title: Origins of the 2009 H1N1 influenza pandemic in swine in Mexico.
abstract: Asia is considered an important source of influenza A virus (IAV) pandemics, owing to large, diverse viral reservoirs in poultry and swine. However, the zoonotic origins of the 2009 A/H1N1 influenza pandemic virus (pdmH1N1) remain unclear, due to conflicting evidence from swine and humans. There is strong evidence that the first human outbreak of pdmH1N1 occurred in Mexico in early 2009. However, no related swine viruses have been detected in Mexico or any part of the Americas, and to date the most closely related ancestor viruses were identified in Asian swine. Here, we use 58 new whole-genome sequences from IAVs collected in Mexican swine to establish that the swine virus responsible for the 2009 pandemic evolved in central Mexico. This finding highlights how the 2009 pandemic arose from a region not considered a pandemic risk, owing to an expansion of IAV diversity in swine resulting from long-distance live swine trade.
authors.affiliation: Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, United States.|Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, United States.
authors.forename: Ignacio
authors.initials: I
authors.lastname: Mena
authors.affiliation: Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, United States.
authors.forename: Martha I
authors.initials: MI
authors.lastname: Nelson
authors.affiliation: Laboratorio Avi-Mex, Mexico City, Mexico.
authors.forename: Francisco
authors.initials: F
authors.lastname: Quezada-Monroy
authors.affiliation: Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States.
authors.forename: Jayeeta
authors.initials: J
authors.lastname: Dutta
authors.affiliation: Laboratorio Avi-Mex, Mexico City, Mexico.
authors.forename: Refugio
authors.initials: R
authors.lastname: Cortes-Fernández
authors.affiliation: Laboratorio Avi-Mex, Mexico City, Mexico.
authors.forename: J Horacio
authors.initials: JH
authors.lastname: Lara-Puente
authors.affiliation: Laboratorio Avi-Mex, Mexico City, Mexico.
authors.forename: Felipa
authors.initials: F
authors.lastname: Castro-Peralta
authors.affiliation: Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States.
authors.forename: Luis F
authors.initials: LF
authors.lastname: Cunha
authors.affiliation: Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, United States.|Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, United States.|Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, United States.|Department of Microbiology and Immunology, Rega Institute, University of Leuven, Leuven, Belgium.
authors.forename: Nídia S
authors.identifier: 0000-0002-2106-1166
authors.initials: NS
authors.lastname: Trovão
authors.affiliation: Laboratorio Avi-Mex, Mexico City, Mexico.
authors.forename: Bernardo
authors.initials: B
authors.lastname: Lozano-Dubernard
authors.affiliation: Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, United States.|Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.|Centre for Immunology, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom.
authors.forename: Andrew
authors.initials: A
authors.lastname: Rambaut
authors.affiliation: Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States.
authors.forename: Harm
authors.initials: H
authors.lastname: van Bakel
authors.affiliation: Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, United States.|Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, United States.|Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, United States.
authors.forename: Adolfo
authors.identifier: 0000-0002-6551-1827
authors.initials: A
authors.lastname: García-Sastre
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D007251:Influenza, Human / Q000453:epidemiology / Q000821:virology*; D008800:Mexico; D009976:Orthomyxoviridae Infections / Q000662:veterinary* / Q000821:virology; D058873:Pandemics; D017422:Sequence Analysis, DNA; D013552:Swine; D013553:Swine Diseases / Q000453:epidemiology / Q000821:virology*; D015047:Zoonoses / Q000453:epidemiology / Q000821:virology*
keywords: 2009 pandemic; epidemiology; evolution; global health; infectious disease; influenza A virus; microbiology; phylogeography; swine; virus; zoonosis