Skip to main content
NCBI home page
Virologica Sinica logoLink to Virologica Sinica
. 2011 Dec 10;26(6):376–385. doi: 10.1007/s12250-011-3208-7

RETRACTED ARTICLE: Phylogenetic analysis of the non-structural (NS) gene of influenza a viruses isolated in Kazakhstan in 2002–2009

Andrey Bogoyavlenskiy 1,✉, Vladimir Berezin 1, Alexey Prilipov 2, Ilya Korotetskiy 1, Irina Zaitseva 1, Aydyn Kydyrmanov 1, Kobey Karamedin 1, Nailya Ishmukhametova 1, Saule Asanova 1, Marat Sayatov 1, Kainar Zhumatov 1
PMCID: PMC8222485  PMID: 22160937

Abstract

Although the important role of the non-structural (NS1 and NEP) gene of influenza A in virulence of the virus is well established, our knowledge about the extent of variation in the NS gene pool of influenza A viruses in their natural reservoirs in Kazakhstan is incomplete. 17 influenza A viruses of different subtypes were studied in this paper. Seven types of haemagglutinin and five different neuraminidase subtypes in eight combinations were found among the isolated viruses. A comparison of nucleotide sequences of isolated viruses revealed a substantial number of silent mutations, which results in high degree of homology in amino acid sequences. By phylogenetic analysis it was shown that two distinct gene pools, corresponding to both NS allele A with 5 Clades and B, were present at the same time in Kazakhstan. The degree of variation within the alleles was very low. In our study allele A viruses had a maximum of 5% amino acid divergence in Clade while allele B viruses had only 4% amino acid divergence.

Key words: Influenza, Nonstructural gene, Phylogenetic analysis

Footnotes

Foundation items: USDA-ISTC(The International Science and Technology Center) partner project #K-747p; Institute of Microbiology and Virology project #0103KZO0126 and #0106KZ00581.

An erratum to this article is available at http://dx.doi.org/10.1007/s12250-013-3374-x.

This article has been retracted at the request of the Editor-in-Chief, as it contains large portions of text that have been duplicated from “Phylogenetic analysis of the non-structural (NS) gene of influenza A viruses isolated from mallards in Northern Europe in 2005” published in Virology Journal (2008) 5:147, without sufficient attribution being given to the article. Despite the data / conclusion being original in the paper, this is violating the journal policy.

References

  • 1.Almond J. W. A single gene determines the host range of influenza virus. Nature. 1977;270:617–618. doi: 10.1038/270617a0. [DOI] [PubMed] [Google Scholar]
  • 2.Bao Y. P., Bolotov, Dernovoy D. The Influenza Virus Resource at the National Center for Biotechnology Information. J. Virol. 2008;82(2):596–601. doi: 10.1128/JVI.02005-07. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 3.Chen Z., Li Y., Krug R. M. Influenza A virus NS1 protein targets poly(A)-binding protein II of the cellular 3′-end processing machinery. EMBO J. 1999;18:2273–2283. doi: 10.1093/emboj/18.8.2273. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 4.European Union Council Directive 92/40/EEC of 19 May Community measures for the control of avian influenza. Official Journal L. 1992;167(06):0001–0016. [Google Scholar]
  • 5.Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution. 1985;39:783–791. doi: 10.2307/2408678. [DOI] [PubMed] [Google Scholar]
  • 6.Gagneux P., Cheriyan M., Hurtado-Ziola N.}. Human-specific regulation of alpha 2-6-linked sialic acids. J Biol Chem. 2003;278:48245–48250. doi: 10.1074/jbc.M309813200. [DOI] [PubMed] [Google Scholar]
  • 7.Hale B. G., Randall R. E., Ortın J. The multifunctional NS1 protein of influenza A Viruses. J Gen Virol. 2008;89:2359–2376. doi: 10.1099/vir.0.2008/004606-0. [DOI] [PubMed] [Google Scholar]
  • 8.Hatta M., Gao P., Halfmann P. Molecular basis for high virulence of Hong Kong H5N1 influenza A viruses. Science. 2001;293:1840–1842. doi: 10.1126/science.1062882. [DOI] [PubMed] [Google Scholar]
  • 9.Inglis S. C., Barrett T., Brown C. M. The Smallest Genome RNA Segment of Influenza Virus Contains Two Genes that May Overlap. Proc Natl Acad Sci USA. 1979;76:3790–3794. doi: 10.1073/pnas.76.8.3790. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10.Kochs G., Garcia-Sastre A., Martinez-Sobrido L. Multiple AntiInterferon Actions of the Influenza A Virus NS1 Protein. J Virol. 2007;81:7011–7021. doi: 10.1128/JVI.02581-06. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 11.Kuiken T., Holmes E. C., McCauley J. Host species barriers to influenza virus infections. Science. 2006;312:394–397. doi: 10.1126/science.1122818. [DOI] [PubMed] [Google Scholar]
  • 12.Krug R. M., Yuan W., Noah D. L. Intracellular warfare between human influenza viruses and human cells: the roles of the viral NS1 protein. Virology. 2003;309:181–189. doi: 10.1016/S0042-6822(03)00119-3. [DOI] [PubMed] [Google Scholar]
  • 13.Lamb R. A., Choppin P. W. Segment 8 of the Influenza Virus Genome is Unique in Coding for Two Polypeptides. Proc Natl Acad Sci USA. 1979;76:4908–4912. doi: 10.1073/pnas.76.10.4908. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 14.Lamb R. A., Lai C. J. Sequence of interrupted and uninterrupted mRNAs and cloned DNA coding for the two overlapping nonstructural proteins of influenza virus. Cell. 1980;21:475–485. doi: 10.1016/0092-8674(80)90484-5. [DOI] [PubMed] [Google Scholar]
  • 15.Li Y., Chen Z. Y., Wang W. The 3′-end-processing factor CPSF is required for the splicing of single-intron pre-mRNAs in vivo. RNA. 2001;7:920–931. doi: 10.1017/S1355838201010226. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 16.Li Z., Jiang Y., Jiao P. The NS1 Gene Contributes to the Virulence of H5N1 Avian Influenza Viruses. J Virol. 2006;80:11115–11123. doi: 10.1128/JVI.00993-06. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 17.Li S., Min J. Y., Krug R. M. Binding of the influenza A virus NS1 protein to PKR mediates the inhibition of its activation by either PACT or double-stranded RNA. Virology. 2006;349:13–21. doi: 10.1016/j.virol.2006.01.005. [DOI] [PubMed] [Google Scholar]
  • 18.Ludwig S., Schultz U., Mandler J. Phylogenetic relationship of the nonstructural (NS) genes of influenza A viruses. Virology. 1991;183:566–577. doi: 10.1016/0042-6822(91)90985-K. [DOI] [PubMed] [Google Scholar]
  • 19.Matrosovich M., Tuzikov A., Bovin N. Early alterations of the receptor-binding properties of H1, H2, and H3 avian influenza virus hemagglutinins after their introduction into mammals. J Virol. 2000;74:8502–8512. doi: 10.1128/JVI.74.18.8502-8512.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 20.Mibayashi M., Martinez-Sobrido L., Loo Y. M. Inhibition of Retinoic Acid-Inducible Gene IMediated Induction of Beta Interferon by the NS1 Protein of Influenza A Virus. J Virol. 2007;81:514–524. doi: 10.1128/JVI.01265-06. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 21.Min J. Y., Krug R. M. The primary function of RNA binding by the influenza A virus NS1 protein in infected cells: Inhibiting the 2′-5′ oligo (A) synthetase/RNase L pathway. Proc Natl Acad Sci USA. 2006;103:7100–7105. doi: 10.1073/pnas.0602184103. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 22.Nemeroff M. E., Barabino S. M. L., Li Y. Influenza Virus NS1 Protein Interacts with the Cellular 30 kDa Subunit of CPSF and Inhibits 3′ End Formation of Cellular PremRNAs. Mol Cell. 1998;1:991–1000. doi: 10.1016/S1097-2765(00)80099-4. [DOI] [PubMed] [Google Scholar]
  • 23.Neumann G., Hughes M. T., Yoshihiro K. Influenza A virus NS2 protein mediates vRNP nuclear export through NES-independent interaction with hCRM1. EMBO J. 2000;19:6751–6758. doi: 10.1093/emboj/19.24.6751. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 24.Obenauer J. C., Denson J., Mehta P. K. Large-Scale Sequence Analysis of Avian Influenza Isolates Science. 2006;311:1576–1580. doi: 10.1126/science.1121586. [DOI] [PubMed] [Google Scholar]
  • 25.Palese P., Shaw M. L. Orthomyxoviridae: the viruses and their replication. In: Knipe D. M., Howley P. M., editors. Fields Virology. 5th edn. Philadelphia: Lippincott Williams & Wilkins; 2007. pp. 1647–1689. [Google Scholar]
  • 26.Qian X. Y., Alonso-Caplen F., Krug R. M. Two functional domains of the influenza virus NS1 protein are required for regulation of nuclear export of mRNA. J Virol. 1994;68:2433–2411. doi: 10.1128/jvi.68.4.2433-2441.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 27.Saitou N., Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406–425. doi: 10.1093/oxfordjournals.molbev.a040454. [DOI] [PubMed] [Google Scholar]
  • 28.Shinya K., Ebina M., Yamada S. Avian flu: influenza virus receptors in the human airway. Nature. 2006;440:435–436. doi: 10.1038/440435a. [DOI] [PubMed] [Google Scholar]
  • 29.Spackman E., Slemons R. D., Winker K. Phylogenetic analyses of type A influenza genes in natural reservoir species in North America reveals genetic variation. Virus Res. 2005;114:89–100. doi: 10.1016/j.virusres.2005.05.013. [DOI] [PubMed] [Google Scholar]
  • 30.Suarez D. L., Perdue M. L. Multiple alignment comparison of the non-structural genes of influenza A viruses. Virus Res. 1998;54:59–69. doi: 10.1016/S0168-1702(98)00011-2. [DOI] [PubMed] [Google Scholar]
  • 31.Subbarao E. K., London W., Murphy B. R. A single amino acid in the PB2 gene of influenza A virus is a determinant of host range. J Virol. 1993;67:1761–1764. doi: 10.1128/jvi.67.4.1761-1764.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 32.Talon J., Horvath C. M., Polley R. Activation of interferon regulatory factor 3 is inhibited by the influenza A virus NS1 protein. J Virol. 2000;74:7989–7996. doi: 10.1128/JVI.74.17.7989-7996.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 33.Tamura K., Dudley J., Nei M. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 2007;24:1596–1599. doi: 10.1093/molbev/msm092. [DOI] [PubMed] [Google Scholar]
  • 34.Tamura K., Nei M., Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci USA. 2004;101:11030–11035. doi: 10.1073/pnas.0404206101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 35.Wang W., Riedel K., Lynch P. RNA binding by the novel helical domain of the influenza virus NS1 protein requires its dimer structure and a small number of specific basic amino acids. RNA. 1999;5:195–205. doi: 10.1017/S1355838299981621. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 36.Yao Y., Mingay L. J., McCauley J. W. Sequences in influenza A virus PB2 protein that determine productive infection for an avian influenza virus in mouse and human cell lines. J Virol. 2001;75:5410–5415. doi: 10.1128/JVI.75.11.5410-5415.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 37.Zohari S., Gyarmati P., Ejdersund A. Phylogenetic analysis of the non-structural (NS) gene of influenza A viruses isolated from mallards in Northern Europe in 2005. Virol J. 2008;5:1–13. doi: 10.1186/1743-422X-5-147. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Virologica Sinica are provided here courtesy of Wuhan Institute of Virology, Chinese Academy of Sciences

RESOURCES