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

To further characterize each virus, all de-multiplexed reads of an interested taxon were filtered, extracted, and de novo assembled with SPAdes Genome Assembler version 3.11.1 for Linux with the assembly options for paired end reads and Burrows Wheeler Aligner mismatch correction [14] . To further validate the assembled contigs, the contigs assembled from each viral genus were blasted against a customized database built specifically for that genus, with the cutoff of 80% similarity and 70% coverage. Totally 9 databases were built, respectively, for each specific virus genus that we detected in the current study, and each database included all public sequences of a genus from NCBI based on taxonomy search. All raw sequencing data obtained from MiSeq has been deposited to NCBI SRA database (Project name: PRJNA432752, SRA accession: SRP132749). Validated contigs were used for further statistic analysis.