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

All detected viruses in this study belong to four viral families (Picornaviridae, Coronaviridae, Astroviridae, Caliciviridae), and 6 out of the 10 virus genera belong to Picornaviridae family (Enterovirus, Posavirus, Sapelovirus, Kobuvirus, Teschovirus, and Pasivirus). Such findings are similar to a previous report [27] . This may have been attributed to the well-understood fact that picornaviruses are highly resistant in the environment and as such, usually survive much longer than other viruses [30] . The environmentally resistant picornaviruses can have a longer exposure time in pigs, increasing the odds of infection and their prevalence when compared to other viruses. Furthermore, the viruses also have better odds of detection in the environment after shedding. Both of these factors can increase the detection rate of picornaviruses from clinical samples, as compared to other viruses. Although the longer surviving feature of picornaviruses makes them easier to detect, such nature may bias their proportion in mixed infections.