Accumulation of Human-Adapting Mutations during Circulation of A(H1N1)pdm09 Influenza Virus in Humans in the United Kingdom

Abstract

The influenza pandemic that emerged in 2009 provided an unprecedented opportunity to study adaptation of a virus recently acquired from an animal source during human transmission. In the United Kingdom, the novel virus spread in three temporally distinct waves between 2009 and 2011. Phylogenetic analysis of complete viral genomes showed that mutations accumulated over time. Second- and third-wave viruses replicated more rapidly in human airway epithelial (HAE) cells than did the first-wave virus. In infected mice, weight loss varied between viral isolates from the same wave but showed no distinct pattern with wave and did not correlate with viral load in the mouse lungs or severity of disease in the human donor. However, second- and third-wave viruses induced less alpha interferon in the infected mouse lungs. NS1 protein, an interferon antagonist, had accumulated several mutations in second- and third-wave viruses. Recombinant viruses with the third-wave NS gene induced less interferon in human cells, but this alone did not account for increased virus fitness in HAE cells. Mutations in HA and NA genes in third-wave viruses caused increased binding to α-2,6-sialic acid and enhanced infectivity in human mucus. A recombinant virus with these two segments replicated more efficiently in HAE cells. A mutation in PA (N321K) enhanced polymerase activity of third-wave viruses and also provided a replicative advantage in HAE cells. Therefore, multiple mutations allowed incremental changes in viral fitness, which together may have contributed to the apparent increase in severity of A(H1N1)pdm09 influenza virus during successive waves.IMPORTANCE Although most people infected with the 2009 pandemic influenza virus had mild or unapparent symptoms, some suffered severe and devastating disease. The reasons for this variability were unknown, but the numbers of severe cases increased during successive waves of human infection in the United Kingdom. To determine the causes of this variation, we studied genetic changes in virus isolates from individual hospitalized patients. There were no consistent differences between these viruses and those circulating in the community, but we found multiple evolutionary changes that in combination over time increased the virus's ability to infect human cells. These adaptations may explain the remarkable ability of A(H1N1)pdm09 virus to continue to circulate despite widespread immunity and the apparent increase in severity of influenza over successive waves of infection.

Adaptive Mutations That Occurred during Circulation in Humans of H1N1 Influenza Virus in the 2009 Pandemic Enhance Virulence in Mice

“…Remarkably, HH15-specific sites in NP 100I, NA 106I, NS1 123V, and HA 202T were highly prevalent in 2009 pH1N1 strains isolated during the 3rd and most severe wave (2010 to 2011) of the pandemic in terms of hospitalizations and deaths among adults compared to the first two waves in the United Kingdom (40). Further, most HH05-specific sites have almost disappeared among circulating strains in the postpandemic phase.…”

Amino acid substitution D222N from fatal influenza infection affects receptor-binding properties of the influenza A(H1N1)pdm09 virus

“…We also addressed the relevance of the mutation S185N, located at the antigenic site Sb (Xu et al, 2010). A different amino acid change, S185T, is reported to be conserved in all A (H1N1)pdm09 viruses in current circulation, and its role in the enhancement of receptor-binding avidity of the early A(H1N1) pdm09 virus has been addressed (de Vries et al, 2013;ECDC 2013;Elderfield et al, 2014;Klimov et al, 2012).…”

Ferret airway epithelial cell cultures support efficient replication of influenza B virus but not mumps virus

“…They were incubated at 37 uC at 5 % CO 2 in maintenance media supplied by Epithelix. (Elderfield et al, 2014).…”