Molecular characterization and sequence analysis of the 2B region of Aichivirus C strains in Japan and Thailand

Okitsu, Shoko; Khamrin, Pattara; Thongprachum, Aksara; Kalesaran, Angela F. C.; Takanashi, Sayaka; Shimizu, Hiroyuki; Maneekarn, Niwat; Mizuguchi, Masashi; Hayakawa, Satoshi; Ushijima, Hiroshi

doi:10.1016/j.meegid.2014.05.010

Cited by 3 publications

(1 citation statement)

References 39 publications

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“…It has been assumed that the 2B protein has multiple functions in different picornaviruses [24]. However, the 2B gene may not be responsible for kobuvirus pathogenesis [25]. The phylogenetic analysis of sequences representing partial 3D regions showed that BKoV strains from Cairo grouped with Chinese strains while those from Sharkia clustered with Korean strains.…”

Section: Discussionmentioning

confidence: 99%

Detection and genetic characterization of bovine kobuvirus from calves in Egypt

et al. 2018

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Kobuviruses are small non-enveloped RNA viruses that probably cause diarrhea in cattle and swine. Since its discovery in 2003, few studies have addressed bovine kobuvirus (BKoV; a species of Aichivirus B) infections. BKoV has been reported in Europe, Asia, and South America, suggesting a worldwide distribution. To investigate the presence of BKoV in Egypt, 36 fecal specimens from diarrheic calves in two different Egyptian provinces (Cairo and Sharkia) were screened by RT-PCR and 24 (66.7%) were found positive for BKoV. RNA from one of the positive samples (BKoV/Egy-1/KY407744) was subjected to next-generation sequencing to determine the complete BKoV genome sequence. When compared to the only recorded BKoV genome sequence (BKoV/U-1/AB084788), the studied strain showed 94 amino acid (aa) substitutions through its entire polyprotein (2463 aa), one nucleotide (nt) insertion and one nt deletion in the 2B gene and 4-nt deletions in the UTRs (2 each). Additionally, five VP1 and seven 3D sequences were obtained from other samples by using RT-PCR and Sanger sequencing. A discrepancy in the phylogenetic topography of VP1 and 3D was observed, where the Egyptian VP1 sequences were classified as a distinct cluster within the proposed lineage 1 (genotype A), which also contained strains from the UK, Brazil, and Japan. While, the 3D sequences from Cairo were related to those of Chinese strains unlike Sharkia ones that were more closer to Korean strains. To the best of our knowledge, this is the first detection and genomic characterization of BKoV in Egypt or indeed Africa.

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Section: Discussionmentioning

confidence: 99%

Detection and genetic characterization of bovine kobuvirus from calves in Egypt

et al. 2018

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Detection and molecular characterization of porcine kobuvirus in piglets in 2009–2013 in northern Thailand

Chuchaona

Khamrin

Yodmeeklin

et al. 2017

Trop Anim Health Prod

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A total of 636 fecal samples collected from piglets with and without diarrhea during 2009 to 2013 were tested for porcine kobuvirus by RT-PCR. From a total of 528 fecal samples collected from piglets with diarrhea and 108 from healthy controls, 505 (95.6%) and 104 (96.3%) were positive for porcine kobuvirus, respectively. The detection rates of porcine kobuvirus were remarkable equally high in both diarrheic and healthy piglets. Phylogenetic analysis revealed that porcine kobuvirus strains detected in both symptomatic and asymptomatic piglets were genetically closely related to each other and also to other porcine kobuviruses reported worldwide. It was interesting to point out that one of the porcine kobuvirus strains isolated from piglet in our study was similar to a porcine-like bovine kobuvirus reference strain isolated previously in South Korea. This finding provided the evidence to support the interspecies transmission of kobuviruses between cattle and swine.

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Complete genome analysis of porcine kobuviruses from the feces of pigs in Japan

Akagami

Ito²,

Niira

et al. 2017

Virus Genes

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Porcine kobuviruses (PoKoVs) are ubiquitously distributed in pig populations worldwide and are thought to be enteric viruses in swine. Although PoKoVs have been detected in pigs in Japan, no complete genome data for Japanese PoKoVs are available. In the present study, 24 nearly complete or complete sequences of the PoKoV genome obtained from 10 diarrheic feces and 14 non-diarrheic feces of Japanese pigs were analyzed using a metagenomics approach. Japanese PoKoVs shared 85.2-100% identity with the complete coding nucleotide (nt) sequences and the closest relationship of 85.1-98.3% with PoKoVs from other countries. Twenty of 24 Japanese PoKoVs carried a deletion of 90 nt in the 2B coding region. Phylogenetic tree analyses revealed that PoKoVs were not grouped according to their geographical region of origin and the phylogenetic trees of the L, P1, P2, and P3 genetic regions showed topologies different from each other. Similarity plot analysis using strains from a single farm revealed partially different similarity patterns among strains from identical farm origins, suggesting that recombination events had occurred. These results indicate that various PoKoV strains are prevalent and not restricted geographically on pig farms worldwide and the coexistence of multiple strains leads to recombination events of PoKoVs and contributes to the genetic diversity and evolution of PoKoVs.

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Molecular characterization and sequence analysis of the 2B region of Aichivirus C strains in Japan and Thailand

Cited by 3 publications

References 39 publications

Detection and genetic characterization of bovine kobuvirus from calves in Egypt

Detection and genetic characterization of bovine kobuvirus from calves in Egypt

Detection and molecular characterization of porcine kobuvirus in piglets in 2009–2013 in northern Thailand

Complete genome analysis of porcine kobuviruses from the feces of pigs in Japan

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