First isolation and genomic characterization of bovine parechovirus from faecal samples of cattle in Japan

Abstract

A novel picornavirus was isolated from the faeces of a diarrhoeic cow using MA-104 cells at the third blind passage. This virus, named Den1/2021/JPN, was completely sequenced using total RNA from the cell culture supernatant by deep sequencing. The genome of Den1/2021/JPN had a standard picornavirus genome organisation with conserved picornaviral motifs. The 5′ untranslated region harboured a type-II internal ribosomal entry site. Den1/2021/JPN was most closely related to a bovine parechovirus (Bo_ParV) named cow/2018/4, which has been recently identified in publicly available databases. Phylogenetic analyses and pairwise sequence comparison revealed that Den1/2021/JPN and Bo_ParV cow/2018/4 clustered with parechoviruses and were most closely related to Parechovirus E identified in birds of prey, exhibiting nucleotide sequence similarity of 64.2–64.5 %, 58.6–59.7 % and 66.3–66.4 % in the polyprotein, P1 and 2C+3 CD coding regions, respectively. This study presents the first report on the isolation of Bo_ParV. Den1/2021/JPN and Bo_ParV cow/2018/4, which are candidates for a novel species in the genus Parechovirus.

Genetic diversity and recombination event in bovine parechovirus infecting Japanese cattle

“…Our qRT-PCR method for Bo_ParV detection could detect Bo_ParV in 10 (6.3%) out of 158 bovine fecal samples. In our previous study, no Bo_ParV positive samples were detected in 46 bovine fecal samples, probably because of the small sample size, sampling area, or year of specimen collection[2]. Kawasaki et al reported that parechovirus infections were detected in 944 of 8284 cow samples from the digestive, lymphatic, and central nervous systems in the SRA and did not observe a significant association between the viral infections and the presence or absence of symptoms[1].However, detailed epidemiological data, such as country, year of sample collection, and age of cows, were not included in their results.…”

“…Bovine parechovirus (Bo_ParV) sequences were firstly identified from the NCBI Sequence Read Archive (SRA), which is a public database of accumulated metagenomic libraries, and a nearly complete Bo_ParV sequence (Bo_ParV/2018/4/KOR) was assembled from the sequence reads from the lower digestive tract of a cow collected in South Korea in 2018 [1]. The first Bo_ParV was isolated in our laboratory in 2021 using cell culture from a bovine fecal sample that was positive for group C rotavirus [2]. This virus, Bo_ParV/Den1/2021/JPN (Den1/2021/JPN), and Bo_ParV/2018/4/KOR (2018/4/KOR) shared sequence homology with each other and were related to parechoviruses, especially the falcon parechovirus (KY645497) belonging to the Parechovirus E within the family Picornaviridae.…”