Neuraminidase subtyping of avian influenza viruses with PrimerHunter-designed primers and quadruplicate primer pools

PLoS ONE

Volumn 8, Issue 11, 2013, Pages

  Huang, Yanyan ^a,b   Khan, Mazhar ^a   Mǎndoiu, Ion I ^c  

^a UNIVERSITY OF CONNECTICUT   (United States)

^b MEMORIAL UNIVERSITY OF NEWFOUNDLAND   (Canada)

^c University of Connecticut   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SIALIDASE; VIRUS RNA;

ARTICLE; AVIAN INFECTIOUS BRONCHITIS VIRUS; AVIAN INFLUENZA VIRUS; GENE AMPLIFICATION; GENETIC ANALYSIS; GENETIC VARIABILITY; INFECTIOUS BURSAL DISEASE VIRUS; NEURAMINIDASE GENE; NEWCASTLE DISEASE PARAMYXOVIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; SENSITIVITY AND SPECIFICITY; VIRUS CULTURE; VIRUS DETECTION; VIRUS GENE;

ANIMALS; BASE SEQUENCE; BIRDS; DNA PRIMERS; INFLUENZA IN BIRDS; MOLECULAR SEQUENCE DATA; NEURAMINIDASE; REAL-TIME POLYMERASE CHAIN REACTION;

EID: 84896691284     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0081842     Document Type: Article

References (27)

1. Webster RG, Bean WJ, Gorman OT, Chambers TM, Kawaoka Y (1992) Evolution and ecology of influenza A viruses. Microbiol Rev 56: 152-179. PubMed: 1579108.
2. Krauss S, Walker D, Pryor SP, Niles L, Chenghong L et al. (2004) Influenza A viruses of migrating wild aquatic birds in North America. Vector Borne Zoonotic Dis 4: 177-189. doi:10.1089/vbz.2004.4.177. PubMed: 15631061. (Pubitemid 39429943)
3. Salomon R, Webster RG (2009) The influenza virus enigma. Cell 136: 402-410. doi:10.1016/j.cell.2009.01.029. PubMed: 19203576.
4. Obenauer JC, Denson J, Mehta PK, Su X, Mukatira S et al. (2006) Large-scale sequence analysis of avian influenza isolates. Science 311: 1576-1580. doi:10.1126/science.1121586. PubMed: 16439620.
5. Subbarao K, Klimov A, Katz J, Regnery H, Lim W et al. (1998) Characterization of an avian influenza A (H5N1) virus isolated from a child with a fatal respiratory illness. Science 279: 393-396. doi:10.1126/science.279. 5349.393. PubMed: 9430591. (Pubitemid 28063376)
6. Kilbourne ED (2006) Influenza pandemics of the 20th century. Emerg Infect Dis 12: 9-14. doi:10.3201/eid1201.051254. PubMed: 16494710.
7. Cardona CJ, Xing Z, Sandrock CE, Davis CE (2009) Avian influenza in birds and mammals. Comp Immunol Microbiol Infect Dis 32: 255-273. doi:10.1016/j.cimid.2008.01.001. PubMed: 18485480.
8. Brown IH, Harris PA, McCauley JW, Alexander DJ (1998) Multiple genetic reassortment of avian and human influenza A viruses in European pigs, resulting in the emergence of an H1N2 virus of novel genotype. J Gen Virol 79: 2947-2955. PubMed: 9880008. (Pubitemid 29002329)
9. Parmley J, Lair S, Leighton FA (2009) Canada's inter-agency wild bird influenza survey. Integr Zool 4: 409-417. doi:10.1111/j.1749-4877.2009.00177.x. PubMed: 21392313.
10. Olsen B, Munster VJ, Wallensten A, Waldenström J, Osterhaus ADME et al. (2006) Global patterns of influenza A virus in wild birds. Science 312: 384-388. doi:10.1126/science.1122438. PubMed: 16627734.
11. Spackman E, Senne DA, Myers TJ, Bulaga LL, Garber LP et al. (2002) Development of a real-time reverse transcriptase PCR assay for type A influenza virus and the avian H5 and H7 hemagglutinin subtypes. J Clin Microbiol 40: 3256-3260. doi:10.1128/JCM.40.9.3256-3260.2002. PubMed: 12202562. (Pubitemid 34977437)
12. Huang Y, Hu B, Wen X, Cao S, Gavrilov BK et al. (2010) Diversified reassortant H9N2 avian influenza viruses in chicken flocks in northern and eastern China. Virus Res 151: 26-32. doi:10.1016/j.virusres.2010.03.010. PubMed: 20347894.
13. Pedersen JC (2008) Neuraminidase-inhibition assay for the identification of influenza A virus neuraminidase subtype or neuraminidase antibody specificity. Methods Mol Biol 436: 67-75. PubMed: 18370042.
14. Suarez DL, Das A, Ellis E (2007) Review of rapid molecular diagnostic tools for avian influenza virus. Avian Dis 51: 201-208. doi: 10.1637/7732-101006-REGR.1. PubMed: 17494554. (Pubitemid 46671280)
15. Ong WT, Omar AR, Ideris A, Hassan SS (2007) Development of a multiplex real-time PCR assay using SYBR Green 1 chemistry for simultaneous detection and subtyping of H9N2 influenza virus type A. J Virol Methods 144: 57-64. doi:10.1016/j.jviromet.2007.03.019. PubMed: 17512062. (Pubitemid 47096847)
16. Wei HL, Bai GR, Mweene AS, Zhou YC, Cong YL et al. (2006) Rapid detection of avian influenza virus a and subtype H5N1 by single step multiplex reverse transcription-polymerase chain reaction. Virus Genes 32: 261-267. doi:10.1007/s11262-005-6910-4. PubMed: 16732478. (Pubitemid 43823154)
17. Bao Y, Bolotov P, Dernovoy D, Kiryutin B, Zaslavsky L et al. (2008) The influenza virus resource at the National Center for Biotechnology Information. J Virol 82: 596-601. doi:10.1128/JVI.02005-07. PubMed: 17942553.
18. Alvarez AC, Brunck ME, Boyd V, Lai R, Virtue E et al. (2008) A broad spectrum, one-step reverse-transcription PCR amplification of the neuraminidase gene from multiple subtypes of influenza A virus. Virol J 5: 77. doi:10.1186/1743-422X-5-77. PubMed: 18613963.
19. Gall A, Hoffmann B, Harder T, Grund C, Ehricht R et al. (2009) Rapid and highly sensitive neuraminidase subtyping of avian influenza viruses by use of a diagnostic DNA microarray. J Clin Microbiol 47: 2985-2988. doi:10.1128/JCM. 00850-09. PubMed: 19587298.
20. Qiu BF, Liu WJ, Peng DX, Hu SL, Tang YH et al. (2009) A reverse transcription-PCR for subtyping of the neuraminidase of avian influenza viruses. J Virol Methods 155: 193-198. doi:10.1016/j.jviromet.2008.10.001. PubMed: 18984006.
21. Fereidouni SR, Starick E, Grund C, Globig A, Mettenleiter TC et al. (2009) Rapid molecular subtyping by reverse transcription polymerase chain reaction of the neuraminidase gene of avian influenza A viruses. Vet Microbiol 135: 253-260. doi:10.1016/j.vetmic.2008.09.077. PubMed: 19028027.
22. Tsukamoto K, Ashizawa T, Nakanishi K, Kaji N, Suzuki K et al. (2009) Use of reverse transcriptase PCR to subtype N1 to N9 neuraminidase genes of avian influenza viruses. J Clin Microbiol 47: 2301-2303. doi: 10.1128/JCM.02366-08. PubMed: 19403772.
23. Tsukamoto K, Javier PC, Shishido M, Noguchi D, Pearce J et al. (2012) 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 50: 37-45. doi:10.1128/JCM.01195-11. PubMed: 22031706.
24. Duitama J, Kumar DM, Hemphill E, Khan M, Mandoiu II et al. (2009) PrimerHunter: a primer design tool for PCR-based virus subtype identification. Nucleic Acids Res 37: 2483-2492. doi:10.1093/nar/gkp073. PubMed: 19264805.
25. Rash S, Gusfield D (2002) String barcoding: Uncovering optimal virus signatures. Proceedings of the Sixth Annual International Conference on Computational Biology. pp. 254-261.
26. Ewens WJ, Grant GR (2006.) Statistical Methods in Bioinformatics: An Introduction (2nd edition). Springer Verlag. 0387400822: 0387400822.
27. Pryor RJ, Wittwer CT (2006) Real-time polymerase chain reaction and melting curve analysis. Methods Mol Biol 336: 19-32. PubMed: 16916250.