Occurrence of mixed populations of influenza A viruses that can be maintained through transmission in a single host and potential for reassortment

Reassortment, which is the rearrangement of viral gene segments in a host cell infected with two different viruses, is an important mechanism for the evolution of influenza viruses. Mixed infections with multiple virus types could lead to reassortment. To better understand the occurrence of quasispecies in a single host, we investigated mixed infections in individual isolates of seasonal influenza A viruses using amantadine sensitivity as a marker. We cultured viruses with amantadine and performed sequencing, restriction fragment length polymorphism analysis, cloning, and quantitative PCR to detect mixed populations. Culturing with amantadine showed evidence of a high number of mixed populations, while the other assays could hardly detect mixed populations. The existence of quasispecies in each isolate was common. However, the proportion of these, which can be less than 1%, is too low to be detected by conventional methods. Such mixed populations in which reassortment occurs may have a significant role in the evolution of viruses.