title: Phylodynamics of H1N1/2009 influenza reveals the transition from host adaptation to immune-driven selection.
abstract: 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.
authors.affiliation: Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore.
authors.forename: Yvonne C F
authors.initials: YCF
authors.lastname: Su
authors.affiliation: 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.
authors.forename: Justin
authors.identifier: http://orcid.org/0000-0001-7572-4300
authors.initials: J
authors.lastname: Bahl
authors.affiliation: Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore.
authors.forename: Udayan
authors.initials: U
authors.lastname: Joseph
authors.affiliation: Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore.
authors.forename: Ka Man
authors.initials: KM
authors.lastname: Butt
authors.affiliation: World Health Organisation Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria 3000, Australia.
authors.forename: Heidi A
authors.initials: HA
authors.lastname: Peck
authors.affiliation: Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, Singapore 119074, Singapore.
authors.forename: Evelyn S C
authors.initials: ESC
authors.lastname: Koay
authors.affiliation: Department of Pathology, Singapore General Hospital, Singapore 169608, Singapore.
authors.forename: Lynette L E
authors.initials: LLE
authors.lastname: Oon
authors.affiliation: World Health Organisation Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria 3000, Australia.
authors.forename: Ian G
authors.initials: IG
authors.lastname: Barr
authors.affiliation: Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore.|World Health Organisation Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria 3000, Australia.|Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.
authors.forename: Dhanasekaran
authors.initials: D
authors.lastname: Vijaykrishna
authors.affiliation: Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore.|World Health Organisation Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria 3000, Australia.|Duke Global Health Institute, Duke University, Durham, North Carolina 27708, USA.
authors.forename: Gavin J D
authors.identifier: http://orcid.org/0000-0001-5031-468X
authors.initials: GJD
authors.lastname: Smith
mesh_terms: D000220:Adaptation, Biological; D000818:Animals; D004285:Dogs; D019143:Evolution, Molecular; D016679:Genome, Viral; D054884:Host-Pathogen Interactions / Q000235:genetics* / Q000276:immunology; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000235:genetics* / Q000276:immunology; D061985:Madin Darby Canine Kidney Cells; D008969:Molecular Sequence Data; D058873:Pandemics; D010802:Phylogeny; D058974:Phylogeography; D012641:Selection, Genetic