Within-host evolutionary dynamics of seasonal and pandemic human influenza A viruses in young children

Abstract

The evolution of influenza viruses is fundamentally shaped by within-host processes. However, the within-host evolutionary dynamics of influenza viruses remain incompletely understood, in part because most studies have focused on within-host virus diversity of infections in otherwise healthy adults based on single timepoint data. Here, we analysed the within-host evolution of 82 longitudinally sampled individuals, mostly young children, infected with A/H3N2 or A/H1N1pdm09 viruses between 2007 and 2009. For A/H1N1pdm09 infections during the 2009 pandemic, nonsynonymous changes were common early in infection but decreased or remained constant throughout infection. For A/H3N2 viruses, early infection was dominated by purifying selection. However, as the A/H3N2 infections progressed for longer-than-average duration (up to 2 weeks) in relatively young or influenza naive individuals, nonsynonymous variants increased in frequencies even though within-host virus titres decreased, leading to the maintenance of virus diversity via mutation-selection balance and provide important opportunities for within-host virus evolution.

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

“…We found the fewest iSNVs in the H1N1 group ( n = 9 ferrets), with an average of 24 iSNVs per ferret, ranging from 3 to 35 across all time points. This is similar to the number of seasonal influenza virus iSNVs reported in humans ( Han et al. 2021 ).…”

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

“…We found the fewest iSNVs per ferret in the CA04 group (n=9 ferrets), with an average of 24 iSNVs per ferret, ranging from 3-83. This is similar to the number of seasonal flu iSNVs reported in humans 35 . The number of iSNVs in the rGD/3 group (n=13 ferrets, grouping both rGD/3 viruses) was also low, with an average of 13 per ferret, ranging from 1-43.…”