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, Tasuku; 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

doi:10.1292/jvms.13-0265

Cited by 11 publications

(9 citation statements)

References 19 publications

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“…Neither cytopathic effect nor the expected RT-PCR products from RNA extracted from cell culture supernatants were observed in any of the inoculated cells, indicating a lack of virus replication in these cell lines. However, using RNA-seq based strategy with DNase treatment before construction of cDNA libraries, we could obtain sufficient viral genomic sequences of RNA viruses from fecal samples not only for picornaviruses but also, in earlier studies, for other viruses such as rotavirus (Minami-Fukuda et al, 2013;Masuda et al, 2014;Nagai et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

Identification and complete genome analysis of a novel bovine picornavirus in Japan

et al. 2015

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We identified novel viruses in feces from cattle with diarrhea collected in 2009 in Hokkaido Prefecture, Japan, by using a metagenomics approach and determined the (near) complete sequences of the virus. Sequence analyses revealed that they had a standard picornavirus genome organization, i.e. 5' untranslated region (UTR) - L- P1 (VP4- VP3- VP2- VP1) - P2 (2A- 2B- 2C) - P3 (3A- 3B- 3C-3D) - 3'UTR- poly(A). They are closely related to other unclassified Chinese picornaviruses; bat picornaviruses group 1-3, feline picornavirus, and canine picornavirus, sharing 45.4-51.4% (P1), 38.0-44.9% (P2), and 49.6-53.3% (P3) amino acid identities, respectively. The phylogenetic analyses and detailed genome characterization showed that they, together with the unclassified Chinese picornaviruses, grouped as a cluster for the P1, 2C, 3CD and VP1 coding regions. These viruses had conserved features (e.g. predicted protein cleavage sites, presence of a leader protein, 2A, 2C, 3C, and 3D functional domains), suggesting they have a common ancestor. Reverse-transcription-PCR assays, using specific primers designed from the 5'UTR sequence of these viruses, showed that 23.0% (20/87) of fecal samples from cattle with diarrhea were positive, indicating the prevalence of these picornavirus in the Japanese cattle population in Hokkaido Prefecture. However, further studies are needed to investigate the pathogenic potential and etiological role of these viruses in cattle.

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Section: Discussionmentioning

confidence: 99%

Identification and complete genome analysis of a novel bovine picornavirus in Japan

et al. 2015

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“…First, convenient genotyping of RVA was carried out using the CLC Genomics Workbench. Mapping sequence reads from five samples to VP4 and VP7 reference sequences of representative strains (Minami-Fukuda et al, 2013) revealed poor alignment with G6, G8, G10, P[1], P[5] and P[11] -the most common bovine genotypes. Near complete sequences of the 11 segments of RVA could be obtained from the resultant contigs generated by reads assembled from five samples.…”

Section: Full Genome Sequencing Of Rvamentioning

confidence: 99%

Identification of novel bovine group A rotavirus G15P[14] strain from epizootic diarrhea of adult cows by de novo sequencing using a next-generation sequencer

Masuda

Nagai

Yamasato

et al. 2014

Veterinary Microbiology

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There are few reports describing diarrhea of adult cattle caused by group A rotaviruses. Here, we report the identification of a novel bovine group A rotavirus from diarrhea of adult cows. A group A rotavirus was detected from an epizootic outbreak of diarrhea in adult cows with a decrease in milk production in Japan in 2013. The comprehensive genomic analyses from fecal samples by viral metagenomics using a next-generation sequencer revealed that it had an unreported genotype combination G15P[14]. The genome constellation of this strain, namely, RVA/Cow-wt/JPN/Tottori-SG/2013/G15P[14] was G15-P[14]-I2-R2-C2-M2-A3-N2-T6-E2-H3 representing VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5, respectively. Each gene segment of Tottori-SG was most closely related to Japanese bovine group A rotaviruses suggesting that Tottori-SG might have derived from multiple reassortment events from group A rotavirus strains circulating among Japanese cattle. No other diarrhea pathogen of adult cattle was detected by routine diagnosis and metagenomics. Viral metagenomics, using a next-generation sequencer, is useful to characterize group A rotaviruses from fecal samples and offers unbiased comprehensive investigations of pathogen.

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“…However, no P types were identified during the genotype detection, which is another limitation of our study. The usefulness of next-generation DNA sequencing has previously been evaluated for the direct detection of bovine rotavirus from fecal samples[ 40 ]. More meticulous rotavirus surveillance should be conducted in Yunnan, China.…”

Section: Discussionmentioning

confidence: 99%

Isolation and characterization of a new candidate human inactivated rotavirus vaccine strain from hospitalized children in Yunnan, China: 2010-2013

Zhou

Zhang

et al. 2018

WJCC

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AIMTo determine the distribution of rotavirus VP7 gene in hospitalized children in Yunnan, China.METHODSA total of 366 stool specimens were collected from hospitalized children in hospitals in Yunnan Province from September 2010 to December 2013. The genomic RNA electropherotypes and the G genotypes of the rotaviruses were determined. A phylogenetic analysis of the VP7 gene was performed. Rotavirus isolation was performed, and characterized by plaque, minimum essential medium, and all genes sequence analysis. Quantification of antibodies for inactivated vaccine prepared with ZTR-68 was examined by enzyme-linked immunosorbent assay and microneutralization assay.RESULTSGroup A human rotavirus was detected in 177 of 366 (48.4%) stool samples using a colloidal gold device assay. The temporal distribution of rotavirus cases showed significant correlation with the mean air temperature. Rotaviruses were isolated from 13% of the rotavirus-positive samples. The predominant genotype was G1 (43.5%), followed by G3 (21.7%), G9 (17.4%), G2 (4.3%), G4 (8.7%), and mixed (4.3%) among a total of 23 rotavirus isolates. A rotavirus strain was isolated from a rotavirus-positive stool sample of a 4-month-old child in The First People’s Hospital of Zhaotong (2010) for use as a candidate human inactivated rotavirus vaccine strain and for further research, and was designated ZTR-68. The genotype of 11 gene segments of strain ZTR-68 (RVA/Human-wt/CHN/ZTR-68/2010/G1P[8]) was characterized. The genotype constellation of strain ZTR-68 was identified as G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. The VP7 and VP4 genotypes of strain ZTR-68 were similar to Wa-like strains.CONCLUSIONSA high prevalence of the G1, G2, and G3 genotypes was detected from 2010 to 2012. However, a dominant prevalence of the G9 genotype was identified as the cause of gastroenteritis in children in Yunnan, China, in 2013. A candidate human inactivated rotavirus vaccine strain, designated ZTR-68 was isolated, characterized, and showed immunogenicity. Our data will be useful for the future formulation and development of a vaccine in China.

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

Cited by 11 publications

References 19 publications

Identification and complete genome analysis of a novel bovine picornavirus in Japan

Identification and complete genome analysis of a novel bovine picornavirus in Japan

Identification of novel bovine group A rotavirus G15P[14] strain from epizootic diarrhea of adult cows by de novo sequencing using a next-generation sequencer

Isolation and characterization of a new candidate human inactivated rotavirus vaccine strain from hospitalized children in Yunnan, China: 2010-2013

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