Detection of Bovine Group A Rotavirus Using Rapid Antigen Detection Kits, RT-PCR and Next-Generation DNA Sequencing

MINAMI-FUKUDA, Fujiko; NAGAI, Makoto; TAKAI, Hikaru; MURAKAMI, Toshiaki; OZAWA, Tadashi; TSUCHIAKA, Shinobu; OKAZAKI, Sachiko; KATAYAMA, Yukie; OBA, Mami; NISHIURA, Naomi; SASSA, Yukiko; OMATSU, Tsutomu; FURUYA, Tetsuya; KOYAMA, Satoshi; SHIRAI, Junsuke; TSUNEMITSU, Hiroshi; FUJII, Yoshiki; KATAYAMA, Kazuhiko; MIZUTANI, Tetsuya

Finally, we demonstrated the detection of RVA from fecal samples using a next-generation DNA sequencer. Exhaustive investigation is useful for directly detecting pathogenic viruses without advance genetic information [2, 10, 19] . In this study, all samples yielded reads of the RVA genome in spite of being negative for RT-PCR. Moreover, the RVA reads from two samples covered all 11 segments of RVA, and the VP4 and VP7 reads could be divided into genotypes using CLC Genomics Workbench by mapping to reference sequences of representative strains of VP4 and VP7 genotypes. Although the cost and expensive equipment make it unlikely that NGS will soon be the diagnostic standard worldwide, the present investigation by RNA-seq is useful for less sequence-depend detection of bovine RVA from fecal samples and screening of the genotypes.