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.DOI: http://dx.doi.org/10.7554/eLife.16777.001

Evidence of Intercontinental Spread and Uncommon Variants of Low-Pathogenicity Avian Influenza Viruses in Ducks Overwintering in Guatemala

“…Genome assembly was refined after several iterations of reference mapping to resolve mixed infections (when present); for the internal gene segments, this was achieved by including two or more reference sequences with sequence identity of <97% for the “mixed” segment and adjusting kmer size in the alignment parameters. The remaining viruses ( n = 23) were sequenced by high-throughput Illumina sequencing as previously described (52). For this set of genomes, it was not possible to resolve individual gene variants for the internal gene segments; thus, mixed infections were identified by observing a high frequency (>10%) of single nucleotide variants across the entire length of one or more gene segments.…”

Human Mobility and the Global Spread of Infectious Diseases: A Focus on Air Travel

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Improved detection of influenza A virus from blue‐winged teals by sequencing directly from swab material

“…A 100 µl volume of either allantoid fluid or swab material was used for RNA extraction using the MagNA Pure LC RNA Isolation Kit-High Performance (Roche) on the MagNaPure LC instrument (Roche). The MS-RT-PCR was set up with minor modifications from a previously described method (Mena et al, 2016;Zhou et al, 2009). Briefly, 2.5 µl of RNA was used as template in a 25 µl MS-RT-PCR (Superscript III high-fidelity RT-PCR kit, ThermoFisher Co.); primer sequences and concentrations were as follows: Opti1-F1 5′-GTTACGCGCCAGCAAAAGCAGG-3′ (0.06 µM); Opti1-F2 5′-GTTACGCGCCAGCGAAAGCAGG-3′ (0.14 µM); Opti1-R1 5′-GTTACGCGCCAGTAGAAACAAGG-3′ (0.2 µM).…”

“…Genome assembly was performed using a pipeline previously developed at Icahn School of Medicine at Mount Sinai by Harm Van Bakel and described (Mena et al, 2016). Briefly, low-quality sequences and adapters were removed by Cutadapt (Martin, 2011) from paired fastq files.…”