Genomic Characterization and Phylogenetic Classification of Bovine Coronaviruses Through Whole Genome Sequence Analysis
Bovine coronavirus (BCoV) is zoonotically transmissible among species, since BCoV-like viruses have been detected in wild ruminants and humans. BCoV causing enteric and respiratory disease is widespread in cattle farms worldwide; however, limited information is available regarding the molecular char...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-02-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/12/2/183 |
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| author | Tohru Suzuki Yoshihiro Otake Satoko Uchimoto Ayako Hasebe Yusuke Goto |
| author_facet | Tohru Suzuki Yoshihiro Otake Satoko Uchimoto Ayako Hasebe Yusuke Goto |
| author_sort | Tohru Suzuki |
| collection | DOAJ |
| description | Bovine coronavirus (BCoV) is zoonotically transmissible among species, since BCoV-like viruses have been detected in wild ruminants and humans. BCoV causing enteric and respiratory disease is widespread in cattle farms worldwide; however, limited information is available regarding the molecular characterization of BCoV because of its large genome size, despite its significant economic impact. This study aimed to better understand the genomic characterization and evolutionary dynamics of BCoV via comparative sequence and phylogenetic analyses through whole genome sequence analysis using 67 BCoV isolates collected throughout Japan from 2006 to 2017. On comparing the genomic sequences of the 67 BCoVs, genetic variations were detected in 5 of 10 open reading frames (ORFs) in the BCoV genome. Phylogenetic analysis using whole genomes from the 67 Japanese BCoV isolates in addition to those from 16 reference BCoV strains, revealed the existence of two major genotypes (classical and US wild ruminant genotypes). All Japanese BCoV isolates originated from the US wild ruminant genotype, and they tended to form the same clusters based on the year and farm of collection, not the disease type. Phylogenetic trees on hemagglutinin-esterase protein (HE), spike glycoprotein (S), nucleocapsid protein (N) genes and ORF1 revealed clusters similar to that on whole genome, suggesting that the evolution of BCoVs may be closely associated with variations in these genes. Furthermore, phylogenetic analysis of BCoV S genes including those of European and Asian BCoVs and human enteric coronavirus along with the Japanese BCoVs revealed that BCoVs differentiated into two major types (European and American types). Moreover, the European and American types were divided into eleven and three genotypes, respectively. Our analysis also demonstrated that BCoVs with different genotypes periodically emerged and predominantly circulated within the country. These findings provide useful information to elucidate the detailed molecular characterization of BCoVs, which have spread worldwide. Further genomic analyses of BCoV are essential to deepen the understanding of the evolution of this virus. |
| first_indexed | 2024-12-21T19:04:12Z |
| format | Article |
| id | doaj.art-a449a98872824fca89bf997e5dcf1ab3 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-12-21T19:04:12Z |
| publishDate | 2020-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-a449a98872824fca89bf997e5dcf1ab32022-12-21T18:53:25ZengMDPI AGViruses1999-49152020-02-0112218310.3390/v12020183v12020183Genomic Characterization and Phylogenetic Classification of Bovine Coronaviruses Through Whole Genome Sequence AnalysisTohru Suzuki0Yoshihiro Otake1Satoko Uchimoto2Ayako Hasebe3Yusuke Goto4Division of Viral Disease and Epidemiology, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 3050856, JapanCentral Tochigi Prefectural Livestock Health and Hygiene Center, Utsunomiya, Tochigi 3210905, JapanShiga Prefectural Livestock Health and Hygiene Center, Omihachiman, Shiga 5230813, JapanCentral Gifu Prefectural Livestock Health and Hygiene Center, Gifu 5011112, JapanCentral Iwate Prefectural Livestock Health and Hygiene Center, Takizawa, Iwate 0200605, JapanBovine coronavirus (BCoV) is zoonotically transmissible among species, since BCoV-like viruses have been detected in wild ruminants and humans. BCoV causing enteric and respiratory disease is widespread in cattle farms worldwide; however, limited information is available regarding the molecular characterization of BCoV because of its large genome size, despite its significant economic impact. This study aimed to better understand the genomic characterization and evolutionary dynamics of BCoV via comparative sequence and phylogenetic analyses through whole genome sequence analysis using 67 BCoV isolates collected throughout Japan from 2006 to 2017. On comparing the genomic sequences of the 67 BCoVs, genetic variations were detected in 5 of 10 open reading frames (ORFs) in the BCoV genome. Phylogenetic analysis using whole genomes from the 67 Japanese BCoV isolates in addition to those from 16 reference BCoV strains, revealed the existence of two major genotypes (classical and US wild ruminant genotypes). All Japanese BCoV isolates originated from the US wild ruminant genotype, and they tended to form the same clusters based on the year and farm of collection, not the disease type. Phylogenetic trees on hemagglutinin-esterase protein (HE), spike glycoprotein (S), nucleocapsid protein (N) genes and ORF1 revealed clusters similar to that on whole genome, suggesting that the evolution of BCoVs may be closely associated with variations in these genes. Furthermore, phylogenetic analysis of BCoV S genes including those of European and Asian BCoVs and human enteric coronavirus along with the Japanese BCoVs revealed that BCoVs differentiated into two major types (European and American types). Moreover, the European and American types were divided into eleven and three genotypes, respectively. Our analysis also demonstrated that BCoVs with different genotypes periodically emerged and predominantly circulated within the country. These findings provide useful information to elucidate the detailed molecular characterization of BCoVs, which have spread worldwide. Further genomic analyses of BCoV are essential to deepen the understanding of the evolution of this virus.https://www.mdpi.com/1999-4915/12/2/183bovine coronaviruswhole genomespike proteinphylogenetic analysisgenotype classification |
| spellingShingle | Tohru Suzuki Yoshihiro Otake Satoko Uchimoto Ayako Hasebe Yusuke Goto Genomic Characterization and Phylogenetic Classification of Bovine Coronaviruses Through Whole Genome Sequence Analysis Viruses bovine coronavirus whole genome spike protein phylogenetic analysis genotype classification |
| title | Genomic Characterization and Phylogenetic Classification of Bovine Coronaviruses Through Whole Genome Sequence Analysis |
| title_full | Genomic Characterization and Phylogenetic Classification of Bovine Coronaviruses Through Whole Genome Sequence Analysis |
| title_fullStr | Genomic Characterization and Phylogenetic Classification of Bovine Coronaviruses Through Whole Genome Sequence Analysis |
| title_full_unstemmed | Genomic Characterization and Phylogenetic Classification of Bovine Coronaviruses Through Whole Genome Sequence Analysis |
| title_short | Genomic Characterization and Phylogenetic Classification of Bovine Coronaviruses Through Whole Genome Sequence Analysis |
| title_sort | genomic characterization and phylogenetic classification of bovine coronaviruses through whole genome sequence analysis |
| topic | bovine coronavirus whole genome spike protein phylogenetic analysis genotype classification |
| url | https://www.mdpi.com/1999-4915/12/2/183 |
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