Orthomyxoviridae Influenzavirus A

The Orthomyxoviridae family of viruses are segmented (8 segments, in the case of influenza A virus), negative-sense, enveloped RNA viruses, which infect vertebrate hosts. (see ICTVdB - The Universal Virus Database, version 4).

Of the viruses belonging to the family Orthomyxoviridae, influenza A virus is the most predominant cause of morbidity and mortality in humans, in which it causes respiratory illness. The natural hosts of all influenza A subtypes are wild birds, primarily those belonging to the family Anatidae (ducks, geese, and swans). Transmission of numerous subtypes to humans and other animals have been documented, but establishment of persistent infection of new subtypes in humans is rare. Apart from waterfowl and humans, transmission of influenza A is known to persist in birds of the order Galliformes, pigs, horses, and dogs.

Influenza A viruses are classified into subtypes based on the antigenic relationships of their two major surface proteins: haemagglutinin (HA), which binds to sialic acid residues on surface proteins of host cells, and induces fusion of the virus membrane with that of the host cell; and neuraminidase (NA), which cleaves sialic acid residues from surface proteins, enabling release of virus particles from host cells.

Until recently, two influenza A subtypes - H1N1 and H3N2 - persisted in humans, and caused seasonal epidemics of influenza in temperate countries, and year-round infections in humans in tropical regions. In 2009, a new variant of H1N1, distantly related to seasonal H1N1, emerged in the human population, and caused the first influenza pandemic of the 21st century - this virus is now referred to as pandemic (H1N1) 2009.

Data Downloads

This project is ongoing and data for this organism will be made available in due course.

[Genome Research Limited]

The Wellcome Trust Sanger Institute is committed to two facets of influenza A virus sequencing: whole genome sequencing; and deep amplicon sequencing.

Our influenza whole genome sequencing is funded by the Wellcome Trust, and involves collaboration with researchers at the Health Protection Agency (HPA), National Institute for Medical Research, London (NIMR), and the Veterinary Laboratories Agency (VLA). We have developed robust approaches to sequencing influenza A genomes using capillary, 454, and Illumina sequencing platforms. The role of these projects is to supplement the sequences of subgenomic genes/segments, which are rapidly generated by our collaborators, with whole genome consensus sequences.

Our deep amplicon sequencing projects are also funded by the Wellcome Trust, and involve collaborations with the Cambridge Infectious Disease Consortium (CIDC) and the Animal Health Trust, Newmarket (AHT). Rather than generating consensus sequence for the whole genome, these projects involve deep sequencing of some genes (usually HA1), to investigate changes in frequency of rare variants over time during infection, both within the period of infection of an individual and through chains of transmission.

Published Genome Data

A/California/07/2009(H1N1)

Studies

ICONIC

Sample

Strain

Run Accession

3034STDY5782406178ERR559524
3034STDY578240499ERR559523
3034STDY578240141_bERR559522
3034STDY578240041_aERR559521
3034STDY578239313U134592ERR559520
3034STDY578238813U186764ERR559519
3034STDY578238313U178837ERR559518
3034STDY578238013U194365ERR559517
3034STDY578237313U157352ERR559516
3034STDY578236713U136701ERR559515
3034STDY578233413U134083ERR559514
3034STDY578232413U112477ERR559513
3034STDY578232313U115604ERR559512
3034STDY578232213U112299ERR559511
3034STDY578231813U108226ERR559510
3034STDY578231413U104208ERR559509
3034STDY578231213U080722ERR559508
3034STDY578231113U080720ERR559507
3034STDY578230913U056533ERR559506
3034STDY578230513U021134ERR559505
3034STDY578230112u734886ERR559504
3034STDY578230013U087087ERR559503
3034STDY578229913U003110ERR559502
3034STDY578228113U094324RPTERR559501
3034STDY578228013U085100ERR559500
3034STDY578227913U094809ERR559499
3034STDY578227013U094117ERR559498
3034STDY578226113U069884ERR559497
3034STDY578226013U069882ERR559496
3034STDY578225913U067912ERR559495
3034STDY578225713U067701ERR559494
3034STDY578225513U067520ERR559493
3034STDY578225413U067247ERR559492
3034STDY578225113U067142ERR559491
3034STDY578225013U061429ERR559490
3034STDY578224913U061412ERR559489
3034STDY578224513U003089ERR559488
3034STDY578224213U042965ERR559487
3034STDY578224113U042961ERR559486
3034STDY578224013U040077ERR559485
3034STDY578222613U104213ERR559484
3034STDY578222413U100457ERR559483
3034STDY578222313U126899ERR559482
3034STDY578222213U126827ERR559481
3034STDY578222013U127578ERR559480
3034STDY578221913U126494ERR559479
3034STDY578221713U126431ERR559478
3034STDY578221613U127683ERR559477
3034STDY578221213U087424ERR559476
3034STDY578220113U127595ERR559475
3034STDY578220013U127321ERR559474
3034STDY578219213U021019ERR559473
3034STDY578218013U037601ERR559472
3034STDY578217912U743134ERR559471
3034STDY578217712U707807ERR559470
3034STDY578217412U582556ERR559469
3034STDY578217612U707806ERR564539
3034STDY578217512U595325ERR564538
3034STDY578250213U127596ERR564518
3034STDY578250113U127320ERR564517
3034STDY578249813U112391ERR564516
3034STDY578249613U134145ERR564515
3034STDY578249513U134084ERR564514
3034STDY578249313U137158ERR564513
3034STDY578249213U115474ERR564512
3034STDY578248913U104418ERR564511
3034STDY578248613U085332ERR564510
3034STDY578248213U094802ERR564509
3034STDY578248013U094389ERR564508
3034STDY578247413U028023ERR564507
3034STDY578247213U028024ERR564506
3034STDY578246612U004384ERR564505

Influenza sequencing

Sample

Strain

Run Accession

001195_07UnknownERR028218
383_05UnknownERR028222
771270_95UnknownERR028223
745769_95UnknownERR028224
636804_96UnknownERR028225
17788_00UnknownERR028226
17787_00UnknownERR028227
39572_01UnknownERR028228
1131_04UnknownERR028229
33780_06UnknownERR028219
200276_92UnknownERR028220
1093_05UnknownERR028221
645913_96UnknownERR028231
100_07UnknownERR028235
303_09UnknownERR028236
90591_97UnknownERR028237
40280_96UnknownERR028238
661263_97UnknownERR028239
88761_97UnknownERR028240
61605_98UnknownERR028241
60797_00UnknownERR028242
43142_01UnknownERR028232
40564_02UnknownERR028233
71251_05UnknownERR028234
3_00UnknownERR045794
68327_98UnknownERR045795
57610_99UnknownERR045796
35320_99UnknownERR045797
254_02UnknownERR045798
010402_03UnknownERR045799
612_06UnknownERR045800
117316_86UnknownERR045801
79851_90UnknownERR045802
114065_90UnknownERR045803
2112_95UnknownERR045804
2111_95UnknownERR045805
177_02UnknownERR045806
279053_93UnknownERR045807
410711_94UnknownERR045808
0214_06UnknownERR045809
002295_02UnknownERR045810
87842_90UnknownERR045811
00003_09UnknownERR045812
375017_93UnknownERR045813
H02AS8_02UnknownERR045814
195852_92UnknownERR045815
252411_92UnknownERR045816
283902_93UnknownERR045817
167655_97UnknownERR045830
203759_92UnknownERR045831
163266_87UnknownERR045832
2899_82UnknownERR045833
425742_94UnknownERR045834
26029_98UnknownERR045835
101692_97UnknownERR045836
193667_98UnknownERR045837
448813_94UnknownERR045838
_1_02UnknownERR045839
53307_00UnknownERR045840
P185_08UnknownERR045841
89_96UnknownERR045818
1513-1_98UnknownERR045819
004772_01UnknownERR045820
145_99UnknownERR045821
285393_93UnknownERR045822
425069_94UnknownERR045823
704563_95UnknownERR045824
_7_98UnknownERR045825
790_97UnknownERR045826
ANNE_H5N1_AUnknownERR045827
ANNE_H5N1_BUnknownERR045828
ANNE_H5N1_CUnknownERR045829
1174_09H1N1ERR027058
15360-3_01H1N1ERR027062
1624_02H1N1ERR027063
800_04H1N1ERR027064
186678-2_05H1N1ERR027065
151672-3_03H1N1ERR027066
272121-1_02H1N1ERR027067
289171_03H1N1ERR027068
159870-2_05H1N1ERR027069
172336_01H1N1ERR027059
1190_02H1N1ERR027060
09_MD0040352RH1N1ERR027061
96_07H1N1ERR027045
483_06H1N1ERR027049
82108_07H1N1ERR027050
112_07H1N1ERR027051
Brno_00H1N1ERR027052
1458_10H1N1ERR027053
1_01H1N1ERR027054
29313_06H1N1ERR027055
132_05H1N1ERR027056
373_10H1N1ERR027046
10_10H1N1ERR027047
1464_10H1N1ERR027048
  • Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans.

    Garten RJ, Davis CT, Russell CA, Shu B, Lindstrom S, Balish A, Sessions WM, Xu X, Skepner E, Deyde V, Okomo-Adhiambo M, Gubareva L, Barnes J, Smith CB, Emery SL, Hillman MJ, Rivailler P, Smagala J, de Graaf M, Burke DF, Fouchier RA, Pappas C, Alpuche-Aranda CM, López-Gatell H, Olivera H, López I, Myers CA, Faix D, Blair PJ, Yu C, Keene KM, Dotson PD, Boxrud D, Sambol AR, Abid SH, St George K, Bannerman T, Moore AL, Stringer DJ, Blevins P, Demmler-Harrison GJ, Ginsberg M, Kriner P, Waterman S, Smole S, Guevara HF, Belongia EA, Clark PA, Beatrice ST, Donis R, Katz J, Finelli L, Bridges CB, Shaw M, Jernigan DB, Uyeki TM, Smith DJ, Klimov AI and Cox NJ

    Science (New York, N.Y.) 2009;325;5937;197-201

  • Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic.

    Smith GJ, Vijaykrishna D, Bahl J, Lycett SJ, Worobey M, Pybus OG, Ma SK, Cheung CL, Raghwani J, Bhatt S, Peiris JS, Guan Y and Rambaut A

    Nature 2009;459;7250;1122-5

  • Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution.

    Ghedin E, Sengamalay NA, Shumway M, Zaborsky J, Feldblyum T, Subbu V, Spiro DJ, Sitz J, Koo H, Bolotov P, Dernovoy D, Tatusova T, Bao Y, St George K, Taylor J, Lipman DJ, Fraser CM, Taubenberger JK and Salzberg SL

    Nature 2005;437;7062;1162-6

Data Use Statement

This sequencing centre plans on publishing the completed and annotated sequences in a peer-reviewed journal as soon as possible. Permission of the principal investigator should be obtained before publishing analyses of the sequence/open reading frames/genes on a chromosome or genome scale. See our data sharing policy.

Sequencing enquiries

Please address all sequencing enquiries to: pathinfo@sanger.ac.uk

* quick link - http://q.sanger.ac.uk/qu979ra6