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Nat Commun. 2015 Aug 6;6:7952. doi: 10.1038/ncomms8952.

Phylodynamics of H1N1/2009 influenza reveals the transition from host adaptation to immune-driven selection.

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Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore.
Division of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas, Houston, Texas 77030, USA.
World Health Organisation Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria 3000, Australia.
Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, Singapore 119074, Singapore.
Department of Pathology, Singapore General Hospital, Singapore 169608, Singapore.
Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.
Duke Global Health Institute, Duke University, Durham, North Carolina 27708, USA.


Influenza A H1N1/2009 virus that emerged from swine rapidly replaced the previous seasonal H1N1 virus. Although the early emergence and diversification of H1N1/2009 is well characterized, the ongoing evolutionary and global transmission dynamics of the virus remain poorly investigated. To address this we analyse >3,000 H1N1/2009 genomes, including 214 full genomes generated from our surveillance in Singapore, in conjunction with antigenic data. Here we show that natural selection acting on H1N1/2009 directly after introduction into humans was driven by adaptation to the new host. Since then, selection has been driven by immunological escape, with these changes corresponding to restricted antigenic diversity in the virus population. We also show that H1N1/2009 viruses have been subject to regular seasonal bottlenecks and a global reduction in antigenic and genetic diversity in 2014.

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