Large-scale sequence analysis reveals novel human-adaptive markers in PB2 segment of seasonal influenza A viruses

Abstract

To elucidate the adaptive strategies of influenza A viruses (IAVs) to human, we proposed a computational approach to identify human-adaptive mutations in seasonal IAVs, which have not been analyzed comprehensively. We compared representative PB2 sequences of 1425 avian IAVs and 2176 human IAVs and identified a total of 42 human-adaptive markers, including 28 and 31 markers in PB2 proteins of seasonal viruses H1N1 and H3N2, respectively. Notably, this comprehensive list encompasses almost all the markers identified in prior computational studies and 21 novel markers including an experimentally verified mutation K526R, suggesting the predictive power of our method. The strength of our analysis derives from the enormous amount of recently available sequences as well as the recognition that human-adaptive mutations are not necessarily conserved across subtypes. We also utilized mutual information to profile the inter-residue coevolution in PB2 protein. A total of 35 and 46 coevolving site pairs are identified in H1N1 and H3N2, respectively. Interestingly, 13 out of the 28 (46.4%) identified markers in H1N1 and 16 out of the 31 (51.6%) in H3N2 are embraced in the coevolving pairs. Many of them are paired with well-characterized human-adaptive mutations, indicating potential epistatic effect of these coevolving residues in human adaptation. Additionally, we reconstructed the PB2 evolutionary history of seasonal IAVs and demonstrated the distinct adaptive pathway of PB2 segment after reassortment from H1 to H3 lineage. Our study may provide clues for further experimental validation of human-adaptive mutations and shed light on the human adaptation process of seasonal IAVs.

Inventory of molecular markers affecting biological characteristics of avian influenza A viruses

“…However, we do not consider this inventory as an exhaustive list. Several studies computationally predict molecular markers of viral adaptation to humans [22–26]. While this work is extremely valuable, experimental validation of the majority of the markers described in these studies is not available and, therefore, necessitated exclusion from this data summary.…”

“…First, the inventory only includes experimentally validated (in vitro or in vivo) markers/mutations. As stated previously, several studies utilize in silico approaches to predict molecular markers of viral adaptation to humans [22–26]. This work is extremely valuable and findings from these computational studies guide future research.…”

The substitution of T271A in PB2 protein could enhance the infectivity and pathogenicity of Eurasian avian-like H1N1 swine influenza viruses in mice

“…Besides, the PB2-T271A mutation could contribute to the efficient transmission of 2009 H1N1 pandemic influenza virus in guinea pigs [9]. Similar results were found in H7N9 and H5N1 influenza viruses [11][12][13]. Besides, the combination of the substitutions PB2-T271A and 590/591 SR increased the viral replication and adaptation of the 2009 pandemic H1N1 and triple reassortant swine influenza viruses (SIVs) in mammals [14].…”

Co-circulation of multiple influenza A reassortants in swine harboring genes from seasonal human and swine influenza viruses

“…As for the aa differences observed between the internal gen cassette of the Sw-L cluster and the sequences located outside the cluster, the T76A mutation in the PB2 protein has been linked an elevated interferon response 64 . Furthermore, the M283I aa change in the PB2 protein has previously been linked to decreased virulence of avian H5 IAV 65,66 and the N456S aa change has, on the other hand, been linked to human adaptations of the H3N2 lineage 67 . For the PB1 protein, the M317I aa change has been identified in a H2N2 after multiple passaging in chicken eggs to create a temperature sensitive IAV strain 68 .…”