Sequence and phylogenetic analysis of highly pathogenic avian influenza H5N1 viruses isolated during 2006-2008 outbreaks in Pakistan reveals genetic diversity

Virology Journal

Volumn 9, Issue , 2012, Pages

  Siddique, Naila ^a,b   Naeem, Khalid ^a   Abbas, Muhammad A ^a   Ahmed, Zaheer ^a   Malik, Salman A ^b  

^a NATIONAL AGRICULTURAL RESEARCH CENTRE   (Pakistan)

^b QUAID I AZAM UNIVERSITY   (Pakistan)

Author keywords

[No Author keywords available]

Indexed keywords

AMANTADINE; NONSTRUCTURAL PROTEIN 2; OSELTAMIVIR; ZANAMIVIR;

AFGHANISTAN; ANTIVIRAL SUSCEPTIBILITY; AVIAN INFLUENZA VIRUS; CLADISTICS; GENE IDENTIFICATION; GENE MUTATION; GENETIC LINKAGE; GENETIC VARIABILITY; GLYCOSYLATION; INFLUENZA VIRUS A H5N1; NONHUMAN; NUCLEOTIDE SEQUENCE; PAKISTAN; PHYLOGENY; POINT MUTATION; RECEPTOR BINDING; REVIEW; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; UNINDEXED SEQUENCE; VIRUS ISOLATION;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ANIMALS; DISEASE OUTBREAKS; GENETIC VARIATION; INFLUENZA A VIRUS, H5N1 SUBTYPE; INFLUENZA IN BIRDS; MOLECULAR SEQUENCE DATA; PAKISTAN; PHYLOGENY; POULTRY; SEQUENCE ANALYSIS, DNA; SEQUENCE DELETION; VIRAL PROTEINS;

AVES;

EID: 84870290860     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-9-300     Document Type: Review

References (42)

1. Genesis of a highly pathogenic and potentially pandemic H5N1 influenza virus in eastern Asia. Li KS, Guan Y, Wang J, Smith GJD, Xu KM, Duan L, Rahardjo AP, Puthavathana P, Buranathai C, Nguyen TD, et al. Nature 2004 430 209 213 10.1038/nature02746 15241415 (Pubitemid 38902429)
2. Characterization of a novel influenza A virus hemagglutinin subtype (H16) obtained from black-headed gulls. Fouchier RA, Munster V, Wallensten A, Bestebroer TM, Herfst S, Smith D, Rimmelzwaan GF, Olsen B, Osterhaus AD, J Virol 2005 79 2814 2822 10.1128/JVI.79.5.2814-2822.2005 15709000 (Pubitemid 40270559)
3. Evolution and ecology of influenza A viruses. Webster RG, Bean WJ, Gorman OT, Chambers TM, Kawaoka Y, Microbiol Rev 1992 56 152 179 1579108
4. Reemerging H5N1 influenza viruses in Hong Kong in 2002 are highly pathogenic to ducks. Sturm-Ramirez KM, Ellis T, Bousfield B, Bissett L, Dyrting K, Rehg JE, Poon L, Guan Y, Peiris M, Webster RG, J Virol 2004 78 4892 4901 10.1128/JVI.78.9.4892-4901.2004 15078970 (Pubitemid 38501109)
5. International Visitors: Birds Come Flying In http://www. wildlifeofpakistan.com/PakistanBirdClub/birdcomeflyingin.html
6. An outbreak of avian influenza in poultry in Pakistan. Naeem K, Hussain M, Vet Rec 1995 137 439 10.1136/vr.137.17.439 8560706
7. Avian influenza A subtype H9N2 in poultry in Pakistan. Naeem K, Ullah A, Manvell RJ, Alexander DJ, Vet Rec 1999 145 560 10.1136/vr.145.19.560 10609578 (Pubitemid 29516283)
8. Use of strategic vaccination for the control of avian influenza in Pakistan. Naeem K, Siddique N, Dev Biol (Basel) 2006 124 145 150 (Pubitemid 43258911)
9. Avian influenza in Pakistan: outbreaks of low- and high-pathogenicity avian influenza in Pakistan during 2003-2006. Naeem K, Siddique N, Ayaz M, Jalalee MA, Avian Dis 2007 51 189 193 10.1637/7617-042506R.1 17494552 (Pubitemid 46671278)
10. Role of Wild Birds in the Spread of Highly Pathogenic Avian Influenza Virus H5N1 and Implications for Global Surveillance. Feare CJ, Avian Dis 2010 54 201 212 10.1637/8766-033109-ResNote.1 20521633
11. Characterization of H5N1 highly pathogenic avian influenza viruses isolated from poultry in Pakistan 2006-2008. Wasilenko J, Pantin-Jackwood M, Khan T, Ahmed A, Rehmani S, Lone N, Swayne D, Spackman E, Virus Genes 2012 44 247 252 10.1007/s11262-011-0689-2 22083300
12. Novel genotypes of H9N2 influenza A viruses isolated from poultry in Pakistan containing NS genes similar to highly pathogenic H7N3 and H5N1 viruses. Iqbal M, Yaqub T, Reddy K, McCauley JW, PLoS One 2009 4 5788 10.1371/journal.pone.0005788 19517011
13. Genome analysis linking recent European and African influenza (H5N1) viruses. Salzberg SL, Kingsford C, Cattoli G, Spiro DJ, Janies DA, Aly MM, Brown IH, Couacy-Hymann E, De Mia GM, Dung DH, et al. Emerg Infect Dis 2007 13 713 718 10.3201/eid1305.070013 17553249 (Pubitemid 46705305)
14. Toward a unified nomenclature system for highly pathogenic avian influenza virus (H5N1). WHO/OIE/FAO, Emerg Infect Dis 2008 14 1 19046502
15. Structural differences among hemagglutinins of influenza A virus subtypes are reflected in their antigenic architecture: analysis of H9 escape mutants. Kaverin NV, Rudneva IA, Ilyushina NA, Lipatov AS, Krauss S, Webster RG, J Virol 2004 78 240 249 10.1128/JVI.78.1.240-249.2004 14671105 (Pubitemid 37549736)
16. Alexander DJ, Highly Pathogenic Avian Influenza (Fowl Plague) Paris: Office International des Epizooties 3 1996
17. Virulence-associated sequence duplication at the hemagglutinin cleavage site of avian influenza viruses. Perdue ML, Garcia M, Senne D, Fraire M, Virus Res 1997 49 173 186 10.1016/S0168-1702(97)01468-8 9213392 (Pubitemid 27252786)
18. The surface glycoproteins of H5 influenza viruses isolated from humans, chickens, and wild aquatic birds have distinguishable properties. Matrosovich M, Zhou N, Kawaoka Y, Webster R, J Virol 1999 73 1146 1155 9882316 (Pubitemid 29036766)
19. Evolution and adaptation of H5N1 influenza virus in avian and human hosts in Indonesia and Vietnam. Smith GJD, Naipospos TSP, Nguyen TD, de Jong MD, Vijaykrishna D, Usman TB, Hassan SS, Nguyen TV, Dao TV, Bui NA, et al. Virology 2006 350 258 268 10.1016/j.virol.2006.03.048 16713612 (Pubitemid 44218982)
20. Human and avian influenza viruses target different cell types in cultures of human airway epithelium. Matrosovich MN, Matrosovich TY, Gray T, Roberts NA, Klenk HD, Proc Natl Acad Sci U S A 2004 101 4620 4624 10.1073/pnas.0308001101 15070767 (Pubitemid 38437460)
21. Avian influenza-situation in Pakistan-update http://www.who.int/csr/don/ 2007-12-27/en/index.html 23288516
22. Cumulative number of confirmed human cases for avian influenza A(H5N1) reported to WHO, 2003-2011 http://www.who.int/influenza/human-animal-interface/ EN-GIP-LatestCumulativeNumberH5N1cases.pdf
23. Structure and receptor specificity of the hemagglutinin from an H5N1 influenza virus. Stevens J, Blixt O, Tumpey TM, Taubenberger JK, Paulson JC, Wilson IA, Science 2006 312 404 410 10.1126/science.1124513 16543414
24. Evolution of H5N1 avian influenza viruses in Asia. WHO, Emerg Infect Dis 2005 11 1515 1521 16318689
25. Structural identification of the antibody-binding sites of Hong Kong influenza haemagglutinin and their involvement in antigenic variation. Wiley DC, Wilson IA, Skehel JJ, Nature 1981 289 373 378 10.1038/289373a0 6162101 (Pubitemid 11135143)
26. The antigenic structure of the influenza virus A/PR/8/34 hemagglutinin (H1 subtype). Caton AJ, Brownlee GG, Yewdell JW, Gerhard W, Cell 1982 31 417 427 10.1016/0092-8674(82)90135-0 6186384 (Pubitemid 13178866)
27. Molecular aspects of avian influenza (H5N1) viruses isolated from humans. Subbarao K, Shaw MW, Rev Med Virol 2000 10 337 348 10.1002/1099-1654(200009/10) 10:5<337::AID-RMV292>3.0.CO;2-V 11015744
28. Characterization of the surface proteins of influenza A (H5N1) viruses isolated from humans in 1997-1998. Bender C, Hall H, Huang J, Klimov A, Cox N, Hay A, Gregory V, Cameron K, Lim W, Subbarao K, Virology 1999 254 115 123 10.1006/viro.1998.9529 9927579 (Pubitemid 29391719)
29. Establishment of multiple sublineages of H5N1 influenza virus in Asia: implications for pandemic control. Chen H, Smith GJ, Li KS, Wang J, Fan XH, Rayner JM, Vijaykrishna D, Zhang JX, Zhang LJ, Guo CT, et al. Proc Natl Acad Sci U S A 2006 103 2845 2850 10.1073/pnas.0511120103 16473931
30. Changes in the haemagglutinin and the neuraminidase genes prior to the emergence of highly pathogenic H7N1 avian influenza viruses in Italy. Banks J, Speidel ES, Moore E, Plowright L, Piccirillo A, Capua I, Cordioli P, Fioretti A, Alexander DJ, Arch Virol 2001 146 963 973 10.1007/s007050170128 11448033 (Pubitemid 32477408)
31. Generation and characterization of recombinant influenza A (H1N1) viruses harboring amantadine resistance mutations. Abed Y, Goyette N, Boivin G, Antimicrob Agents Chemother 2005 49 556 559 10.1128/AAC.49.2.556-559.2005 15673732 (Pubitemid 40175661)
32. A single amino acid in the PB2 gene of influenza A virus is a determinant of host range. Subbarao EK, London W, Murphy BR, J Virol 1993 67 1761 1764 8445709 (Pubitemid 23088345)
33. Lethal H5N1 influenza viruses escape host anti-viral cytokine responses. Seo SH, Hoffmann E, Webster RG, Nat Med 2002 8 950 954 10.1038/nm757 12195436 (Pubitemid 35033698)
34. PDZ domains: fundamental building blocks in the organization of protein complexes at the plasma membrane. Fanning AS, Anderson JM, J Clin Invest 1999 103 767 772 10.1172/JCI6509 10079096 (Pubitemid 29152621)
35. Persistent host markers in pandemic and H5N1 influenza viruses. Finkelstein DB, Mukatira S, Mehta PK, Obenauer JC, Su X, Webster RG, Naeve CW, J Virol 2007 81 10292 10299 10.1128/JVI.00921-07 17652405 (Pubitemid 47463304)
36. Molecular changes associated with the transmission of avian influenza a H5N1 and H9N2 viruses to humans. Shaw M, Cooper L, Xu X, Thompson W, Krauss S, Guan Y, Zhou N, Klimov A, Cox N, Webster R, et al. J Med Virol 2002 66 107 114 10.1002/jmv.2118 11748666 (Pubitemid 34183725)
37. Virus Propagation in Embryonating Eggs. Senne DA, A laboratory manual for the isolation and identification of avian pathogens Kennett Square, PA: American Association of Avian Pathologists, Swayne DE, Gilsson JR, Jackwood MW, Pearson JE, Reed WM, 4 1998 235 240
38. Highly Pathogenic Avian Influenza. OIE, Manual of Diagnostic Tests and Vaccines for Terrestrial Animals (Mammals, Birds and Bees). Volume 1 Paris: Office International des Epizooties 4 2004 258 269
39. Hemagglutination-inhibition test for avian influenza virus subtype identification and the detection and quantitation of serum antibodies to the avian influenza virus. Pedersen JC, Methods Mol Biol 2008 436 53 66 18370041
40. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Tamura K, Dudley J, Nei M, Kumar S, Mol Biol Evol 2007 24 1596 1599 10.1093/molbev/msm092 17488738 (Pubitemid 47236692)
41. Using CLUSTAL for multiple sequence alignments. Higgins DG, Thompson JD, Gibson TJ, Methods Enzymol 1996 266 383 402 8743695 (Pubitemid 26165878)
42. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Kumar S, Tamura K, Nei M, Brief Bioinform 2004 5 150 163 10.1093/bib/5.2.150 15260895