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

Porcine sapelovirus was molecularly characterized in this study. One complete genomic sequence of the PSV (USA/IA033375/2015) was obtained in this study, and the genomic organization was described in detail elsewhere [16] . Phylogenetic analysis based on the PDCoV 64 5 1 0 0 0 1 0 0 2 Enterovirus 1035 143 24 7 1 2 0 1 0 0 Kobuvirus 638 76 36 13 6 10 1 2 1 3 Mamastrovirus 3880 362 128 71 61 11 7 (Fig. 4b) . Second, the other two Korean strains (SK/ KS04105 and SK/KS055217) and USA/ISU-SHIC/2016 strain have a 9-nt insertion (AGARCARWT) between position 2681 and 2682which are the same as the 3′ end of the 24-nt insertion above. Interestingly, these two strains also have a 9-nt deletion (AACCCAGAC) between position 2674 and 2681 right before the 9-nt insertion, as compared to the other six strains. Therefore, this 9-nt deletion and insertion resulted in one aa mutation from TQT to EQL (Fig. 4b) . Third, as compared to the UK V13 strain, all the other 9 strains have three "T" separated insertions between position 6246 and 6255 of the polyprotein gene, leading to changes in nt sequence from "TTGCGCGA" to "TTTGCTGCTGA", which results in one aa insertion and altering the aa sequence from "LR" to "FAA".