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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.

Original publication




Journal article


Emerg Infect Dis

Publication Date





1795 - 1805


China, H7N9, adaptation, avian influenza, avian influenza virus, diversity, hemagglutination inhibition assay, influenza, molecular epidemiology, molecular evolution, phylogenetics, respiratory infections, virus subtypes, viruses, Amino Acid Sequence, Animals, Antigenic Variation, Birds, China, Evolution, Molecular, Genetic Variation, Genome, Viral, Genotype, Geography, Medical, History, 21st Century, Humans, Influenza A Virus, H7N9 Subtype, Influenza in Birds, Influenza, Human, Phylogeny, RNA, Viral