Data from: Origins of the 2009 H1N1 influenza pandemic in swine in Mexico
Mena, Ignacio, Icahn School of Medicine at Mount Sinai
Nelson, Martha I., National Institutes of Health
Quezada-Monroy, Francisco, Laboratorio Avi-Mex, Mexico City, Mexico
Dutta, Jayeeta, Icahn School of Medicine at Mount Sinai
Cortes-Fernández, Refugio, Icahn School of Medicine at Mount Sinai
Lara-Puente, J. Horacio, Laboratorio Avi-Mex, Mexico City, Mexico
Castro-Peralta, Felipa, National Institutes of Health
Cunha, Luis F., Icahn School of Medicine at Mount Sinai
Sequeira-Trovão, Nídia, KU Leuven, National Institutes of Health
Lozano-Dubernard, Bernardo, Laboratorio Avi-Mex, Mexico City, Mexico
Rambaut, Andrew, University of Edinburgh, National Institutes of Health
van Bakel, Harm, Icahn School of Medicine at Mount Sinai
García-Sastre, Adolfo, Icahn School of Medicine at Mount Sinai
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.
Usage Notes
XML files. Datasets for swine influenza phylogenetic analysis
Datasets containing sets of sequences used for the phylogenetic analysis of the different genomic segments of swine influenza
XML files.zip
Supplementary Data file 1
acknowledgement of the authors and research laboratories that contributed sequence data
Data set 1.csv
Supplementary Data file 2
acknowledgement of the authors and research laboratories that contributed sequence data
Data set 2.csv
Supplementary data file 3
2009 pandemic H1N1 genome sequences used in the analysis
Data set 3.csv
genebank acc numbers
accession numbers of the 58 new genomes of swine influenza from Mexico analyzed in this study
Figure 1 - source data 1
source data used in figure 1 of the manuscript
Figure 2 - figure supplement 1
Characteristics of the 58 swIAVs collected in Mexico for this study.
Figure 6 - source data 1
Pairwise information on imports of live swine from specific countries is available from 1996-2012. Data available from the United Nations' Commodity Trade Statistics Database, http://comtrade.un.org.
Figure 7- source data 1
Times to the most recent common ancestor (tMRCA) and posterior probabilities (>0.01) used in figure 7
Figure 7--source data 1.csv
Location
