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

Complete sequences of the polyprotein gene were obtained for four kobuvirus strains (US/ISU20245/2015, US/ISU20448-1/201, US/ISU25220/2015, US/ISU41447/ 2015) in this study. Kobuvirus has been detected in multiple species [19] , and the 4 kobuvirus sequences identified in this study were genetically most closely related to Aichivirus C. The polyprotein gene of ISU20245, ISU20448-1, ISU25220, and ISU41447is 7470-nt, 7467-nt, 7377-nt, and 7377-nt long, respectively. All polyprotein genes of each Aichivirus C compose L, VP0, VP3, VP1, P2 (2A-2C), and P3 (3A-3D) genes similar to other reported Aichivirus C sequences [19] [20] [21] Comparing the Aichivirus C polyprotein genes available in GenBank revealed all Aichivirus C could phylogenetically be classified into three genogroups with the representative HUN/S-1HUN/2007 strain, the first Aichivirus C (PKV-1) reported from Hungary in 2007, belonging to Group II (Fig. 5a) It was previously reported that the HUN/S-1HUN/ 2007 strain encoded two continuous copies of a 30-aa-long motif insertion within the 2B region, AANR-VAESIETTAS(/T)V(/A)VREADLARST.