Intrahost Dynamics of Influenza Virus Reassortment

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 givenmatched 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 2 102 PFU, one parental virus was absent from each guinea pig throughout the time course, indicat-ing the presence of a bottleneck. With an intermediate dose of 2 103 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 2 106 PFU, however, reassort-ment 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 ge-notypes produced. Our data reveal the potential for reassortment to contribute to intrahost diversity in mixed influenza virus infection