Multiple Natural Substitutions in Avian Influenza A Virus PB2 Facilitate Efficient Replication in Human Cells

Abstract

A strong restriction of the avian influenza A virus polymerase in mammalian cells generally limits viral host-range switching. Although substitutions like E627K in the PB2 polymerase subunit can facilitate polymerase activity to allow replication in mammals, many human H5N1 and H7N9 viruses lack this adaptive substitution. Here, several previously unknown, naturally occurring, adaptive substitutions in PB2 were identified by bioinformatics, and their enhancing activity was verified using in vitro assays. Adaptive substitutions enhanced polymerase activity and virus replication in mammalian cells for avian H5N1 and H7N9 viruses but not for a partially human-adapted H5N1 virus. Adaptive substitutions toward basic amino acids were frequent and were mostly clustered in a putative RNA exit channel in a polymerase crystal structure. Phylogenetic analysis demonstrated divergent dependency of influenza viruses on adaptive substitutions. The novel adaptive substitutions found in this study increase basic understanding of influenza virus host adaptation and will help in surveillance efforts. IMPORTANCEInfluenza viruses from birds jump the species barrier into humans relatively frequently. Such influenza virus zoonoses may pose public health risks if the virus adapts to humans and becomes a pandemic threat. Relatively few amino acid substitutions-most notably in the receptor binding site of hemagglutinin and at positions 591 and 627 in the polymerase protein PB2-have been identified in pandemic influenza virus strains as determinants of host adaptation, to facilitate efficient virus replication and transmission in humans. Here, we show that substantial numbers of amino acid substitutions are functionally compensating for the lack of the above-mentioned mutations in PB2 and could facilitate influenza virus emergence in humans.

How host genetics dictates successful viral zoonosis

“…Mutations in viral PB2 PB2-E627K, others observed as well [63][64][65] SIVcpz APOBEC3H restriction factor…”

Evaluation of the Biological Properties and Cross-Reactive Antibody Response to H10 Influenza Viruses in Ferrets

“…in the lungs. To determine if the H10 viruses carried mutations or gene constellations that are associated with replication in mammals, we analyzed the available PB2 gene sequences for known mammalian-adaptive mutations (33). As shown in Table 1 and as previously described (8,21), only 3 viruses carried known mutations, and the JX/13 virus had internal protein gene segments donated by H9N2 viruses (21).…”

“…For analysis of HA sequences, the signal peptide was deleted from the HA, and unique mutations identified in the H10 sequences were converted to H3 numbering (57). For analysis of the PB2 sequences, all available sequences were analyzed for previously described mutations (33).…”

Codon adaptation biases among sylvatic and urban genotypes of Dengue virus type 2

“…In fact, recent outbreaks caused by other emerging viruses [e.g. Ebola virus, Influenza A virus (H1N1), Middle East respiratory syndrome coronavirus (MERS-CoV)], have occurred due to the zoonotic spillover and adaptation of the virus to replication in human cells (Dudas et al, 2018;Mänz et al, 2016;Plowright et al, 2017;Urbanowicz et al, 2016). In this context, as previous analyses have suggested (Moncayo et al, 2004), our findings support the notion that for the sylvatic strains to effectively colonize the urban environment, the virus needs a number of silent, adaptive nucleotide substitutions to optimize the codon usage to invertebrate host cells, while maintaining a compositional base balance suitable for efficient alternate spread among both human and insect hosts.…”