1887

Abstract

To genetically explore the fusion protein gene () in human parainfluenza virus type 1 (HPIV1) and type 3 (HPIV3) strains, we analysed them in patients with acute respiratory infections in Eastern Japan from 2011 to 2015.

We constructed phylogenetic trees based on the HPIV and HPIV3 gene using the maximum likelihood method and conducted -distance and selective pressure analyses. We also predicted the linear epitopes of the protein in the prototype strains. Furthermore, we mapped the amino acid substitutions of the proteins.

Nineteen strains of HPIV1 and 53 strains of HPIV3 were detected among the clinical acute respiratory infection cases. The phylogenetic trees indicated that the HPIV1 and HPIV3 strains were classified into clusters II and III and cluster C, respectively. The -distance values of the HPIV1 and HPIV3 genes were <0.03. Two positive selection sites were inferred in the HPIV1 (aa 8 and aa 10), and one positive selection site was inferred in the HPIV3 (aa 108), but over 10 negative selection sites were inferred. Four epitopes were predicted for the HPIV1 prototype strains, while five epitopes were predicted for the HPIV3 prototype strain. A positive selection site (aa 108) or the HPIV3 F protein was involved in the predicted epitope. Additionally, we found that an amino acid substitution (R73K) in the LC76627 HPIV3 strain presumably may affect the resistance to neutralization by antibodies.

The gene of HPIV1 and HPIV3 was relatively well conserved in the eastern part of Japan during the investigation period.

Keyword(s): F genes , HPIV1 and HPIV3
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2017-02-01
2020-01-27
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References

  1. Karron RA, Collins PL. Parainfluenza viruses. In Knipe DM, Howley PM. (editors) Fields Virology, 5th ed. Philadelphia: Lippincott Williams & Wilkins; 2007; pp1497–1526
    [Google Scholar]
  2. Parrott RH, Vargosko A, Luckey A, Kim HW, Cumming C et al. Clinical features of infection with hemadsorption viruses. N Engl J Med 1959;260:731–738 [CrossRef][PubMed]
    [Google Scholar]
  3. Parrott RH, Vargosko AJ, Kimhw Bell JA, Chanock RM. Acute respiratory diseases of viral etiology. III. parainfluenza. Myxoviruses. Am J Public Health Nations Health 1962;52:907–917[PubMed][CrossRef]
    [Google Scholar]
  4. Griffin MR, Walker FJ, Iwane MK, Weinberg GA, Staat MA et al. Epidemiology of respiratory infections in young children: insights from the new vaccine surveillance network. Pediatr Infect Dis J 2004;23:S188–S192[PubMed][CrossRef]
    [Google Scholar]
  5. Kusel MM, de Klerk NH, Kebadze T, Vohma V, Holt PG et al. Early-life respiratory viral infections, atopic sensitization, and risk of subsequent development of persistent asthma. J Allergy Clin Immunol 2007;119:1105–1110 [CrossRef][PubMed]
    [Google Scholar]
  6. Palese P, Shaw ML. Orthomyxoviridae. In Knipe DM, Howley PM. (editors) Fields Virology, 5th ed. Philadelphia: Lippincott Williams & Wilkins; 2007; pp.1647–1689
    [Google Scholar]
  7. Collins PL, Crowe JE. Respiratory syncytial virus and metapneumovirus. In Knipe DM, Howley PM. (editors) Fields Virology, 5th ed. Philadelphia: Lippincott Williams & Wilkins; 2007; pp1601–1646
    [Google Scholar]
  8. Lamb RA, Park GD. Paramyxoviridae: the viruses and their replication. In Knipe DM, Howley PM. (editors) Fields Virology, 5th ed. Philadelphia: Lippincott Williams & Wilkins; 2007; pp1449–1496
    [Google Scholar]
  9. Henrickson KJ. Parainfluenza viruses. Clin Microbiol Rev 2003;16:242–264 [CrossRef][PubMed]
    [Google Scholar]
  10. Ito M, Nishio M, Komada H, Ito Y, Tsurudome M. An amino acid in the heptad repeat 1 domain is important for the haemagglutinin-neuraminidase-independent fusing activity of simian virus 5 fusion protein. J Gen Virol 2000;81:719–727 [CrossRef][PubMed]
    [Google Scholar]
  11. Russell CJ, Jardetzky TS, Lamb RA. Conserved glycine residues in the fusion peptide of the paramyxovirus fusion protein regulate activation of the native state. J Virol 2004;78:13727–13742 [CrossRef][PubMed]
    [Google Scholar]
  12. Sergel TA, Mcginnes LW, Morrison TG. A single amino acid change in the Newcastle disease virus fusion protein alters the requirement for HN protein in fusion. J Virol 2000;74:5101–5107 [CrossRef][PubMed]
    [Google Scholar]
  13. Seth S, Vincent A, Compans RW. Mutations in the cytoplasmic domain of a paramyxovirus fusion glycoprotein rescue syncytium formation and eliminate the hemagglutinin-neuraminidase protein requirement for membrane fusion. J Virol 2003;77:167–178 [CrossRef][PubMed]
    [Google Scholar]
  14. Griffin DE. Measles viruses. In Knipe DM, Howley PM. (editors) Fields Virology, 5th ed. Philadelphia: Lippincott Williams & Wilkin; 2007; pp1551–1585
    [Google Scholar]
  15. Carbone KM, Rubin S. Mumps viruses. In Knipe DM, Howley PM. (editors) Fields Virology, 5th ed. Philadelphia: Lippincott Williams & Wilkins; 2007; pp1527–1550
    [Google Scholar]
  16. Mizuta K, Saitoh M, Kobayashi M, Tsukagoshi H, Aoki Y et al. Detailed genetic analysis of hemagglutinin-neuraminidase glycoprotein gene in human parainfluenza virus type 1 isolates from patients with acute respiratory infection between 2002 and 2009 in Yamagata prefecture, Japan. Virol J 2011;8:533 [CrossRef][PubMed]
    [Google Scholar]
  17. Beck ET, He J, Nelson MI, Bose ME, Fan J et al. Genome sequencing and phylogenetic analysis of 39 human parainfluenza virus type 1 strains isolated from 1997-2010. PLoS One 2012;7:e46048 [CrossRef][PubMed]
    [Google Scholar]
  18. Košutić-Gulija T, Slovic A, Ljubin-Sternak S, Mlinarić-Galinović G, Forčić D. A study of genetic variability of human parainfluenza virus type 1 in Croatia, 2011-2014. J Med Microbiol 2016;65:793–803 [CrossRef][PubMed]
    [Google Scholar]
  19. Prinoski K, Côté MJ, Kang CY, Dimock K. Evolution of the fusion protein gene of human parainfluenza virus 3. Virus Res 1992;22:55–69 [CrossRef][PubMed]
    [Google Scholar]
  20. Almajhdi FN. Hemagglutinin-neuraminidase gene sequence- based reclassification of human parainfluenza virus 3 variants. Intervirology 2015;58:35–40 [CrossRef][PubMed]
    [Google Scholar]
  21. Godoy C, Peremiquel-Trillas P, Andrés C, Gimferrer L, Uriona SM et al. A molecular epidemiological study of human parainfluenza virus type 3 at a tertiary university hospital during 2013-2015 in Catalonia, Spain. Diagn Microbiol Infect Dis 2016;86:153–159 [CrossRef][PubMed]
    [Google Scholar]
  22. Roth JP, Li JK, Smee DF, Morrey JD, Barnard DL. A recombinant infectious human parainfluenza virus type 3 expressing the enhanced green fluorescent protein for use in high-throughput antiviral assays. Antiviral Res 2009;82:12–21 [CrossRef][PubMed]
    [Google Scholar]
  23. Yang HT, Jiang Q, Zhou X, Bai MQ, Si HL et al. Identification of a natural human serotype 3 parainfluenza virus. Virol J 2011;8:58 [CrossRef][PubMed]
    [Google Scholar]
  24. Mizuta K, Tsukagoshi H, Ikeda T, Aoki Y, Abiko C et al. Molecular evolution of the haemagglutinin-neuraminidase gene in human parainfluenza virus type 3 isolates from children with acute respiratory illness in Yamagata prefecture, Japan. J Med Microbiol 2014;63:570–577 [CrossRef][PubMed]
    [Google Scholar]
  25. van Wyke Coelingh KL, Winter CC, Murphy BR. Nucleotide and deduced amino acid sequence of hemagglutinin-neuraminidase genes of human type 3 parainfluenza viruses isolated from 1957 to 1983. Virology 1988;162:137–143 [CrossRef][PubMed]
    [Google Scholar]
  26. Bellau-Pujol S, Vabret A, Legrand L, Dina J, Gouarin S et al. Development of three multiplex RT-PCR assays for the detection of 12 respiratory RNA viruses. J Virol Methods 2005;126:53–63 [CrossRef][PubMed]
    [Google Scholar]
  27. Itagaki T, Abiko C, Ikeda T, Aoki Y, Seto J et al. Sequence and phylogenetic analyses of Saffold cardiovirus from children with exudative tonsillitis in Yamagata, Japan. Scand J Infect Dis 2010;42:950–952 [CrossRef][PubMed]
    [Google Scholar]
  28. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013;30:2725–2729 [CrossRef][PubMed]
    [Google Scholar]
  29. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980;16:111–120[PubMed][CrossRef]
    [Google Scholar]
  30. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425[PubMed]
    [Google Scholar]
  31. Tanabe AS. Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional and separate models for combined molecular phylogenetic analyses of multilocus sequence data. Mol Ecol Resour 2011;11:914–921 [CrossRef][PubMed]
    [Google Scholar]
  32. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010;59:307–321 [CrossRef][PubMed]
    [Google Scholar]
  33. Pond SL, Frost SD. Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 2005;21:2531–2533 [CrossRef][PubMed]
    [Google Scholar]
  34. Rubinstein ND, Mayrose I, Martz E, Pupko T. Epitopia: a web-server for predicting B-cell epitopes. BMC Bioinformatics 2009;10:287 [CrossRef]
    [Google Scholar]
  35. El-Manzalawy Y, Dobbs D, Honavar V. Predicting linear B-cell epitopes using string kernels. J Mol Recognit 2008;21:243–255 [CrossRef][PubMed]
    [Google Scholar]
  36. Larsen JE, Lund O, Nielsen M. Improved method for predicting linear B-cell epitopes. Immunome Res 2006;2:2 [CrossRef][PubMed]
    [Google Scholar]
  37. Rice P, Longden I, Bleasby A. EMBOSS: the European molecular biology open software suite. Trends Genet 2000;16:276–277 [CrossRef][PubMed]
    [Google Scholar]
  38. Kobayashi M, Matsushima Y, Motoya T, Sakon N, Shigemoto N et al. Molecular evolution of the capsid gene in human norovirus genogroup II. Sci Rep 2016;6:29400 [CrossRef][PubMed]
    [Google Scholar]
  39. Kimura H, Nagasawa K, Tsukagoshi H, Matsushima Y, Fujita K et al. Molecular evolution of the fusion protein gene in human respiratory syncytial virus subgroup A. Infect Genet Evol 2016;43:398–406 [CrossRef][PubMed]
    [Google Scholar]
  40. Webb B, Sali A. Protein structure modeling with MODELLER. Methods Mol Biol 2014;1137:1–15 [CrossRef][PubMed]
    [Google Scholar]
  41. Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 1997;59:2714–2723[CrossRef]
    [Google Scholar]
  42. Lovell SC, Davis IW, Arendall WB 3rd, de Bakker PI, Word JM et al. Structure validation by Calpha geometry: phi, psi and Cbeta deviation. Proteins 2003;50:437–450[CrossRef]
    [Google Scholar]
  43. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM et al. UCSF Chimera – a visualization system for exploratory research and analysis. J Comput Chem 2004;25:1605–1612 [CrossRef][PubMed]
    [Google Scholar]
  44. Coelingh KV, Winter CC. Naturally occurring human parainfluenza type 3 viruses exhibit divergence in amino acid sequence of their fusion protein neutralization epitopes and cleavage sites. J Virol 1990;64:1329–1334[PubMed]
    [Google Scholar]
  45. Luque LE, Bridges OA, Mason JN, Boyd KL, Portner A et al. Residues in the heptad repeat a region of the fusion protein modulate the virulence of Sendai virus in mice. J Virol 2010;84:810–821 [CrossRef][PubMed]
    [Google Scholar]
  46. Tappert MM, Smith DF, Air GM. Fixation of oligosaccharides to a surface may increase the susceptibility to human parainfluenza virus 1, 2, or 3 hemagglutinin-neuraminidase. J Virol 2011;85:12146–12159 [CrossRef][PubMed]
    [Google Scholar]
  47. Mao N, Ji Y, Xie Z, Wang H, Wang H et al. Human parainfluenza virus-associated respiratory tract infection among children and genetic analysis of HPIV-3 strains in Beijing, China. PLoS One 2012;7:e43893 [CrossRef][PubMed]
    [Google Scholar]
  48. Holmes EC. Virus evolution. In Knipe DM, Howley PM. (editors) Fields Virology, 6th ed. Philadelphia: Lippincott Willams & Wilkins; 2013; pp286–313
    [Google Scholar]
  49. Ponomarenko JV, van Regenmortel MH. B cell epitope prediction. Structural Bioinformatics 2009;849–879
    [Google Scholar]
  50. Greenough TC, Babcock GJ, Roberts A, Hernandez HJ, Thomas WD et al. Development and characterization of a severe acute respiratory syndrome-associated coronavirus-neutralizing human monoclonal antibody that provides effective immunoprophylaxis in mice. J Infect Dis 2005;191:507–514 [CrossRef][PubMed]
    [Google Scholar]
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