A simple method for the parallel deep sequencing of full influenza A genomes

Journal of Virological Methods

Volumn 178, Issue 1-2, 2011, Pages 243-248

  Kampmann, Marie Louise ^a,b   Fordyce, Sarah L ^a,b   Ávila Arcos, María C ^a   Rasmussen, Morten ^a   Willerslev, Eske ^a   Nielsen, Lars P ^b   Gilbert, M Thomas P ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b STATENS SERUM INSTITUT   (Denmark)

Author keywords

Full genome sequencing; High throughput sequencing; Influenza A

Indexed keywords

VIRUS RNA;

ANIMAL CELL; ARTICLE; CONTROLLED STUDY; DEEP SEQUENCING; GENE AMPLIFICATION; GENE MAPPING; GENE SEQUENCE; GENETIC VARIABILITY; HUMAN; HUMAN CELL; INFLUENZA VIRUS A; INFLUENZA VIRUS A H1N1; INFLUENZA VIRUS A H5N1; MOLECULAR LIBRARY; NONHUMAN; PARALLEL DESIGN; PRIORITY JOURNAL; RNA EXTRACTION; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; VIRUS GENOME; VIRUS STRAIN;

ANIMALS; GENOME, VIRAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INFLUENZA A VIRUS, H1N1 SUBTYPE; INFLUENZA A VIRUS, H5N1 SUBTYPE; RNA, VIRAL;

ANIMALIA; SUIDAE;

EID: 80955148866     PISSN: 01660934     EISSN: 18790984     Source Type: Journal    
DOI: 10.1016/j.jviromet.2011.09.001     Document Type: Article

References (16)

1. Chen H., Cheung C.L., Tai H., Zhao P., Chan J.F., Cheng V.C., Chan K.H., Yuen K.Y. Oseltamivir-resistant influenza A pandemic (H1N1) 2009 virus, Hong Kong, China. Emerg. Infect. Dis. 2009, 15:1970-1972.
2. DePristo M., Banks E., Poplin R., Garimella K., Maguire J., Hartl C., Philippakis A., del Angel G., Rivas M.A., Hanna M., McKenna A., Fennell T., Kernytsky A., Sivachenko A., Cibulskis K., Gabriel S., Altshuler D., Daly M. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 2011, 43:491-498.
3. Domingo E., Baranowski E., Ruiz-Jarabo C.M., Martin-Hernandez A.M., Saiz J.C., Escarmis C. Quasispecies structure and persistence of RNA viruses. Emerg. Infect. Dis. 1998, 4:521-527.
4. Fouchier R.A.M., Munster V., Wallensten A., Bestebroer T.M., Herfst S., Smith D., Rimmelzwaan G.F., Olsen B., Osterhaus A.D.M.E. Characterization of a novel influenza A virus hemagglutinin subtype (H16) obtained from black-headed gulls. J. Virol. 2005, 79. 2824-2822.
5. Ghedin E., Sengamalay N.A., Shumway M., Zaborsky J., Feldblyum T., Subbu V., Spiro D.J., Sitz J., Koo H., Bolotov P., Dernovoy D., Tatusova T., Bao Y., St George K., Taylor J., Lipman D.J., Fraser C.M., Taubenberger J.K., Salzberg S.L. Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature 2005, 437:1162-1166.
6. Hoffmann E., Stech J., Guan Y., Webster R.G., Perez D.R. Universal primer set for the full-length amplification of all influenza A viruses. Arch. Virol. 2001, 146:2275-2289.
7. Höper D., Hoffmann B., Beer M. Simple, sensitive and swift sequencing of complete H5N1 avian influenza virus genomes. J. Clin. Microbiol. 2009, 47:674-679.
8. Kuroda M., Katano H., Nakajima N., Tobiume M., Ainai A., Sekizuka T., Hasegawa H., Tashiro M., Sasaki Y., Arakawa Y., Hata S., Watanabe M., Sata T. Characterization of quasispecies of pandemic 2009 influenza A virus (A/H1N1/2009) by de novo sequencing using a next-generation DNA sequencer. PLoS One 2010, 5:e10256.
9. Li H., Durbin R. Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics 2009, 25:1754-1760.
10. Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. The sequence alignment/map (SAM) format and SAMtools. Bioinformatics 2009, 25:2078-2079. 1000 Genome Project Data Processing Subgroup.
11. McKenna A., Hanna M., Banks E., Sivachenko A., Cibulskis K., Kernytsky A., Garimella K., Altshuler D., Gabriel S., Daly M., DePristo M.A. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010, 20:1297-1303.
12. Neumann G., Kawaoka Y. Generation of influenza A virus from cloned cDNAs-historical perspective and outlook for the new millennium. Rev. Med. Virol. 2002, 12:13-30.
13. Palese P. The genes of influenza virus. Cell 1977, 10:1-10.
14. Wang M.Z., Tai C.Y., Mendel D.B. Mechanism by which mutations at His274 alter sensitivity of influenza A virus N1 neuraminidase to oseltamivir carboxylate and zanamivir. Antimicrob. Agents Chemother. 2002, 46:3809-3816.
15. World Health Organization A revision of the system of nomenclature for influenza viruses: a WHO Memorandum. Bull. World Health Organ. 1980, 58:585-591.
16. Zhou B., Donnelly M.E., Scholes D.T., St George K., Hatta M., Kawaoka Y., Wentworth D.E. Single reaction genome amplification accelerates sequencing and vaccine production for classical and swine origin human influenza A viruses. J. Virol. 2009, 83:10309-10313.