title: Intrahost dynamics of influenza virus reassortment.
abstract: The segmented nature of the influenza virus genome allows reassortment between coinfecting viruses. This process of genetic exchange vastly increases the diversity of circulating influenza viruses. The importance of reassortment to public health is clear from its role in the emergence of a number of epidemiologically important viruses, including novel pandemic and epidemic strains. To gauge its impact on within-host genomic variation, we tracked reassortment in coinfected guinea pigs over time and given matched or discordant doses of coinfecting viruses. To ensure unbiased detection of reassortants, we used parental viruses of equivalent fitness that differ only by noncoding nucleotide changes. These viruses were based on the isolate A/Panama/2007/1999 (H3N2). At a dose of 2 × 10(2) PFU, one parental virus was absent from each guinea pig throughout the time course, indicating the presence of a bottleneck. With an intermediate dose of 2 × 10(3) PFU, genomic diversity present in nasal lavage samples increased from 1 to 3 days postinfection (dpi) and then declined by 6 dpi. With a high dose of 2 × 10(6) PFU, however, reassortment levels were high (avg. 59%) at 1 dpi and remained stable. Even late in the course of infection, parental viruses were not eclipsed by reassortants, suggesting that a uniformly high multiplicity of infection was not achieved in vivo. Inoculation with ∼10-fold discordant doses did not reduce reassortment relative to equivalent inputs but markedly changed the spectrum of genotypes produced. Our data reveal the potential for reassortment to contribute to intrahost diversity in mixed influenza virus infection.
  
  
  OBJECTIVE
  Influenza virus reassortment is prevalent in nature and is a major contributor to the diversity of influenza viruses circulating in avian, swine, human and other host species. This diversity, in turn, increases the potential for influenza viruses to evade selective pressures or adapt to new host environments. As examples, reassortment was key to the emergence of the 1957, 1968, and 2009 pandemics; the unusually severe influenza epidemics of 2003, 1951, and 1947; and the rise in adamantane resistance among currently circulating human H3N2 viruses. We reveal here the diversity of viral genotypes generated over time in a host coinfected with two influenza viruses. We found that intrahost diversity driven by reassortment is dynamic and dependent on the amount of each virus initiating infection. Our results demonstrate the readiness with which reassortant influenza viruses arise, offering new insight into this important mechanism of influenza virus evolution.
authors.affiliation: Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA.
authors.forename: Hui
authors.initials: H
authors.lastname: Tao
authors.affiliation: Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA.
authors.forename: John
authors.initials: J
authors.lastname: Steel
authors.affiliation: Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA anice.lowen@emory.edu.
authors.forename: Anice C
authors.initials: AC
authors.lastname: Lowen
mesh_terms: D000818:Animals; D004285:Dogs; D019143:Evolution, Molecular; D005260:Female; D016679:Genome, Viral; D006168:Guinea Pigs / Q000821:virology*; D006801:Humans; D061985:Madin Darby Canine Kidney Cells; D009975:Orthomyxoviridae / Q000235:genetics* / Q000276:immunology / Q000302:isolation & purification; D009976:Orthomyxoviridae Infections / Q000235:genetics* / Q000276:immunology / Q000821:virology; D016865:Reassortant Viruses / Q000235:genetics* / Q000276:immunology
references.citation: Clin Chem. 2003 Jun;49(6 Pt 1):853-60
references.pmid: 12765979
references.citation: J Virol. 2009 Apr;83(7):2803-18
references.pmid: 19153237
references.citation: Virus Genes. 1995;11(2-3):209-15
references.pmid: 8828147
references.citation: J Infect Dis. 1970 Apr;121(4):419-26
references.pmid: 5441118
references.citation: J Virol. 2013 Apr;87(8):4330-8
references.pmid: 23365443
references.citation: Science. 2009 Jul 10;325(5937):197-201
references.pmid: 19465683
references.citation: Nature. 2012 May 02;486(7403):420-8
references.pmid: 22722205
references.citation: Nature. 2005 Oct 20;437(7062):1162-6
references.pmid: 16208317
references.citation: PLoS Biol. 2005 Sep;3(9):e300
references.pmid: 16026181
references.citation: J Virol. 2009 Sep;83(17):8832-41
references.pmid: 19553313
references.citation: PLoS Pathog. 2006 Dec;2(12):e125
references.pmid: 17140286
references.citation: Emerg Infect Dis. 2006 Jan;12(1):9-14
references.pmid: 16494710
references.citation: PLoS Pathog. 2008 Aug 22;4(8):e1000133
references.pmid: 18725925
references.citation: Proc Natl Acad Sci U S A. 1999 Apr 27;96(9):5095-100
references.pmid: 10220424
references.citation: Proc Natl Acad Sci U S A. 2009 May 5;106(18):7565-70
references.pmid: 19380727
references.citation: Proc Soc Exp Biol Med. 1966 Jul;122(3):800-4
references.pmid: 5918954
references.citation: Proc Natl Acad Sci U S A. 2006 Jun 27;103(26):9988-92
references.pmid: 16785447
references.citation: Nature. 2008 May 29;453(7195):615-9
references.pmid: 18418375
references.citation: Nature. 2014 Apr 10;508(7495):254-7
references.pmid: 24531761
references.citation: PLoS Pathog. 2009 Jan;5(1):e1000252
references.pmid: 19119420
references.citation: J Virol. 2013 Jul;87(14):8064-74
references.pmid: 23678180
references.citation: PLoS Pathog. 2008 Feb 29;4(2):e1000012
references.pmid: 18463694
references.citation: PLoS Pathog. 2013;9(6):e1003421
references.pmid: 23785286
references.citation: J Virol. 2010 May;84(10):5329-35
references.pmid: 20219907
references.citation: J Virol. 2008 Oct;82(20):10052-8
references.pmid: 18684820
references.citation: J Virol. 2010 Jul;84(14):6943-54
references.pmid: 20444896
references.citation: J Virol. 2014 Mar;88(5):2844-57
references.pmid: 24371052
references.citation: PLoS Pathog. 2012 Dec;8(12):e1003081
references.pmid: 23308065
references.citation: J Virol. 2010 Nov;84(21):11219-26
references.pmid: 20739532
references.citation: Proc Natl Acad Sci U S A. 2011 Nov 15;108(46):E1156-63
references.pmid: 22065783
references.citation: J Virol. 2013 Apr;87(8):4768-71
references.pmid: 23388708
references.citation: PLoS Pathog. 2007 Oct 19;3(10):1470-6
references.pmid: 17953482
references.citation: Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):12084-8
references.pmid: 21730147
references.citation: J Gen Virol. 2012 Sep;93(Pt 9):1996-2007
references.pmid: 22718569
references.citation: PLoS Pathog. 2012;8(5):e1002730
references.pmid: 22693449