Ancient Evolutionary History of Human Papillomavirus Type 16, 18 and 58 Variants Prevalent Exclusively in Japan
Human papillomavirus (HPV) is a sexually transmitted virus with an approximately 8-kilo base DNA genome, which establishes long-term persistent infection in anogenital tissues. High levels of genetic variations, including viral genotypes and intra-type variants, have been described for HPV genomes,...
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MDPI AG
2022-02-01
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| Online Access: | https://www.mdpi.com/1999-4915/14/3/464 |
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| author | Kohsei Tanaka Gota Kogure Mamiko Onuki Koji Matsumoto Takashi Iwata Daisuke Aoki Iwao Kukimoto |
| author_facet | Kohsei Tanaka Gota Kogure Mamiko Onuki Koji Matsumoto Takashi Iwata Daisuke Aoki Iwao Kukimoto |
| author_sort | Kohsei Tanaka |
| collection | DOAJ |
| description | Human papillomavirus (HPV) is a sexually transmitted virus with an approximately 8-kilo base DNA genome, which establishes long-term persistent infection in anogenital tissues. High levels of genetic variations, including viral genotypes and intra-type variants, have been described for HPV genomes, together with geographical differences in the distribution of genotypes and variants. Here, by employing a maximum likelihood method, we performed phylogenetic analyses of the complete genome sequences of HPV16, HPV18 and HPV58 available from GenBank (<i>n</i> = 627, 146 and 157, respectively). We found several characteristic clusters that exclusively contain HPV genomes from Japan: two for HPV16 (sublineages A4 and A5), one for HPV18 (sublineage A1) and two for HPV58 (sublineages A1 and A2). Bayesian phylogenetic analyses of concatenated viral gene sequences showed that divergence of the most recent common ancestor of these Japan-specific clades was estimated to have occurred ~98,000 years before present (YBP) for HPV16 A4, ~39,000 YBP for HPV16 A5, ~38,000 YBP for HPV18 A1, ~26,000 for HPV58 A1 and ~25,000 YBP for HPV58 A2. This estimated timeframe for the divergence of the Japan-specific clades suggests that the introduction of these HPV variants into the Japanese archipelago dates back to at least ~25,000 YBP and provides a scenario of virus co-migration with ancestral Japanese populations from continental Asia during the Upper Paleolithic period. |
| first_indexed | 2024-03-09T12:19:18Z |
| format | Article |
| id | doaj.art-def2b454b618436d84fa5103a7e6dda8 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-09T12:19:18Z |
| publishDate | 2022-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-def2b454b618436d84fa5103a7e6dda82023-11-30T22:43:50ZengMDPI AGViruses1999-49152022-02-0114346410.3390/v14030464Ancient Evolutionary History of Human Papillomavirus Type 16, 18 and 58 Variants Prevalent Exclusively in JapanKohsei Tanaka0Gota Kogure1Mamiko Onuki2Koji Matsumoto3Takashi Iwata4Daisuke Aoki5Iwao Kukimoto6Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo 208-0011, JapanPathogen Genomics Center, National Institute of Infectious Diseases, Tokyo 208-0011, JapanDepartment of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo 142-8666, JapanDepartment of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo 142-8666, JapanDepartment of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-0016, JapanDepartment of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-0016, JapanPathogen Genomics Center, National Institute of Infectious Diseases, Tokyo 208-0011, JapanHuman papillomavirus (HPV) is a sexually transmitted virus with an approximately 8-kilo base DNA genome, which establishes long-term persistent infection in anogenital tissues. High levels of genetic variations, including viral genotypes and intra-type variants, have been described for HPV genomes, together with geographical differences in the distribution of genotypes and variants. Here, by employing a maximum likelihood method, we performed phylogenetic analyses of the complete genome sequences of HPV16, HPV18 and HPV58 available from GenBank (<i>n</i> = 627, 146 and 157, respectively). We found several characteristic clusters that exclusively contain HPV genomes from Japan: two for HPV16 (sublineages A4 and A5), one for HPV18 (sublineage A1) and two for HPV58 (sublineages A1 and A2). Bayesian phylogenetic analyses of concatenated viral gene sequences showed that divergence of the most recent common ancestor of these Japan-specific clades was estimated to have occurred ~98,000 years before present (YBP) for HPV16 A4, ~39,000 YBP for HPV16 A5, ~38,000 YBP for HPV18 A1, ~26,000 for HPV58 A1 and ~25,000 YBP for HPV58 A2. This estimated timeframe for the divergence of the Japan-specific clades suggests that the introduction of these HPV variants into the Japanese archipelago dates back to at least ~25,000 YBP and provides a scenario of virus co-migration with ancestral Japanese populations from continental Asia during the Upper Paleolithic period.https://www.mdpi.com/1999-4915/14/3/464human papillomavirusBayesian phylogeneticsmost recent common ancestorupper paleolithic eraJapanese archipelago |
| spellingShingle | Kohsei Tanaka Gota Kogure Mamiko Onuki Koji Matsumoto Takashi Iwata Daisuke Aoki Iwao Kukimoto Ancient Evolutionary History of Human Papillomavirus Type 16, 18 and 58 Variants Prevalent Exclusively in Japan Viruses human papillomavirus Bayesian phylogenetics most recent common ancestor upper paleolithic era Japanese archipelago |
| title | Ancient Evolutionary History of Human Papillomavirus Type 16, 18 and 58 Variants Prevalent Exclusively in Japan |
| title_full | Ancient Evolutionary History of Human Papillomavirus Type 16, 18 and 58 Variants Prevalent Exclusively in Japan |
| title_fullStr | Ancient Evolutionary History of Human Papillomavirus Type 16, 18 and 58 Variants Prevalent Exclusively in Japan |
| title_full_unstemmed | Ancient Evolutionary History of Human Papillomavirus Type 16, 18 and 58 Variants Prevalent Exclusively in Japan |
| title_short | Ancient Evolutionary History of Human Papillomavirus Type 16, 18 and 58 Variants Prevalent Exclusively in Japan |
| title_sort | ancient evolutionary history of human papillomavirus type 16 18 and 58 variants prevalent exclusively in japan |
| topic | human papillomavirus Bayesian phylogenetics most recent common ancestor upper paleolithic era Japanese archipelago |
| url | https://www.mdpi.com/1999-4915/14/3/464 |
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