Longitudinal epidemiology of human coronavirus OC43 in Yamagata, Japan, 2010–2017: Two groups based on spike gene appear one after another
Human coronavirus OC43 (HCoV‐OC43) is divided into genotypes A to H based on genetic recombination including the spike (S) gene. To investigate the longitudinal transition of the phylogenetic feature of the HCoV‐OC43 S gene in a community, phylogenetic analysis of the S1 region of the S gene was con...
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| Veröffentlicht in: | Journal of medical virology 2021-02, Vol.93 (2), p.945-951 |
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| creator | Komabayashi, Kenichi Matoba, Yohei Tanaka, Shizuka Seto, Junji Aoki, Yoko Ikeda, Tatsuya Shimotai, Yoshitaka Matsuzaki, Yoko Itagaki, Tsutomu Mizuta, Katsumi |
| description | Human coronavirus OC43 (HCoV‐OC43) is divided into genotypes A to H based on genetic recombination including the spike (S) gene. To investigate the longitudinal transition of the phylogenetic feature of the HCoV‐OC43 S gene in a community, phylogenetic analysis of the S1 region of the S gene was conducted using 208 strains detected in Yamagata during 2010 to 2017 with reference strains of the genotype. The S1 sequences were divisible into four groups: A to D. All Yamagata strains belonged to either group B or group D. In group B, 46 (90.2%) out of 51 Yamagata strains were clustered with those of genotype E reference strains (cluster E). In group D, 28 (17.8%) and 122 (77.7%) out of 157 Yamagata strains were clustered, respectively, with genotype F and genotype G reference strains. In cluster G, 28 strains formed a distinct cluster. Monthly distributions of HCoV‐OC43 in Yamagata in 2010 to 2017 revealed that group B and group D appeared one after another. In group B, the cluster E strains were prevalent recurrently. In conclusion, epidemics of HCoV‐OC43 in Yamagata, Japan might be attributable to two genetically different groups: group B showed a recurrent epidemic of strains belonging to a single phylogenetic cluster and group D showed epidemic strains belonging to multiple clusters.
Highlights
Longitudinal transition of the phylogenetic feature of the HCoV‐OC43 spike gene in a community.
Epidemics of HCoV‐OC43 in Yamagata, Japan might be attributable to two genetically different groups. |
| doi_str_mv | 10.1002/jmv.26361 |
| format | Article |
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Highlights
Longitudinal transition of the phylogenetic feature of the HCoV‐OC43 spike gene in a community.
Epidemics of HCoV‐OC43 in Yamagata, Japan might be attributable to two genetically different groups.</description><identifier>ISSN: 0146-6615</identifier><identifier>EISSN: 1096-9071</identifier><identifier>DOI: 10.1002/jmv.26361</identifier><identifier>PMID: 32720708</identifier><language>eng</language><publisher>United States: Wiley Subscription Services, Inc</publisher><subject>acute respiratory infection ; Adolescent ; Adult ; Child ; Child, Preschool ; Clusters ; Coronaviridae ; Coronavirus Infections - epidemiology ; Coronavirus Infections - virology ; Coronavirus OC43, Human - classification ; Coronavirus OC43, Human - genetics ; Coronaviruses ; Epidemics ; Epidemiology ; Evolution, Molecular ; Female ; Genotype ; Genotype & phenotype ; Genotypes ; Humans ; Infant ; Infant, Newborn ; influenza‐like illness ; Longitudinal Studies ; Male ; Middle Aged ; outpatient clinic ; phylogenetic tree ; Phylogenetics ; Phylogeny ; Recombination ; Recombination, Genetic ; RNA, Viral - genetics ; S gene ; Sequence Analysis, DNA ; Spike Glycoprotein, Coronavirus - genetics ; Spikes ; Strains (organisms) ; Virology ; Young Adult</subject><ispartof>Journal of medical virology, 2021-02, Vol.93 (2), p.945-951</ispartof><rights>2020 Wiley Periodicals LLC</rights><rights>2020 Wiley Periodicals LLC.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3971-79bed62f48fd3d37f864f8a2661a6fc8706d25b30dd3d6a53f64d751f98fc6053</citedby><cites>FETCH-LOGICAL-c3971-79bed62f48fd3d37f864f8a2661a6fc8706d25b30dd3d6a53f64d751f98fc6053</cites><orcidid>0000-0002-9612-3261 ; 0000-0003-2227-5315 ; 0000-0003-2757-5886 ; 0000-0003-4636-8460 ; 0000-0001-8965-9925 ; 0000-0003-0900-8845</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fjmv.26361$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fjmv.26361$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,778,782,1414,27911,27912,45561,45562</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32720708$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Komabayashi, Kenichi</creatorcontrib><creatorcontrib>Matoba, Yohei</creatorcontrib><creatorcontrib>Tanaka, Shizuka</creatorcontrib><creatorcontrib>Seto, Junji</creatorcontrib><creatorcontrib>Aoki, Yoko</creatorcontrib><creatorcontrib>Ikeda, Tatsuya</creatorcontrib><creatorcontrib>Shimotai, Yoshitaka</creatorcontrib><creatorcontrib>Matsuzaki, Yoko</creatorcontrib><creatorcontrib>Itagaki, Tsutomu</creatorcontrib><creatorcontrib>Mizuta, Katsumi</creatorcontrib><title>Longitudinal epidemiology of human coronavirus OC43 in Yamagata, Japan, 2010–2017: Two groups based on spike gene appear one after another</title><title>Journal of medical virology</title><addtitle>J Med Virol</addtitle><description>Human coronavirus OC43 (HCoV‐OC43) is divided into genotypes A to H based on genetic recombination including the spike (S) gene. To investigate the longitudinal transition of the phylogenetic feature of the HCoV‐OC43 S gene in a community, phylogenetic analysis of the S1 region of the S gene was conducted using 208 strains detected in Yamagata during 2010 to 2017 with reference strains of the genotype. The S1 sequences were divisible into four groups: A to D. All Yamagata strains belonged to either group B or group D. In group B, 46 (90.2%) out of 51 Yamagata strains were clustered with those of genotype E reference strains (cluster E). In group D, 28 (17.8%) and 122 (77.7%) out of 157 Yamagata strains were clustered, respectively, with genotype F and genotype G reference strains. In cluster G, 28 strains formed a distinct cluster. Monthly distributions of HCoV‐OC43 in Yamagata in 2010 to 2017 revealed that group B and group D appeared one after another. In group B, the cluster E strains were prevalent recurrently. In conclusion, epidemics of HCoV‐OC43 in Yamagata, Japan might be attributable to two genetically different groups: group B showed a recurrent epidemic of strains belonging to a single phylogenetic cluster and group D showed epidemic strains belonging to multiple clusters.
Highlights
Longitudinal transition of the phylogenetic feature of the HCoV‐OC43 spike gene in a community.
Epidemics of HCoV‐OC43 in Yamagata, Japan might be attributable to two genetically different groups.</description><subject>acute respiratory infection</subject><subject>Adolescent</subject><subject>Adult</subject><subject>Child</subject><subject>Child, Preschool</subject><subject>Clusters</subject><subject>Coronaviridae</subject><subject>Coronavirus Infections - epidemiology</subject><subject>Coronavirus Infections - virology</subject><subject>Coronavirus OC43, Human - classification</subject><subject>Coronavirus OC43, Human - genetics</subject><subject>Coronaviruses</subject><subject>Epidemics</subject><subject>Epidemiology</subject><subject>Evolution, Molecular</subject><subject>Female</subject><subject>Genotype</subject><subject>Genotype & phenotype</subject><subject>Genotypes</subject><subject>Humans</subject><subject>Infant</subject><subject>Infant, Newborn</subject><subject>influenza‐like illness</subject><subject>Longitudinal Studies</subject><subject>Male</subject><subject>Middle Aged</subject><subject>outpatient clinic</subject><subject>phylogenetic tree</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Recombination</subject><subject>Recombination, Genetic</subject><subject>RNA, Viral - genetics</subject><subject>S gene</subject><subject>Sequence Analysis, DNA</subject><subject>Spike Glycoprotein, Coronavirus - genetics</subject><subject>Spikes</subject><subject>Strains (organisms)</subject><subject>Virology</subject><subject>Young Adult</subject><issn>0146-6615</issn><issn>1096-9071</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp10c1u1DAUBWALgei0sOAFkCU2VGraazuxE3ZoxF81qJuCxCq6E9uph8RO7Umr2fEA7HhDngSXKSyQWF3L_nQk30PIMwanDICfbcabUy6FZA_IgkEjiwYUe0gWwEpZSMmqA3KY0gYA6obzx-RAcMVBQb0g31fB9247a-dxoGZy2owuDKHf0WDp1Tyip12IweONi3OiF8tSUOfpFxyxxy2e0HOc0J9QDgx-fvuRh3pFL28D7WOYp0TXmIymwdM0ua-G9sYbitNkMObLfLRbEyn6sL0y8Ql5ZHFI5un9PCKf3r65XL4vVhfvPixfr4pONIoVqlkbLbkta6uFFsrWsrQ18vxTlLarFUjNq7UAnZ8lVsLKUquK2aa2nYRKHJGX-9wphuvZpG07utSZYUBvwpxaXvIaqoapMtMX_9BNmGPe1Z1SogZoVJPV8V51MaQUjW2n6EaMu5ZBe1dRmytqf1eU7fP7xHk9Gv1X_ukkg7M9uHWD2f0_qT3_-Hkf-QvVg5pA</recordid><startdate>202102</startdate><enddate>202102</enddate><creator>Komabayashi, Kenichi</creator><creator>Matoba, Yohei</creator><creator>Tanaka, Shizuka</creator><creator>Seto, Junji</creator><creator>Aoki, Yoko</creator><creator>Ikeda, Tatsuya</creator><creator>Shimotai, Yoshitaka</creator><creator>Matsuzaki, Yoko</creator><creator>Itagaki, Tsutomu</creator><creator>Mizuta, Katsumi</creator><general>Wiley Subscription Services, Inc</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7TK</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-9612-3261</orcidid><orcidid>https://orcid.org/0000-0003-2227-5315</orcidid><orcidid>https://orcid.org/0000-0003-2757-5886</orcidid><orcidid>https://orcid.org/0000-0003-4636-8460</orcidid><orcidid>https://orcid.org/0000-0001-8965-9925</orcidid><orcidid>https://orcid.org/0000-0003-0900-8845</orcidid></search><sort><creationdate>202102</creationdate><title>Longitudinal epidemiology of human coronavirus OC43 in Yamagata, Japan, 2010–2017: Two groups based on spike gene appear one after another</title><author>Komabayashi, Kenichi ; 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To investigate the longitudinal transition of the phylogenetic feature of the HCoV‐OC43 S gene in a community, phylogenetic analysis of the S1 region of the S gene was conducted using 208 strains detected in Yamagata during 2010 to 2017 with reference strains of the genotype. The S1 sequences were divisible into four groups: A to D. All Yamagata strains belonged to either group B or group D. In group B, 46 (90.2%) out of 51 Yamagata strains were clustered with those of genotype E reference strains (cluster E). In group D, 28 (17.8%) and 122 (77.7%) out of 157 Yamagata strains were clustered, respectively, with genotype F and genotype G reference strains. In cluster G, 28 strains formed a distinct cluster. Monthly distributions of HCoV‐OC43 in Yamagata in 2010 to 2017 revealed that group B and group D appeared one after another. In group B, the cluster E strains were prevalent recurrently. In conclusion, epidemics of HCoV‐OC43 in Yamagata, Japan might be attributable to two genetically different groups: group B showed a recurrent epidemic of strains belonging to a single phylogenetic cluster and group D showed epidemic strains belonging to multiple clusters.
Highlights
Longitudinal transition of the phylogenetic feature of the HCoV‐OC43 spike gene in a community.
Epidemics of HCoV‐OC43 in Yamagata, Japan might be attributable to two genetically different groups.</abstract><cop>United States</cop><pub>Wiley Subscription Services, Inc</pub><pmid>32720708</pmid><doi>10.1002/jmv.26361</doi><tpages>7</tpages><orcidid>https://orcid.org/0000-0002-9612-3261</orcidid><orcidid>https://orcid.org/0000-0003-2227-5315</orcidid><orcidid>https://orcid.org/0000-0003-2757-5886</orcidid><orcidid>https://orcid.org/0000-0003-4636-8460</orcidid><orcidid>https://orcid.org/0000-0001-8965-9925</orcidid><orcidid>https://orcid.org/0000-0003-0900-8845</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | acute respiratory infection Adolescent Adult Child Child, Preschool Clusters Coronaviridae Coronavirus Infections - epidemiology Coronavirus Infections - virology Coronavirus OC43, Human - classification Coronavirus OC43, Human - genetics Coronaviruses Epidemics Epidemiology Evolution, Molecular Female Genotype Genotype & phenotype Genotypes Humans Infant Infant, Newborn influenza‐like illness Longitudinal Studies Male Middle Aged outpatient clinic phylogenetic tree Phylogenetics Phylogeny Recombination Recombination, Genetic RNA, Viral - genetics S gene Sequence Analysis, DNA Spike Glycoprotein, Coronavirus - genetics Spikes Strains (organisms) Virology Young Adult |
| title | Longitudinal epidemiology of human coronavirus OC43 in Yamagata, Japan, 2010–2017: Two groups based on spike gene appear one after another |
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