A viral metagenomics approach was used to investigate fecal samples of Japanese calves with and without diarrhea. Of the different viral pathogens detected, read counts gave nearly complete astrovirus-related RNA sequences in 15 of the 146 fecal samples collected in three distinct areas (Hokkaido, Ishikawa, and Kagoshima Prefectures) between 2009 and 2015. Due to the lack of genetic information about bovine astroviruses (BoAstVs) in Japan, these sequences were analyzed in this study. Nine of the 15 Japanese BoAstVs were closely related to Chinese BoAstVs and clustered into a lineage (tentatively named lineage 1) in all phylogenetic trees. Three of 15 strains were phylogenetically separate from lineage 1, showing low sequence identities, and clustered instead with an American strain isolated from cattle with respiratory disease (tentatively named lineage 2). Interestingly, two of 15 strains clustered with lineage 1 in the open reading frame (ORF)1a and ORF1b regions, while they clustered with lineage 2 in the ORF2 region. Remarkably, one of 15 strains exhibited low amino acid sequence similarity to other BoAstVs and was clustered separately with porcine astrovirus type 5 in all trees, and ovine astrovirus in the ORF2 region, suggesting past interspecies transmission.
We investigated the sensitivity of human rotavirus rapid antigen detection (RAD)
kits, RT-PCR and next-generation DNA sequencing (NGS) for detection of bovine group A
rotavirus (RVA). The Dipstick ‘Eiken’ Rota (Dipstick) showed the highest sensitivity out
of the seven RAD kits against all selected strains in limited dilution analyses, which was
consistent with the results for equine rotavirus previously reported. RT-PCR had
100–103-fold higher sensitivity than the Dipstick. NGS using
thirteen RT-PCR-negative fecal samples revealed that all samples yielded RVA reads and
especially that two of them covered all 11 genome segments. Moreover, mapping reads to
reference sequences allowed genotyping. The NGS would be sensitive and useful for analysis
of less dependent on specific primers and screening of genotypes.
Mammalian orthoreovirus (MRV) is a non-enveloped double-stranded RNA virus with a broad host range. MRVs are prevalent worldwide and have been isolated from various hosts, including humans, dogs, cats, wild boars, sewage, and pigs, in Japan. However, Japanese porcine MRV has not been genetically characterized yet. While investigating porcine enteric viruses including MRV, five MRVs were isolated from the feces of Japanese pigs using the MA104 cell culture. Genetic analysis of the S1 gene revealed that the Japanese porcine MRV strain isolates could be classified as MRV-2 and MRV-3. Whole genome analysis showed that Japanese porcine MRVs exhibited genetic diversity, although they shared homology with porcine MRV sequences deposited in the DDBJ/EMBL/GenBank database. Several potential intra-genetic reassortment events among MRV strains from pigs, sewage, and humans have been detected in Japan, suggesting zoonotic transmission. Furthermore, homologous recombination events were identified in the M1 and S1 genes of Japanese porcine MRV. These findings imply that different strains of Japanese porcine MRVs share a porcine MRV genomic backbone and have evolved through intra-genetic reassortment and homologous recombination events.
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