Identifying influenza viruses with resequencing microarrays

Emerging Infectious Diseases

Volumn 12, Issue 4, 2006, Pages 638-646

  Wang, Zheng ^a,b   Daum, Luke T ^c   Vora, Gary J ^a   Metzgar, David ^d   Walter, Elizabeth A ^e   Canas, Linda C ^c   Malanoski, Anthony P ^a   Lin, Baochuan ^a   Stenger, David A ^a  

^a NAVAL RESEARCH LABORATORY   (United States)

^b NOVA RESEARCH INC   (United States)

^c Air Force Materiel Command   (United States)

^d NAVAL MEDICAL CENTER SAN DIEGO   (United States)

^e Lackland Air Force Base ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA HYBRIDIZATION; DNA SEQUENCE; GENE AMPLIFICATION; GENE SEQUENCE; GENETIC VARIABILITY; GENOTYPE; INFLUENZA VIRUS; INFLUENZA VIRUS B; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; VIRUS IDENTIFICATION; VIRUS STRAIN;

EID: 33645471454     PISSN: 10806040     EISSN: 10806059     Source Type: Journal    
DOI: 10.3201/eid1204.051441     Document Type: Article

References (30)

1. Cox NJ, Subbarao K. Global epidemiology of influenza: past and present. Annu Rev Med. 2000;51:407-21.
2. Horimoto T, Kawaoka Y. Influenza: lessons from past pandemics, warnings from current incidents. Nat Rev Microbiol. 2005;3:591-600.
3. Webby RJ, Webster RG. Are we ready for pandemic influenza? Science. 2003;302:1519-22.
4. World Health Organization. Cumulative number of confirmed human cases of avian influenza A/(H5N1) reported to WHO (Jan 30, 2006). Geneva: The Organization; 2006.
5. Hacia JG. Resequencing and mutational analysis using oligonucleotide microarrays. Nat Genet. 1999;21:42-7.
6. Warrington JA, Shah NA, Chen X, Janis M, Liu C, Kondapalli S, et al. New developments in high-throughput resequencing and variation detection using high density microarrays. Hum Mutat. 2002;19:402-9.
7. Cutler DJ, Zwick ME, Carrasquillo MM, Yohn CT, Tobin KP, Kashuk C, et al. High-throughput variation detection and genotyping using microarrays. Genome Res. 2001;11:1913-25.
8. Vahey M, Nau ME, Barrick S, Cooley JD, Sawyer R, Sleeker AA, et al. Performance of the Affymetrix GeneChip HIV PRT 440 platform for antiretroviral drug resistance genotyping of human immunodeficiency virus type 1 clades and viral isolates with length polymorphisms. J Clin Microbiol. 1999;37:2533-7.
9. Gingeras TR, Ghandour G, Wang E, Berno A, Small PM, Drobniewski F, et al. Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays. Genome Res. 1998;8:435-48.
10. Wilson KH, Wilson WJ, Radosevich JL, DeSantis TZ, Viswanathan VS, Kuczmarski TA, et al. High-density microarray of small-subunit ribosomal DNA probes. Appl Environ Microbiol. 2002;68:2535-41.
11. Zwick ME, McAfee F, Cutler DJ, Read TD, Ravel J, Bowman GR, et al. Microarray-based resequencing of multiple Bacillus anthracis isolates. Genome Biol. 2005;6:R10.
12. Winzeler EA, Richards DR, Conway AR, Goldstein AL, Kalman S, McCullough MJ, et al. Direct allelic variation scanning of the yeast genome. Science. 1998;281:1194-7.
13. Wang DG, Fan JB, Siao CJ, Breno A, Young P, Sapolsky R, et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science. 1998;280:1077-82.
14. Lin B, Wang Z, Vora GJ, Thornton JA, Schnur JM, Thach DC, et al. Broad spectrum respiratory tract pathogen identification using resequencing DNA microarray. Genome Res. 2006 Feb 15; [Epub ahead of print].
15. Canas LC, Lohman K, Pavlin JA, Endy T, Singh DL, Pandey P, et al. The Department of Defense laboratory-based global influenza surveillance system. Mil Med. 2000;165 (Suppl 2):52-6.
16. Daum LT, Canas LC, Smith CB, Klimov A, Huff W, Barnes W, et al. Genetic and antigenic analysis of the first A/New Caledonia/20/99-like H1N1 influenza isolates reported in the Americas. Emerg Infect Dis. 2002;8:408-12.
17. Daum LT, Shaw MW, Klimov AI, Canas LC, Macias EA, Niemeyer D, et al. Influenza A (H3N2) outbreak, Nepal. Emerg Infect Dis. 2005;11:1186-91.
18. Wang D, Coscoy L, Zylberberg M, Avila PC, Boushey HA, Ganem D, et al. Microarray-based detection and genotyping of viral pathogens. Proc Natl Acad Sci U S A. 2002;99:15687-92.
19. Macken C, Lu H, Goodman J, Boykin L. Options for the control of influenza. In: Osterhaus AD, Cox N, Hampson AW, editors. The value of a database in surveillance and vaccine selection. Amsterdam: Elsevier Science; 2001. p. 103-6.
20. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389-402.
21. Holmes EC, Ghedin E, Miller N, Taylor J, Bao Y, St George K, et al. Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol. 2005;3:e300.
22. Centers for Disease Control and Prevention. 2004-05 U.S. influenza season summary. [cited 2006 Jan 30]. Available from http://www.cdc.gov/flu/weekly/ weeklyarchives2004-2005/04-05summary.htm
23. Wareing MD, Tannock GA. Live attenuated vaccines against influenza: a historical review. Vaccine. 2001;19:3320-30.
24. Ellis JS, Zambon MC. Molecular diagnosis of influenza. Rev Med Virol. 2002;12:375-89.
25. Warsen AE, Krug MJ, LaFrentz S, Stanek DR, Loge FJ, Call DR. Simultaneous discrimination between 15 fish pathogens by using 16S ribosomal DNA PCR and DNA microarrays. Appl Environ Microbiol. 2004;70:4216-21.
26. Roth SB, Jalava J, Ruuskanen O, Ruohola A, Nikkari S. Use of an oligonucleotide array for laboratory diagnosis of bacteria responsible for acute upper respiratory infections. J Clin Microbiol. 2004;42:4268-74.
27. Chizhikov V, Rasooly A, Chumakov K, Levy DD. Microarray analysis of microbial virulence factors. Appl Environ Microbiol. 2001;67:3258-63.
28. Wang Z, Vora GJ, Stenger DA. Detection and genotyping of Entamoeba histolytica, Entamoeba dispar, Giardia lamblia, and Cryptosporidium parvum by oligonucleotide microarray. J Clin Microbiol. 2004;42:3262-71.
29. Ghedin E, Sengamalay NA, Shumway M, Zaborsky J, Feldblyum T, Subbu V, et al. Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature. 2005;437:1162-6.
30. The World Health Organization Global Influenza Program Surveillance Network. Evolution of H5N1 avian influenza viruses in Asia. Emerg Infect Dis. 2005;11:1515-21.