Full genome analysis of bovine astrovirus from fecal samples of cattle in Japan: identification of possible interspecies transmission of bovine astrovirus.

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.

Diversity in VP3, NSP3, and NSP4 of rotavirus B detected from Japanese cattle.

Bovine rotavirus B (RVB) is an etiological agent of diarrhea mostly in adult cattle. Currently, a few sequences of viral protein (VP)1, 2, 4, 6, and 7 and nonstructural protein (NSP)1, 2, and 5 of bovine RVB are available in the DDBJ/EMBL/GenBank databases, and none have been reported for VP3, NSP3, and NSP4. In order to fill this gap in the genetic characterization of bovine RVB strains, we used a metagenomics approach and sequenced and analyzed the complete coding sequences (CDS) of VP3, NSP3, and NSP4 genes, as well as the partial or complete CDS of other genes of RVBs detected from Japanese cattle. VP3, NSP3, and NSP4 of bovine RVBs shared low nucleotide sequence identities (63.3-64.9% for VP3, 65.9-68.2% for NSP3, and 52.6-56.2% for NSP4) with those of murine, human, and porcine RVBs, suggesting that bovine RVBs belong to a novel genotype. Furthermore, significantly low amino acid sequence identities were observed for NSP4 (36.1-39.3%) between bovine RVBs and the RVBs of other species. In contrast, hydrophobic plot analysis of NSP4 revealed profiles similar to those of RVBs of other species and rotavirus A (RVA) strains. Phylogenetic analyses of all gene segments revealed that bovine RVB strains formed a cluster that branched distantly from other RVBs. These results suggest that bovine RVBs have evolved independently from other RVBs but in a similar manner to other rotaviruses. These findings provide insights into the evolution and diversity of RVB strains.

Reinfection of adult cattle with rotavirus B during repeated outbreaks of epidemic diarrhea.

Rotavirus B (RVB) infection in cattle is poorly understood. The objective of this study was to describe the epidemiological features of repeated outbreaks of epidemic diarrhea due to RVB infection in adult cattle on a large dairy farm complex in Japan. In October 2002, approximately 550 adult cows and approximately 450 in February 2005 had acute watery diarrhea at several farms on the complex. Four months before the first outbreak, RVB antibody-positive rates at subsequently affected farms were significantly lower than at non-affected farms (30% to 32% versus 61% to 67%). During the acute phase of both outbreaks, RVB antibody-positive rates in diarrheal cows tested were as low as 15% to 26%. Most of the farms affected in the second outbreak were also involved in the first outbreak. Some adult cows with RVB diarrhea in the first outbreak showed not only RVB seroresponse, but also RVB shedding in the second outbreak, although none of these cows developed diarrhea. Nucleotide sequences of the VP7 and VP4 genes revealed a close relationship between RVB strains in both outbreaks. Taken together, these results indicate that outbreaks of epidemic RVB diarrhea in adult cows might be influenced by herd immunity and could occur repeatedly at the same farms over several years. To our knowledge, this is the first report on repeated RVB infections in the same cattle.

L'infection par le rotavirus B (RVB) chez les bovins est peu comprise. L'objectif de la présente étude était de décrire les caractéristiques épidémiologiques de poussées de cas répétées de diarrhée épidémique dues à une infection par le RVB chez des bovins adultes dans un grand complexe laitier au Japon. En octobre 2002, environ 550 vaches adultes et environ 450 en février 2005 présentaient une diarrhée aqueuse aigüe dans plusieurs fermes sur le complexe. Quatre mois avant le premier épisode, les taux d'anticorps anti-RVB dans les fermes subséquemment affectées étaient significativement plus faibles que dans les fermes non-affectées (30 % à 32 % vs 61 % à 67 %). Pendant la phase aigüe des deux épidémies, les taux d'anticorps anti-RVB chez les vaches diarrhéiques testées étaient aussi bas que 15 % à 26 %. La plupart des fermes affectées dans la deuxième épidémie étaient également impliquées dans la première épidémie. Quelques vaches adultes avec une diarrhée à RVB dans la première épidémie avaient non seulement une réponse sérologique positive envers le RVB, mais excrétaient également le RVB durant la deuxième épidémie, bien qu'aucun de ces vaches ne présenta de diarrhée. Les séquences nucléotidiques des gènes VP7 et VP4 ont révélé une proche parenté entre les deux souches de RVB des deux épidémies. Pris globalement, ces résultats indiquent que les épisodes de diarrhée épidémique causée par RVB chez des vaches adultes peuvent être influencés par l'immunité du troupeau et peuvent survenir de manière répétée sur une même ferme pendant plusieurs années. Selon nous, il s'agirait du premier rapport de cas d'infections à répétition par le RVB chez les mêmes bovins.(Traduit par Docteur Serge Messier).

Phylogenetic analysis of bovine viral diarrhea viruses using five different genetic regions.

Phylogenetic analysis of the five different regions (5' non-coding region (5'NCR), N(pro), E2, NS3 and NS5B-3'NCR) of 48 Japanese and reported bovine viral diarrhea virus (BVDV) genomes was performed. Japanese BVDVs were segregated into BVDV1 subdivided into six subgroups and BVDV2. One isolate, So CP/75, isolated in 1975 and previously proposed as subgroup 1e according to its 5'NCR sequence, was quite unique and formed an independent lineage in the tree of any region. Another isolate, 190CP, obtained from an experimental mucosal disease case was classified as subgroup 1e, defined by Becher et al. in the 5'NCR, N(pro) and E2 regions, whereas it was classified as subgroup 1a in the NS5B-3'NCR region. The genomic sequences of the American isolates ILLC and ILLNC obtained from the GenBank database were assigned into subgroup 1b in the 5'NCR, N(pro), E2 and NS5B-3'NCR regions, whereas they were assigned into subgroup 1a in the NS3 region, suggesting that recombination between the virus strains classified into different subgroups had occurred in an animal. These findings suggest that phylogenetic analysis of several genetic regions is useful for the further characterization of field BVDV isolates.

Detection of bovine group a rotavirus using rapid antigen detection kits, rt-PCR and next-generation DNA sequencing.

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 10°-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.

Effect of cellooligosaccharide or synbiotic feeding on growth performance, fecal condition and hormone concentrations in Holstein calves.

We investigated the effect of cellooligosaccharide (CE) or a combination of dextran and Lactobacillus casei ssp. casei strain JCM1134(T) (synbiotic; SB) feeding on growth performance, fecal condition and hormone concentrations in Holstein calves. Fifty-two female Holstein calves were randomly assigned to three treatment groups: CE feeding group (n = 16), SB feeding group (n = 18), and control group (n = 18). Body weight at 90 days of age, as well as daily body weight gain (DG) and feed efficiency after weaning to 90 days of age were greater (P < 0.05) in the CE feeding group than in the control group. The total fecal score tended to be lower (P < 0.1) in the SB feeding group than in the control group. Plasma insulin concentration was higher (P < 0.05) in the CE feeding group than in the control group at 90 days of age. Our results indicate that CE feeding improved DG and feed efficiency in calves. On the other hand, there was less effect on growth performance and fecal Escherichia coli counts in calves fed SB.