Metagenomic analysis of the RNA fraction of the fecal virome indicates high diversity in pigs infected by porcine endemi
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RESEARCH
Open Access
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 Qi Chen1†, Leyi Wang2†, Ying Zheng1, Jianqiang Zhang1, Baoqing Guo1, Kyoung-Jin Yoon1, Phillip C. Gauger1, Karen M. Harmon1, Rodger G. Main1 and Ganwu Li1*
Abstract Background: Emergence and re-emergence of porcine epidemic diarrhea virus (PEDV) in North America, Asia and Europe has caused severe economic loss to the global swine industry. However, the virome of PEDV infected pigs and its effect on disease severity remains unknown. The advancements of sequencing technology have made it possible to characterize the entire microbiome of different body sites for any host. Methods: The objective of this study was to characterize the RNA virome in PEDV-positive pigs using the hypothesis-free metagenomics approach based on next-generation sequencing. Specifically, 217 PEDV-positive swine fecal swab samples collected from diarrheic piglets over 17 US states during 2015–2016 were analyzed. Results: A Kraken algorithm-based bioinformatics analysis revealed the presence of up to 9 different RNA genera besides PEDV (Alphacoronavirus genus), including Mamastrovirus (52%, 113/217), Enterovirus (39%, 85/217), Sapelovirus (31%, 67/217), Posavirus (30%, 66/217), Kobuvirus (23%, 49/217), Sapovirus (13%, 28/217), Teschovirus (10%, 22/217), Pasivirus (9%, 20/217), and Deltacoronavirus (3%, 6/217). There were 58 out of 217 piglets (27%) have PEDV infection alone whereas the remaining 159 (73%) shed 2 up to 9 different viruses. Conclusion: These findings demonstrated that PEDV infected diarrheic pigs had an extensive RNA viral flora consisting of four different families: Astroviridae, Picornaviridae, Caliciviridae, and Coronaviridae. Keywords: PEDV, RNA virome, Coinfection, Metagenomic analysis
Background Diarrhea in pigs, especially in piglets, is a major issue affecting global swine industry. A diverse array of viral pathogens are implicated in piglet diarrhea, including porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), porcine deltacoronavirus (PDCoV), porcine rotavirus (PRoV), porcine bocavirus, Aichivirus C (formerly named as porcine kobuvirus 1 [PKV-1]), porcine sapovirus, porcine sapelovirus (PSV), * Correspondence: [email protected] † Qi Chen and Leyi Wang contributed equally to this work. 1 Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1907 ISU C-Drive, VMRI#1, Ames, IA 50011, USA Full list of author information is available at the end of the article
and porcine astrovirus as well as others [1]. Among them, PEDV, TGEV, PDCoV and PRoV have been well characterized for their role in clinical diarrhea and have been considered as major swine enteric viral pathogens while the causative role of the other agents in diarrheic disease has been characterized to a significantly less extent or remains to be further studied. PEDV is an enveloped, si
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