Weak selection and stochastic processes limit the emergence of antigenic variants during household transmission of influenza A viruses

Influenza viruses undergo antigenic drift, the gradual accumulation of mutations that cause antigenic changes in the viral surface proteins hemagglutinin (HA) and neuraminidase (NA). Although selection for antigenic variants is detectable on the global scale, the processes by which antigenic variants are generated and selected in individual hosts remain unclear. It has been hypothesized that selection for antigenic variants may occur during the establishment of a new infection, rather than over time in a single host. Here, we leveraged a large household cohort study to assess whether selection was detectable between acutely infected hosts. We investigated influenza A virus evolution using specimens from 384 children and household contacts with RT-PCR-confirmed influenza A infection, representing infections with A(H1N1)pdm09 and A(H3N2) viruses from 2017-19. In agreement with prior studies, we found that acute infections involved weak purifying selection across the viral genome. In addition, we identified 40 transmission events occurring in 31 households. During transmission, evolution between hosts was characterized by tight transmission bottlenecks and weak purifying selection. We found variability in the strength and direction of selection on antigenic regions of HA, but no clear evidence for selection of antigenic variants during transmission. Together, our results indicate that stochastic processes and weak natural selection dominate most acute influenza A virus infections and transmission events, and that selection of antigenic variants during transmission between acutely infected hosts is likely to be exceedingly rare. Author SummaryInfluenza viruses clearly evolve under selective pressure from immune responses in human populations, but recent work suggests that within individual infections random effects are stronger than selection. New viral variants that spread globally must nonetheless emerge in one person and be transmitted onwards--how does this happen? We characterized viral genomes collected over two influenza seasons from 384 children and their household contacts. We detected 40 transmissions among 31 of the households, allowing us to examine how selection acts during infection and transmission. We found that influenza virus genetic diversity is low in infected individuals, and mutations arising in one person are rarely transmitted to their household contacts, consistent with prior reports that influenza virus evolution is tightly constrained within hosts. We further examined all transmission events for evidence of selection between hosts, finding only one mutation that could plausibly affect antibody recognition. However, we found no evidence that this mutation was favored by natural selection. Our results suggest that chance events, together with weak selection, are the main forces affecting influenza virus evolution within and between hosts during typical acute infections. Selection for new variants may be more likely to occur over longer transmission chains and/or during prolonged infections.