Complete-Proteome Mapping of Human Influenza A Adaptive Mutations: Implications for Human Transmissibility of Zoonotic Strains

Background

There is widespread concern that H5N1 avian influenza A viruses will emergeas a pandemic threat, if they become capable of human-to-human (H2H)transmission. Avian strains lack this capability, which suggests that itrequires important adaptive mutations. We performed a large-scalecomparative analysis of proteins from avian and human strains, to produce acatalogue of mutations associated with H2H transmissibility, and to detecttheir presence in avian isolates.

Methodology/Principal Findings

We constructed a dataset of influenza A protein sequences from 92,343 publicdatabase records. Human and avian sequence subsets were compared, using amethod based on mutual information, to identifycharacteristic sites where human isolates presentconserved mutations. The resulting catalogue comprises 68 characteristicsites in eight internal proteins. Subtype variability prevented theidentification of adaptive mutations in the hemagglutinin and neuraminidaseproteins. The high number of sites in the ribonucleoprotein complex suggestsinterdependence between mutations in multiple proteins. Characteristic sitesare often clustered within known functional regions, suggesting theirfunctional roles in cellular processes. By isolating and concatenatingcharacteristic site residues, we defined adaptationsignatures, which summarize the adaptive potential of specificisolates. Most adaptive mutations emerged within three decades after the1918 pandemic, and have remained remarkably stable thereafter. Two lineageswith stable internal protein constellations have circulated among humanswithout reassorting. On the contrary, H5N1 avian and swine viruses reassortfrequently, causing both gains and losses of adaptive mutations.

Conclusions

Human host adaptation appears to be complex and systemic, involving nearlyall influenza proteins. Adaptation signatures suggest that the ability ofH5N1 strains to infect humans is related to the presence of an unusuallyhigh number of adaptive mutations. However, these mutations appear unstable,suggesting low pandemic potential of H5N1 in its current form. In addition,adaptation signatures indicate that pandemic H1N1/09 strain possessesmultiple human-transmissibility mutations, though not an unusually highnumber with respect to swine strains that infected humans in the past.Adaptation signatures provide a novel tool for identifying zoonotic strainswith the potential to infect humans.