Evolution of 2009 H1N1 influenza viruses during the pandemic correlates with increased viral pathogenicity and transmissibility in the ferret model

Abstract

There is increasing evidence that 2009 pandemic H1N1 influenza viruses have evolved after pandemic onset giving rise to severe epidemics in subsequent waves. However, it still remains unclear which viral determinants might have contributed to disease severity after pandemic initiation. Here, we show that distinct mutations in the 2009 pandemic H1N1 virus genome have occurred with increased frequency after pandemic declaration. Among those, a mutation in the viral hemagglutinin was identified that increases 2009 pandemic H1N1 virus binding to human-like α2,6-linked sialic acids. Moreover, these mutations conferred increased viral replication in the respiratory tract and elevated respiratory droplet transmission between ferrets. Thus, our data show that 2009 H1N1 influenza viruses have evolved after pandemic onset giving rise to novel virus variants that enhance viral replicative fitness and respiratory droplet transmission in a mammalian animal model. These findings might help to improve surveillance efforts to assess the pandemic risk by emerging influenza viruses.

Sweep Dynamics (SD) plots: Computational identification of selective sweeps to monitor the adaptation of influenza A viruses

“…For the 2009S season, we detected a selective sweep at seven amino acid positions throughout the viral genome (in PA (L581M), HA (S203T) (position 202 in Otte et al 34 ), NP (V100I, I373T), NA (V106I, N248D) and NS1 (I123V)) ( Figure 2C, 2D, 2E, 2F and 2I, Supplementary Table 1), which were also described in Otte et al 34 . All of these changes rapidly became predominant in this season and continued to rise in frequency until they were close to fixation in 2010N, suggesting that the new amino acid was present in nearly all sampled isolates in this season.…”

“…Hereby, particularly the receptor binding properties of HA play an important role. We have also previously shown that HA S203T increases binding to α2,6-linked sialic acids (corresponds to position 202 in Otte et al 34 )…”

“…Five of seven detected sweep-related changes were also described in this study as emerging changes in the first wave of the pandemic, with frequencies close to 100% in the second wave in 2010N, similar to the frequencies we observed in our analysis (frequencies between 91% and 99%, with slight differences most likely due to differing time frames and datasets in both analyses 36 . Moreover, all seven adaptive mutations were associated with enhanced respiratory droplet transmission in a ferret model, suggesting their crucial role to sustain with the mammalian host 34 . The ability of influenza A viruses to transmit from human-to-human is considered to be key in pandemic spread.…”

“…that are predominantly expressed in the upper respiratory tract of humans, a key site in virus transmission among humans 34,37,38 .…”

Comparative In Vitro and In Vivo Analysis of H1N1 and H1N2 Variant Influenza Viruses Isolated from Humans between 2011 and 2016

“…Other tested variant viruses had activation pH values of Ն5.6 and transmitted less efficiently between ferrets, but it is not clear whether poor transmissibility of these viruses was attributed to the higher HA activation pH and/or additional viral traits. Growing evidence indicates that swine can facilitate adaptations of zoonotic influenza viruses to humans, including increased binding to alpha-2,6 SA receptors, increased replication at temperatures found in mammalian respiratory tracts, increased pathogenicity and transmissibility, and decreased HA activation pH (64,65). As virulence and transmissibility are multifactorial traits, additional determinants such as virus morphology, HA-NA balance, and the ability to evade innate immune responses may also be important (66).…”