The effective population size and mutation rate of influenza A virus in acutely infected individuals
McCrone, J. T.; Woods, R. J.; Martin, E. T.; Monto, A. S.; Lauring, A. S.
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The global evolutionary dynamics of influenza viruses ultimately derive from processes that take place within and between infected individuals. Recent work suggests that within-host populations are dynamic, but an in vivo estimate of mutation rate and population size in naturally infected individuals remains elusive. Here we model the within-host dynamics of influenza A viruses using high depth of coverage sequence data from 200 acute infections in an outpatient, community setting. Using a Wright-Fisher model, we estimate a within-host effective population size of 32-72 and an in vivo mutation rate of 3.4x10-6 per nucleotide per generation.
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