Origins of the 2009 H1N1 influenza pandemic in swine in Mexico
Ignacio Mena,
Martha I Nelson,
Francisco Quezada-Monroy,
Jayeeta Dutta,
Refugio Cortes-Fernández,
J Horacio Lara-Puente,
Felipa Castro-Peralta,
Luis F Cunha,
Nídia S Trovão,
Bernardo Lozano-Dubernard,
Andrew Rambaut,
Harm van Bakel,
Adolfo García-Sastre
Affiliations
Ignacio Mena
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
Martha I Nelson
Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, United States
Francisco Quezada-Monroy
Laboratorio Avi-Mex, Mexico City, Mexico
Jayeeta Dutta
Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
Refugio Cortes-Fernández
Laboratorio Avi-Mex, Mexico City, Mexico
J Horacio Lara-Puente
Laboratorio Avi-Mex, Mexico City, Mexico
Felipa Castro-Peralta
Laboratorio Avi-Mex, Mexico City, Mexico
Luis F Cunha
Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
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
Bernardo Lozano-Dubernard
Laboratorio Avi-Mex, Mexico City, Mexico
Andrew Rambaut
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
Harm van Bakel
Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
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
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.
