Viral ecology determined by metagenomic sequencing within multi-sourced swine markets located in the southeastern United States

摘要

Commingled markets are often located near live production sites, and represent a collection point for diseases that could spread to the region. Surveillance of markets, where pigs from multiple sources are commingled, utilizing metagenomics sequencingcould be useful in identifying emerging/reemerging pathogens. Metagenomic sequencing can be used to identify viruses without a priori sequence information. This new technology is different from traditional sequencing methods because it allows thousandsof base pairs to be sequenced without the use of a known primer. This permits for a more comprehensive view of all viruses present in a sample. When compared to the traditional Sanger method of sequencing, metagenomic sequencing creates almost one million reads of shot tet sequences and is cheaper per base pair. The Sanger method cost approximately $0.30 per base pair while metagenomic sequencing costs around $0.02 per base pair. Metagenomic sequencing has been used to identify several emerging pathogens in swine such as enterovirus G and a novel influenza virus in swine. Metagenomic sequencing can also be used to identify bacterial genomes although that was not the goal of this study. The objective of this study was to identify viruses found in pigs sent to markets in the southeast region of the United States.