A/California/05/2009(H1N1))		 FJ966955 FJ966958 FJ966957 FJ966952 FJ966953 FJ966956 FJ966954
Influenza A virus
(A/California/06/2009(H1N1))		 FJ966963 FJ966965 FJ966964 FJ966960 FJ966961 FJ966962
Influenza A virus
(A/California/07/2009(H1N1))		 FJ966976 FJ966978 FJ966977 FJ966974 FJ966975
Influenza A virus
(A/California/09/2009(H1N1))		 FJ966971 FJ966973 FJ966972
Influenza A virus
(A/Texas/04/2009(H1N1))		 FJ966982 FJ966979 FJ966981 FJ966980
FJ966983
Influenza A virus
(A/Texas/05/2009(H1N1))		 FJ966970 FJ966959 FJ966967 FJ966969 FJ966968 FJ966966
via ncbi.nlm.nih.gov

From "2009 H1N1 influenza Outbreak, Influenza Virus Resource."

Many thanks to David Hale, @lostonroute66, for the link - via Twitter of course!

Posted via web from Jen's Posterous

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1 comment:

Anonymous said...

why are there only 2 mutations in the Mexican sequences ?
They give no date or host details,
but according to Cordova the first case was 13.Apr.
So, had the Mexican virus survived in the environment (pork ?) for
months without replicating, without mutating ?
This is unusual for influenza.

May 8, 2009 at 10:02 AM

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