Real-time RT-PCR assay to differentiate clades of H5N1 avian influenza viruses circulating in Vietnam

Journal of Virological Methods

Volumn 193, Issue 2, 2013, Pages 452-458

  Kis, Z ^a,b   Jones, J ^a   Creanga, A ^a   Ferdinand, K ^a   Inui, K ^c   Gerloff, N ^a   Davis, C T ^a   Nguyen, T ^d,e   Donis, R O ^a  

^a CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

^b NATIONAL CENTER FOR EPIDEMIOLOGY   (Hungary)

^c Food and Agriculture Organization   (Viet Nam)

^d VIETNAM NATIONAL UNIVERSITY OF AGRICULTURE   (Viet Nam)

^e National Centre for Veterinary Diagnostics   (Viet Nam)

Author keywords

Clade differentiation; H5N1; Highly pathogenic avian influenza; Real time RT PCR; Vietnam

Indexed keywords

INFLUENZA VIRUS HEMAGGLUTININ;

ARTICLE; AVIAN INFLUENZA VIRUS; CLADISTICS; CONTROLLED STUDY; INFLUENZA VIRUS A H5N1; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; VIET NAM;

CLADE-DIFFERENTIATION; H5N1; HIGHLY PATHOGENIC AVIAN INFLUENZA; REAL-TIME RT-PCR; VIETNAM;

ANIMALS; BIRDS; DNA PRIMERS; HEMAGGLUTININ GLYCOPROTEINS, INFLUENZA VIRUS; HUMANS; INFLUENZA A VIRUS, H5N1 SUBTYPE; INFLUENZA IN BIRDS; INFLUENZA, HUMAN; MOLECULAR EPIDEMIOLOGY; REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; VIETNAM; VIROLOGY;

EID: 84882769700     PISSN: 01660934     EISSN: 18790984     Source Type: Journal    
DOI: 10.1016/j.jviromet.2013.06.023     Document Type: Article

References (28)

1. Abdelwhab El-S.M., Arafa A.S., Erfan A.M., Aly M.M., Hafez H.M. Modified H5 real-time reverse transcriptase-PCR oligonucleotides for detection of divergent avian influenza H5N1 viruses in Egypt. Avian Dis. 2010, 54:1301-1305.
2. Abdelwhab El-S.M., Erfan A.M., Grund C., Ziller M., Arafa A.S., Beer M., Aly M.M., Hafez H.M., Harder T.C. Simultaneous detection and differentiation by multiplex real time RT-PCR of highly pathogenic avian influenza subtype H5N1 classic (clade 2.2.1 proper) and escape mutant (clade 2.2.1 variant) lineages in Egypt. Virol. J. 2010, 7:260-267.
3. Beato M.S., Capua I. Transboundary spread of highly pathogenic avian influenza through poultry commodities and wild birds: a review. Rev. Sci. Technol. 2011, 1:51-61.
4. Buchy P., Fourment M., Mardy S., Sorn S., Holl D., Ly S., Vong S., Enouf V., Peiris J.S.M., Van Der Werf S. Molecular epidemiology of clade 1 influenza A viruses (H5N1), Southern Indochina Peninsula, 2004-2007. Emerg. Infect. Dis. 2009, 15:1641-1644.
5. Davis C.T., Balish A.L., O'Neill E., Nguyen C.V., Cox N.J., Xiyan X., Klimov A., Nguyen T., Donis R.O. Detection and characterization of clade 7 high pathogenicity avian influenza H5N1 viruses in chickens seized at ports of entry and live poultry markets in Vietnam. Avian Dis. 2010, 54(1 Suppl.):307-312.
6. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32:1792-1797.
7. Food and Agriculture Organization Approaches to controlling, preventing and eliminating H5N1 Highly Pathogenic Avian Influenza in endemic countries. Animal Production and Health Paper. No. 171. Rome 2011, (accessed 20.02.13). http://www.fao.org/docrep/014/i2150e/i2150e.pdf.
8. Gao R., Gao Y., Wen L., Shao M., Zou S., Li C., Yang L., Li X., Wang W., Shu Y. Development and implementation of the quality control panel of RT-PCR and real time RT-PCR for avian influenza A (H5N1) surveillance network in mainland China. BMC Infect. Dis. 2011, 11:67-75.
9. Islam M.R., Haque M.E., Giasuddin M., Chowdhury E.H., Samad M.A., Parvin R., Nooruzzaman M., Rahman M.M., Monoura P. New introduction of clade 2.3.2.1 avian influenza virus (H5N1) into Bangladesh. Transbound Emerg. Dis. 2011, 59:460-463.
10. Li X.H., Tian H.D., Heiner M., Li D.M. Global occurrence and spread of highly pathogenic avian influenza virus of the subtype H5N1. Avian Dis. 2011, 55:21-28.
11. Li Y., Shi J., Zhong G., Deng G., Tian G., Ge J., Zeng X., Song J., Zhao D., Liu L., Jiang Y., Guan Y., Bu Z., Chen H. Continued evolution of H5N1 influenza viruses in wild birds, domestic poultry, and humans in China from 2004 to 2009. J. Virol. 2010, 84:8389-8397.
12. L'Vov D.K., Zhchelkanov M., Vlasov N.A., Prilipov A.G., Deriabin P.G., Fediakina I.T., Galkina I.V., Zaberezhnyi A.D. The first break-through of the genotype 2.3.2 of high-virulence influenza A virus A/H5N1, which is new for Russia, in the Far East. Vopr. Virusol. 2008, 53:4-8.
13. Moore C., Telles J.N., Corden S., Gao R.B., Vernet G., Van Aarle P., Shu Y.L. Development and validation of a commercial real-time NASBA assay for the rapid confirmation of influenza A H5N1 virus in clinical samples. J. Virol. Methods 2010, 170:173-176.
14. Nguyen T.D., Nguyen T.V., Vijaykrishna D., Webster R.G., Guan Y., Peiris M.J.S., Smith G.J. Multiple sublineages of influenza A virus (H5N1), Vietnam, 2005-2007. Emerg. Infect. Dis. 2008, 14:632-636.
15. Nguyen T., Rivailler P., Davis C.T., Hoa D.T., Balish A., Dang N.H., Jones J., Vui D.T., Simpson N., Huong N.T., Shu B., Loughlin R., Ferdinand K., Lindstrom S.E., York I.A., Klimov A.I., Donis R.O. Evolution of highly pathogenic avian influenza (H5N1) virus populations in Vietnam between 2007 and 2010. Virology 2012, 432:405-416.
16. Sakoda Y., Sugar S., Batchluun D., Erdene-Ochir T., Okamatsu M. Characterization of H5N1 highly pathogenic avian influenza virus strains isolated from migratory waterfowl in Mongolia on the way back from the southern Asia to their northern territory. Virology 2010, 406:88-94.
17. Takakuwa H., Yamashiro T., Le M.Q., Phuong L.S., Ozaki H., Tsunekuni R., Usui T., Ito H., Morimatsu M., Tomioka Y., Yamaguchi T., Ito T., Murase T., Ono E., Otsuki K. Molecular epidemiology of avian influenza viruses circulating among healthy poultry flocks in farms in northern Vietnam. Prev. Vet. Med. 2012, 103:192-200.
18. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 28:2731-2739.
19. Tan T., Pawestri H.P., My N.N., Minh H.M., Syahrial H., Vu T.N., van Doorn H.R., Wertheim H.F., Van Vinh C.N., Quang H.D., Farrar J.J., Tinh H.T., Sedyaningsih E.R., de Jong M.D. A real-time RT-PCR for detection of clade 1 and 2 H5N1 Influenza A virus using Locked Nucleic Acid (LNA) TaqMan probes. Virol. J. 2010, 7:46-51.
20. Tsukamoto K., Javier P.C., Shishido M., Noguchi D., Pearce J., Kang H.M., Jeong O.M., Lee Y.J., Nakanishi K., Ashizawa T. SYBR green-based real-time reverse transcription-PCR for typing and subtyping of all hemagglutinin and neuraminidase genes of avian influenza viruses and comparison to standard serological subtyping tests. J. Clin. Microbiol. 2012, 50:37-45.
21. Wan X.F., Dong L., Lan Y., Long L.P., Xu C., Zou S., Li Z., Wen L., Cai Z., Wang W., Li X., Yuan F., Sui H., Zhang Y., Dong J., Sun S., Gao Y., Wang M., Bai T., Yang L., Li D., Yang W., Yu H., Wang S., Feng Z., Wang Y., Guo Y., Webby R.J., Shu Y. Indications that live poultry markets are a major source of human H5N1 influenza virus infection in China. J. Virol. 2011, 85:13432-13438.
22. Wan X.F., Nguyen T., Davis C.T., Smith C.B., Zhao Z.M., Carrel M., Inui K., Do H.T., Mai D.T., Jadhao S., Balish A., Shu B., Luo F., Emch M., Matsuoka Y., Lindstrom S.E., Cox N.J., Nguyen C.V., Klimov A., Donis R.O. Evolution of highly pathogenic H5N1 avian influenza viruses in Vietnam between 2001 and 2007. PLoS ONE 2008, 3:e3462.
23. Wibawa H., Henning J., Wong F., Selleck P., Junaidi A., Bingham J., Daniels P., Meers J. A molecular and antigenic survey of H5N1 highly pathogenic avian influenzavirus isolates from small holder duck farms in Central Java, Indonesia during 2007-2008. Virol. J. 2011, 8:425-429.
24. World Health Organization, 2012. Cumulative number of confirmed human cases of avian influenza A(H5N1) reported to WHO. (accessed 31.12.12). http://www.who.int/influenza/human_animal_interface/en/.
25. World Health Organization, 2012. Antigenic and genetic characteristics of zoonotic influenza viruses and development of candidate vaccine viruses for pandemic preparedness. (accessed 20.02.12). http://www.who.int/influenza/vaccines/virus/201209_h5h7h9_vaccinevirusupdate.pdf.
26. WHO/OIE/FAO H5N1 Evolution Working Group Toward a unified nomenclature system for highly pathogenic avian influenza virus (H5N1). Emerg. Infect. Dis. 2008, 14(7):e1. 10.3201/eid1407.071681.
27. WHO/OIE/FAO H5N1 Evolution Working Group Continuing progress towards a unified nomenclature for the highly pathogenic H5N1 avian influenza viruses: divergence of clade 2.2 viruses. Influenza Other Respir. Viruses 2009, 3:59-62.
28. WHO/OIE/FAO H5N1 Evolution Working Group Continued evolution of highly pathogenic avian influenza A(H5N1): updated nomenclature. Influenza Other Respir. Viruses 2012, 6:1-5.