Phylodynamics of Influenza A/H1N1pdm09 in India Reveals Circulation Patterns and Increased Selection for Clade 6b Residues and Other High Mortality Mutants

The severity and observed case fatality ratio (CFR) of influenza A/H1N1pdm09 in India exceeds current global estimates. Reasons for this beyond health resource constraints remain unclear. This study aimed to investigate genetic factors that could explain the high CFR while also quantifying transmission dynamics. We collected all full-length hemagglutinin (HA) A/H1N1pdm09 sequences sampled in India from 2009 to 2017 from GISAID (N=613). Using BEASTv1.10.4 we calculated dN/dS ratios, evaluated transmission routes, and quantified the effect of various factors on transmission. To control for sampling bias, we replicated the analysis across five randomly down-sampled subsets. We compared dN/dS ratios to two subsets (N=4,063 taxa each) randomly drawn from a global sample of all full-length HA A/H1N1pdm09 sequences uploaded to GISAID from the same period (N=21,209). We found increased dN/dS ratios at several residue positions within the antigenic domains of HA. Selection at position 222 was up to eight times greater relative to globally circulating strains. Increased ratios were also found at sites 186 and 256 where no selection was detected among either global subset. Maharashtra state was the most significant state spreading A/H1N1pdm09 to other states in both the complete and down sampled replicate analysis. Commercial airline travel was associated with increased inter-state transmission. We found increased dN/dS ratios in India at several sites with residue changes associated with increased disease severity (D222N/G, S84N, A265T) relative to isolates circulating globally that might explain the increased CFR in India. Site 186 has significant antigenic implications at equivalent positions in A/H3N2 (site 189) which warrants further investigation. The quantification of commercial passenger travel and identification of Maharashtra as a key source of A/H1N1pdm09 transmission indicates opportunities for disease control. These results have important implications for future A/H1N1pdm09 surveillance and control within India but also risk prediction around the world.