Molecular evolution, diversity and adaptation of H7N9 viruses in China during 2013-2017

Lu, J and Raghwani, J and Pryce, R and Bowden, T A and Thézé, J and Huang, S and Song, Y and Zou, L and Liang, L and Bai, R and Jing, Y and Zhou, P and Kang, M and Yi, L and Wu, J and Pybus, O G and Ke, C (2018) Molecular evolution, diversity and adaptation of H7N9 viruses in China during 2013-2017. Emerging Infectious Diseases, 24 (10).

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The substantial increase in prevalence and emergence of antigenically divergent or highly pathogenic influenza A(H7N9) viruses during 2016–17 raises concerns about the epizootic potential of these viruses. We investigated the evolution and adaptation of H7N9 viruses by analyzing available data and newly generated virus sequences isolated in Guangdong Province, China, during 2015–2017. Phylogenetic analyses showed that circulating H7N9 viruses belong to distinct lineages with differing spatial distributions. Hemagglutination inhibition assays performed on serum samples from patients infected with these viruses identified 3 antigenic clusters for 16 strains of different virus lineages. We used ancestral sequence reconstruction to identify parallel amino acid changes on multiple separate lineages. We inferred that mutations in hemagglutinin occur primarily at sites involved in receptor recognition or antigenicity. Our results indicate that highly pathogenic strains likely emerged from viruses circulating in eastern Guangdong Province during March 2016 and are associated with a high rate of adaptive molecular evolution.

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