Metagenomic analysis of the RNA fraction of the fecal virome indicates high diversity in pigs infected by porcine endemic diarrhea virus in the United States

Chen, Qi; Wang, Leyi; Zheng, Ying; Zhang, Jianqiang; Guo, Baoqing; Yoon, Kyoung-Jin; Gauger, Phillip C.; Harmon, Karen M.; Main, Rodger G.; Li, Ganwu

Next-generation sequencing technology, characterized by massive sequence output, low cost, and short turnaround time, have significantly changed the path of new pathogen discoveries. There are various potential applications of HTS in clinical virology, such as whole viral genome reconstruction, the discovery of uncharacterized and/or novel viral pathogens, the detection of mixed infections, the identification of viral variants and quasispecies, outbreak tracking, the disease surveillance, and the characterization of host responses. These applications have revolutionized infectious disease diagnostics and clinical microbiology. Therefore, HTS technology has obvious advantages over traditional diagnostic methods. However, most clinical samples are very "dirty" and composed of both host and microbial nucleic acids; in most cases, 99% of nucleic acid contained in samples belong to either the host or other microorganisms of no interest. As a result, searching for particular microbial nucleic acids is similar to searching for "a needle in a haystack". Therefore, metagenomics approach for mixed infection detection and novel viral discovery relies extensively on bioinformatics to tackle the huge amounts of sequence data.