Avian H7N9 influenza viruses are evolutionarily constrained by stochastic processes during replication and transmission in mammals

Abstract

H7N9 avian influenza viruses (AIV) have caused over 1,500 documented human infections since emerging in 2013. Although wild type H7N9 AIV can be transmitted by respiratory droplets in ferrets, they have not yet caused widespread outbreaks in humans. Previous studies have revealed molecular determinants of H7N9 AIV virus host-switching, but little is known about potential evolutionary constraints on this process. Here, we compare patterns of sequence evolution for H7N9 AIV and mammalian H1N1 viruses during replication and transmission in ferrets. We show that three main factors—purifying selection, stochasticity, and very narrow transmission bottlenecks—combine to severely constrain the ability of H7N9 AIV to effectively adapt to mammalian hosts in isolated, acute spillover events. We find rare evidence of natural selection favoring new, potentially mammal-adapting mutations within ferrets, but no evidence of natural selection acting during transmission. We conclude that human-adapted H7N9 viruses are unlikely to emerge during typical spillover infections. Our findings are instead consistent with a model in which the emergence of a human-transmissible virus would be a rare and unpredictable, though highly consequential, “jackpot” event. Strategies to limit the total number of spillover infections will limit opportunities for the virus to win this evolutionary lottery.

Viral expansion after transfer is a primary driver of influenza A virus transmission bottlenecks

“…The reduction in diversity between virus populations in donor animals and those that become established in recipients seen here is highly consistent with prior studies carried out both in human cohorts and experimental animals [19–21, 24]. Our conclusion that early viral dynamics in the recipient make a major contribution to this loss of diversity is, however, novel.…”

“…In human cohort studies, sample collection is typically triggered by the onset of symptoms reported by the study subject, such that the very early stages of infection are often not sampled [19]. Similarly, previous studies of the influenza A virus transmission bottleneck in experimental models did not characterize viral populations present early after transmission [20, 24].…”

“…The observation that many viral genomes were conveyed through the environment during both direct and aerosol exposures is somewhat surprising in light of prior studies that compared different types of exposure [20, 24]. This result was also unanticipated based on the potential for expelled aerosols to be diluted in air [40].…”

“…More relaxed bottlenecks have been reported in natural hosts aside from humans, suggesting roles for host biology and/or modes of transmission in shaping species-specific between-host dynamics [22, 23]. Finally, avian influenza A virus transmission in mammals has been shown to involve a tight bottleneck with reductions in viral diversity attributed to either stochastic or selective forces [24–26].…”

“…More relaxed bottlenecks have been reported in natural hosts aside from humans, suggesting roles for host biology and/or modes of transmission in shaping species-specific between-host dynamics [22,23]. Finally, avian influenza A virus transmission in mammals has been shown to involve a tight bottleneck with reductions in viral diversity attributed to either stochastic or selective forces [24][25][26]. While it is known that diversity is lost during influenza A virus transmission, it is unclear at which point -in the donor host, the environment, or the recipient host -this takes place.…”