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Since March 2013, three waves of human infection with avian influenza A(H7N9) virus have been detected in China. To investigate virus transmission within and across epidemic waves, we used surveillance data and whole-genome analysis of viruses sampled in Guangdong during 2013-2015. We observed a geographic shift of human A(H7N9) infections from the second to the third waves. Live poultry market interventions were undertaken in epicenter cities; however, spatial phylogenetic analysis indicated that the third-wave outbreaks in central Guangdong most likely resulted from local virus persistence rather than introduction from elsewhere. Although the number of clinical cases in humans declined by 35% from the second to the third waves, the genetic diversity of third-wave viruses in Guangdong increased. Our results highlight the epidemic risk to a region reporting comparatively few A(H7N9) cases. Moreover, our results suggest that live-poultry market interventions cannot completely halt A(H7N9) virus persistence and dissemination.

Original publication




Journal article


Emerg Infect Dis

Publication Date





2104 - 2112


A(H7N9), China, Influenza virus, influenza, live-poultry market, phylogeny, phylogeography, viruses, Animals, Bayes Theorem, China, Disease Outbreaks, Genetic Variation, Genotype, Humans, Incidence, Influenza A Virus, H7N9 Subtype, Influenza, Human, Phylogeny, Population Surveillance, Poultry, RNA, Viral, Spatio-Temporal Analysis