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

We were able to obtain 487 k raw reads (112 Mb data) per sample on average, and 386 k reads (67 Mb data) after raw data trimming. Fifty-eight out of the 217 sequenced fecal swab samples (27%) were found to contain PEDV as the only RNA virus under study conditions (Fig. 2 Fig. 2 ). One hundred and forty-eight samples (68%) contained at least 2 to 6 different viral genera while 10 samples (5%) had 7 to 8 viral genera detected including alphacoronavirus. There was no sample found to be infected with all 10 detected viral genera in the current study. The above taxonomic classification results from Kraken analysis based on nucleic acid level were also confirmed by Kaiju on protein level, as shown by the same total 10 viral genera detection, and the high agreement (average agreement rate = 90.5%) in taxonomic classification between the two programs.