1887

Abstract

To gain insight into the evolution of influenza A viruses (IAVs) during infection of vaccinated pigs, we experimentally infected a 3-week-old naive pig with a triple-reassortant H1N1 IAV and placed the seeder pig in direct contact with a group of age-matched vaccinated pigs ( = 10). We indexed the genetic diversity and evolution of the virus at an intra-host level by deep sequencing the entire genome directly from nasal swabs collected at two separate samplings during infection. We obtained 13 IAV metagenomes from 13 samples, which included the virus inoculum and two samples from each of the six pigs that tested positive for IAV during the study. The infection produced a population of heterogeneous alleles (sequence variants) that was dynamic over time. Overall, 794 polymorphisms were identified amongst all samples, which yielded 327 alleles, 214 of which were unique sequences. A total of 43 distinct haemagglutinin proteins were translated, two of which were observed in multiple pigs, whereas the neuraminidase (NA) was conserved and only one dominant NA was found throughout the study. The genetic diversity of IAVs changed dynamically within and between pigs. However, most of the substitutions observed in the internal gene segments were synonymous. Our results demonstrated remarkable IAV diversity, and the complex, rapid and dynamic evolution of IAV during infection of vaccinated pigs that can only be appreciated with repeated sampling of individual animals and deep sequence analysis.

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2015-10-01
2019-10-21
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References

  1. Ali A. , Daniels J.B. , Zhang Y. , Rodriguez-Palacios A. , Hayes-Ozello K. , Mathes L. , Lee C.W. . ( 2011;). Pandemic and seasonal human influenza virus infections in domestic cats: prevalence, association with respiratory disease, and seasonality patterns. J Clin Microbiol 49: 4101–4105 [CrossRef] [PubMed].
    [Google Scholar]
  2. Allerson M. , Deen J. , Detmer S.E. , Gramer M.R. , Joo H.S. , Romagosa A. , Torremorell M. . ( 2013;). The impact of maternally derived immunity on influenza A virus transmission in neonatal pig populations. Vaccine 31: 500–505 [CrossRef] [PubMed].
    [Google Scholar]
  3. Anderson T.K. , Campbell B.A. , Nelson M.I. , Lewis N.S. , Janas-Martindale A. , Killian M.L. , Vincent A.L. . ( 2015;). Characterization of co-circulating swine influenza A viruses in North America and the identification of a novel H1 genetic clade with antigenic significance. Virus Res 201: 24–31 [CrossRef] [PubMed].
    [Google Scholar]
  4. André P. , Kim A. , Khrapko K. , Thilly W.G. . ( 1997;). Fidelity and mutational spectrum of Pfu DNA polymerase on a human mitochondrial DNA sequence. Genome Res 7: 843–852 [PubMed].
    [Google Scholar]
  5. Archer J. , Baillie G. , Watson S.J. , Kellam P. , Rambaut A. , Robertson D.L. . ( 2012;). Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II. BMC Bioinformatics 13: 47 [CrossRef] [PubMed].
    [Google Scholar]
  6. Arnold K. , Bordoli L. , Kopp J. , Schwede T. . ( 2006;). The swiss-model workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22: 195–201 [CrossRef] [PubMed].
    [Google Scholar]
  7. Bandelt H.J. , Forster P. , Röhl A. . ( 1999;). Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16: 37–48 [CrossRef] [PubMed].
    [Google Scholar]
  8. Bao Y. , Bolotov P. , Dernovoy D. , Kiryutin B. , Tatusova T. . ( 2007;). flan: a web server for influenza virus genome annotation. Nucleic Acids Res 35: (Web Server), W280–W284 [CrossRef] [PubMed].
    [Google Scholar]
  9. Belshaw R. , Pybus O.G. , Rambaut A. . ( 2007;). The evolution of genome compression and genomic novelty in RNA viruses. Genome Res 17: 1496–1504 [CrossRef] [PubMed].
    [Google Scholar]
  10. Bidzhieva B. , Zagorodnyaya T. , Karagiannis K. , Simonyan V. , Laassri M. , Chumakov K. . ( 2014;). Deep sequencing approach for genetic stability evaluation of influenza A viruses. J Virol Methods 199: 68–75 [CrossRef] [PubMed].
    [Google Scholar]
  11. Blanc A. , Ruchansky D. , Clara M. , Achaval F. , Le Bas A. , Arbiza J. . ( 2009;). Serologic evidence of influenza A and B viruses in South American fur seals (Arctocephalus australis). J Wildl Dis 45: 519–521 [CrossRef] [PubMed].
    [Google Scholar]
  12. Bourret V. , Croville G. , Mariette J. , Klopp C. , Bouchez O. , Tiley L. , Guérin J.L. . ( 2013;). Whole-genome, deep pyrosequencing analysis of a duck influenza A virus evolution in swine cells. Infect Genet Evol 18: 31–41 [CrossRef] [PubMed].
    [Google Scholar]
  13. Bourret V. , Croville G. , Mansuy J.M. , Mengelle C. , Mariette J. , Klopp C. , Genthon C. , Izopet J. , Guérin J.L. . ( 2015;). Intra-host viral variability in children clinically infected with H1N1(2009) pandemic influenza. Infect Genet Evol 33: 47–54 [CrossRef] [PubMed].
    [Google Scholar]
  14. Caton A.J. , Brownlee G.G. , Yewdell J.W. , Gerhard W. . ( 1982;). The antigenic structure of the influenza virus A/PR/8/34 hemagglutinin (H1 subtype). Cell 31: 417–427 [CrossRef] [PubMed].
    [Google Scholar]
  15. Chen R. , Holmes E.C. . ( 2010;). Hitchhiking and the population genetic structure of avian influenza virus. J Mol Evol 70: 98–105 [CrossRef] [PubMed].
    [Google Scholar]
  16. Chen-Harris H. , Borucki M.K. , Torres C. , Slezak T.R. , Allen J.E. . ( 2013;). Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs. BMC Genomics 14: 96 [CrossRef] [PubMed].
    [Google Scholar]
  17. Ciacci-Zanella J.R. , Vincent A.L. , Prickett J.R. , Zimmerman S.M. , Zimmerman J.J. . ( 2010;). Detection of anti-influenza A nucleoprotein antibodies in pigs using a commercial influenza epitope-blocking enzyme-linked immunosorbent assay developed for avian species. J Vet Diagn Invest 22: 3–9 [CrossRef] [PubMed].
    [Google Scholar]
  18. Corzo C.A. , Culhane M. , Juleen K. , Stigger-Rosser E. , Ducatez M.F. , Webby R.J. , Lowe J.F. . ( 2013;). Active surveillance for influenza A virus among swine, midwestern United States, 2009-2011. Emerg Infect Dis 19: 954–960 [CrossRef] [PubMed].
    [Google Scholar]
  19. Cummings S.M. , McMullan M. , Joyce D.A. , van Oosterhout C. . ( 2010;). Solutions for PCR, cloning and sequencing errors in population genetic analysis. Conserv Genet 11: 1095–1097 [CrossRef].
    [Google Scholar]
  20. de Groot J. , Ruis M.A. , Scholten J.W. , Koolhaas J.M. , Boersma W.J. . ( 2001;). Long-term effects of social stress on antiviral immunity in pigs. Physiol Behav 73: 145–158 [CrossRef] [PubMed].
    [Google Scholar]
  21. Debbink K. , Lindesmith L.C. , Ferris M.T. , Swanstrom J. , Beltramello M. , Corti D. , Lanzavecchia A. , Baric R.S. . ( 2014;). Within-host evolution results in antigenically distinct GII.4 noroviruses. J Virol 7244–7255.[CrossRef]
    [Google Scholar]
  22. Deem M.W. , Pan K. . ( 2009;). The epitope regions of H1-subtype influenza A, with application to vaccine efficacy. Protein Eng Des Sel 22: 543–546 [CrossRef] [PubMed].
    [Google Scholar]
  23. Diaz A. , Allerson M. , Culhane M. , Sreevatsan S. , Torremorell M. . ( 2013;). Antigenic drift of H1N1 influenza A virus in pigs with and without passive immunity. Influenza Other Respir Viruses 7: (Suppl 4), 52–60 [CrossRef] [PubMed].
    [Google Scholar]
  24. Diaz A. , Perez A. , Sreevatsan S. , Davies P. , Culhane M. , Torremorell M. . ( 2015;). Association between influenza A virus infection and pigs subpopulations in endemically infected breeding herds. PLoS One 10: e0129213 [CrossRef] [PubMed].
    [Google Scholar]
  25. Direksin K. , Joo H. , Goyal S.M. . ( 2002;). An immunoperoxidase monolayer assay for the detection of antibodies against swine influenza virus. J Vet Diagn Invest 14: 169–171 [CrossRef] [PubMed].
    [Google Scholar]
  26. Domingo E. , Martínez-Salas E. , Sobrino F. , de la Torre J.C. , Portela A. , Ortín J. , López-Galindez C. , Pérez-Breña P. , Villanueva N. , other authors . ( 1985;). The quasispecies (extremely heterogeneous) nature of viral RNA genome populations: biological relevance - a review. Gene 40: 1–8 [CrossRef] [PubMed].
    [Google Scholar]
  27. Domingo E. , Sheldon J. , Perales C. . ( 2012;). Viral quasispecies evolution. Microbiol Mol Biol Rev 76: 159–216 [CrossRef] [PubMed].
    [Google Scholar]
  28. Ducatez M.F. , Hause B. , Stigger-Rosser E. , Darnell D. , Corzo C. , Juleen K. , Simonson R. , Brockwell-Staats C. , Rubrum A. , other authors . ( 2011;). Multiple reassortment between pandemic (H1N1) 2009 and endemic influenza viruses in pigs. United States. Emerg Infect Dis 17: 1624–1629 [CrossRef] [PubMed].
    [Google Scholar]
  29. Goto N. , Prins P. , Nakao M. , Bonnal R. , Aerts J. , Katayama T. . ( 2010;). BioRuby: bioinformatics software for the Ruby programming language. Bioinformatics 26: 2617–2619 [CrossRef] [PubMed].
    [Google Scholar]
  30. Hedman J. , Nordgaard A. , Rasmusson B. , Ansell R. , Rådström P. . ( 2009;). Improved forensic DNA analysis through the use of alternative DNA polymerases and statistical modeling of DNA profiles. Biotechniques 47: 951–958 [CrossRef] [PubMed].
    [Google Scholar]
  31. Hensley S.E. , Das S.R. , Bailey A.L. , Schmidt L.M. , Hickman H.D. , Jayaraman A. , Viswanathan K. , Raman R. , Sasisekharan R. , other authors . ( 2009;). Hemagglutinin receptor binding avidity drives influenza A virus antigenic drift. Science 326: 734–736 [CrossRef] [PubMed].
    [Google Scholar]
  32. Hoelzer K. , Murcia P.R. , Baillie G.J. , Wood J.L.N. , Metzger S.M. , Osterrieder N. , Dubovi E.J. , Holmes E.C. , Parrish C.R. . ( 2010;). Intrahost evolutionary dynamics of canine influenza virus in naive and partially immune dogs. J Virol 84: 5329–5335 [CrossRef] [PubMed].
    [Google Scholar]
  33. Kitikoon P. , Nelson M.I. , Killian M.L. , Anderson T.K. , Koster L. , Culhane M.R. , Vincent A.L. . ( 2013;). Genotype patterns of contemporary reassorted H3N2 virus in US swine. J Gen Virol 94: 1236–1241 [CrossRef] [PubMed].
    [Google Scholar]
  34. Knauer M.T. , Hostetler C.E. . ( 2013;). US swine industry productivity analysis, 2005 to 2010. J Swine Health Prod 21: 248–252.
    [Google Scholar]
  35. Korber B. . ( 2000;). HIV signature and sequence variation analysis. . In Computational Analysis of HIV Molecular Sequences, pp. 55–72. Edited by Rodrigo A. G. , Learn G. H. . Dordrecht: Kluwer;.
    [Google Scholar]
  36. Larkin M.A. , Blackshields G. , Brown N.P. , Chenna R. , McGettigan P.A. , McWilliam H. , Valentin F. , Wallace I.M. , Wilm A. , other authors . ( 2007;). Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947–2948 [CrossRef] [PubMed].
    [Google Scholar]
  37. Lemey P. , Rambaut A. , Pybus O.G. . ( 2006;). HIV evolutionary dynamics within and among hosts. AIDS Rev 8: 125–140 [PubMed].
    [Google Scholar]
  38. Lorusso A. , Vincent A.L. , Harland M.L. , Alt D. , Bayles D.O. , Swenson S.L. , Gramer M.R. , Russell C.A. , Smith D.J. , other authors . ( 2011;). Genetic and antigenic characterization of H1 influenza viruses from United States swine from 2008. J Gen Virol 92: 919–930 [CrossRef] [PubMed].
    [Google Scholar]
  39. Lundberg K.S. , Shoemaker D.D. , Adams M.W.W. , Short J.M. , Sorge J.A. , Mathur E.J. . ( 1991;). High-fidelity amplification using a thermostable DNA polymerase isolated from Pyrococcus furiosus . Gene 108: 1–6 [CrossRef] [PubMed].
    [Google Scholar]
  40. Meguro H. , Bryant J.D. , Torrence A.E. , Wright P.F. . ( 1979;). Canine kidney cell line for isolation of respiratory viruses. J Clin Microbiol 9: 175–179 [PubMed].
    [Google Scholar]
  41. Murcia P.R. , Baillie G.J. , Daly J. , Elton D. , Jervis C. , Mumford J.A. , Newton R. , Parrish C.R. , Hoelzer K. , other authors . ( 2010;). Intra- and interhost evolutionary dynamics of equine influenza virus. J Virol 84: 6943–6954 [CrossRef] [PubMed].
    [Google Scholar]
  42. Murcia P.R. , Hughes J. , Battista P. , Lloyd L. , Baillie G.J. , Ramirez-Gonzalez R.H. , Ormond D. , Oliver K. , Elton D. , other authors . ( 2012;). Evolution of an Eurasian avian-like influenza virus in naïve and vaccinated pigs. PLoS Pathog 8: e1002730 [CrossRef] [PubMed].
    [Google Scholar]
  43. Murcia P.R. , Baillie G.J. , Stack J.C. , Jervis C. , Elton D. , Mumford J.A. , Daly J. , Kellam P. , Grenfell B.T. , other authors . ( 2013;). Evolution of equine influenza virus in vaccinated horses. J Virol 87: 4768–4771 [CrossRef] [PubMed].
    [Google Scholar]
  44. Nei M. , Gojobori T. . ( 1986;). Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3: 418–426 [PubMed].
    [Google Scholar]
  45. Nelson M.I. , Lemey P. , Tan Y. , Vincent A. , Lam T.T.Y. , Detmer S. , Viboud C. , Suchard M.A. , Rambaut A. , other authors . ( 2011;). Spatial dynamics of human-origin H1 influenza A virus in North American swine. PLoS Pathog 7: e1002077 [CrossRef] [PubMed].
    [Google Scholar]
  46. Nelson M.I. , Gramer M.R. , Vincent A.L. , Holmes E.C. . ( 2012;). Global transmission of influenza viruses from humans to swine. J Gen Virol 93: 2195–2203 [CrossRef] [PubMed].
    [Google Scholar]
  47. Oh S.H. , Whitley N.C. . ( 2011;). Pork production in China, Japan and South Korea. Asian-Australas J Anim Sci 24: 1629–1636 [CrossRef].
    [Google Scholar]
  48. Ramakrishnan M.A. , Tu Z.J. , Singh S. , Chockalingam A.K. , Gramer M.R. , Wang P. , Goyal S.M. , Yang M. , Halvorson D.A. , Sreevatsan S. . ( 2009;). The feasibility of using high resolution genome sequencing of influenza A viruses to detect mixed infections and quasispecies. PLoS One 4: e7105 [CrossRef] [PubMed].
    [Google Scholar]
  49. Rambaut A. , Holmes E. . ( 2009;). The early molecular epidemiology of the swine-origin A/H1N1 human influenza pandemic. PLoS Curr 1: RRN1003 [CrossRef] [PubMed].
    [Google Scholar]
  50. Roedig J.V. , Rapp E. , Höper D. , Genzel Y. , Reichl U. . ( 2011;). Impact of host cell line adaptation on quasispecies composition and glycosylation of influenza A virus hemagglutinin. PLoS One 6: e27989 [CrossRef] [PubMed].
    [Google Scholar]
  51. Romagosa A. , Allerson M. , Gramer M. , Joo H.S. , Deen J. , Detmer S. , Torremorell M. . ( 2011;). Vaccination of influenza A virus decreases transmission rates in pigs. Vet Res 42: 120 [CrossRef] [PubMed].
    [Google Scholar]
  52. Ross M.G. , Russ C. , Costello M. , Hollinger A. , Lennon N.J. , Hegarty R. , Nusbaum C. , Jaffe D.B. . ( 2013;). Characterizing and measuring bias in sequence data. Genome Biol 14: R51 [CrossRef] [PubMed].
    [Google Scholar]
  53. Russell C.A. , Jones T.C. , Barr I.G. , Cox N.J. , Garten R.J. , Gregory V. , Gust I.D. , Hampson A.W. , Hay A.J. , other authors . ( 2008;). The global circulation of seasonal influenza A (H3N2) viruses. Science 320: 340–346 [CrossRef] [PubMed].
    [Google Scholar]
  54. Salemi M. . ( 2013;). The intra-host evolutionary and population dynamics of human immunodeficiency virus type 1: a phylogenetic perspective. Infect Dis Rep 5: (Suppl 1), e3 [CrossRef] [PubMed].
    [Google Scholar]
  55. Shao W. , Boltz V.F. , Spindler J.E. , Kearney M.F. , Maldarelli F. , Mellors J.W. , Stewart C. , Volfovsky N. , Levitsky A. , other authors . ( 2013;). Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of low-frequency drug resistance mutations in HIV-1 DNA. Retrovirology 10: 18 [CrossRef] [PubMed].
    [Google Scholar]
  56. Simonsen L. , Spreeuwenberg P. , Lustig R. , Taylor R.J. , Fleming D.M. , Kroneman M. , Van Kerkhove M.D. , Mounts A.W. , Paget W.J. , GLaMOR Collaborating Teams . ( 2013;). Global mortality estimates for the 2009 influenza pandemic from the GLaMOR project: a modeling study. PLoS Med 10: e1001558 [CrossRef] [PubMed].
    [Google Scholar]
  57. Slomka M.J. , Densham A.L.E. , Coward V.J. , Essen S. , Brookes S.M. , Irvine R.M. , Spackman E. , Ridgeon J. , Gardner R. , other authors . ( 2010;). Real time reverse transcription (RRT)-polymerase chain reaction (PCR) methods for detection of pandemic (H1N1) 2009 influenza virus and European swine influenza A virus infections in pigs. Influenza Other Respir Viruses 4: 277–293 [CrossRef] [PubMed].
    [Google Scholar]
  58. Spackman E. , Suarez D.L. . ( 2008;). Type A influenza virus detection and quantitation by real-time RT-PCR. Methods Mol Biol 436: 19–26 [PubMed].
    [Google Scholar]
  59. Tao H. , Steel J. , Lowen A.C. . ( 2014;). Intrahost dynamics of influenza virus reassortment. J Virol 88: 7485–7492 [CrossRef] [PubMed].
    [Google Scholar]
  60. Taubenberger J.K. , Kash J.C. . ( 2010;). Influenza virus evolution, host adaptation, and pandemic formation. Cell Host Microbe 7: 440–451 [CrossRef] [PubMed].
    [Google Scholar]
  61. Tong S. , Zhu X. , Li Y. , Shi M. , Zhang J. , Bourgeois M. , Yang H. , Chen X. , Recuenco S. , other authors . ( 2013;). New World bats harbor diverse influenza A viruses. PLoS Pathog 9: e1003657 [CrossRef] [PubMed].
    [Google Scholar]
  62. Torremorell M. , Allerson M. , Corzo C. , Diaz A. , Gramer M. . ( 2012;). Transmission of influenza A virus in pigs. Transbound Emerg Dis 59: (Suppl 1), 68–84 [CrossRef] [PubMed].
    [Google Scholar]
  63. Tu Z. , He Y.L. , Lu H. , Xu L. , Yang Z.B. , Yang C. , Chen W.J. . ( 2013;). Mutant spectrum of Dengue type 1 virus in the plasma of patients from the 2006 epidemic in South China. Int J Infect Dis 17: e1080–e1081 [CrossRef] [PubMed].
    [Google Scholar]
  64. Vincent A.L. , Ma W. , Lager K.M. , Janke B.H. , Webby R.J. , García-Sastre A. , Richt J.A. . ( 2007;). Efficacy of intranasal administration of a truncated NS1 modified live influenza virus vaccine in swine. Vaccine 25: 7999–8009 [CrossRef] [PubMed].
    [Google Scholar]
  65. Vincent A.L. , Ma W.J. , Lager K.M. , Janke B.H. , Richt J.A. . ( 2008;). Swine influenza viruses: a North American perspective. Adv Virus Res 72: 127–154.[CrossRef]
    [Google Scholar]
  66. Wei K. , Sun H. , Sun Z. , Sun Y. , Kong W. , Pu J. , Ma G. , Yin Y. , Yang H. , other authors . ( 2014;). Influenza A virus acquires enhanced pathogenicity and transmissibility after serial passages in swine. J Virol 88: 11981–11994 [CrossRef] [PubMed].
    [Google Scholar]
  67. Wu J.Y. , Jiang X.T. , Jiang Y.X. , Lu S.Y. , Zou F. , Zhou H.W. . ( 2010;). Effects of polymerase, template dilution and cycle number on PCR based 16S rRNA diversity analysis using the deep sequencing method. BMC Microbiol 10: 255 [CrossRef] [PubMed].
    [Google Scholar]
  68. Zhou B. , Donnelly M.E. , Scholes D.T. , St George K. , Hatta M. , Kawaoka Y. , Wentworth D.E. . ( 2009;). Single-reaction genomic amplification accelerates sequencing and vaccine production for classical and swine origin human influenza A viruses. J Virol 83: 10309–10313 [CrossRef] [PubMed].
    [Google Scholar]
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