Analysis of the genomic diversity of human papillomavirus type 31 in cervical samples reveals the presence of novel sublineages in clade C
Human papillomavirus 31 (HPV31) is the fourth most frequent high-risk HPV (HR-HPV) genotype identified in cervical cancer (CC) worldwide and in Mexico. It has been recently classified into three lineages (A, B, and C) and eight sublineages (A1, A2, B1, B2, and C1 – C4). Here, we report the complete...
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| Veröffentlicht in: | Archives of virology 2022-12, Vol.167 (12), p.2795-2800 |
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| creator | Fragoso-Fonseca, David Esaú Ruiz-Hernández, Ubaldo Emilio Trujillo-Salgado, Brenda Berenice Manuell-Barrios, Rita Teresita Garcés-Ayala, Fabiola del Mazo-López, Juan Carlos Méndez-Tenorio, Alfonso Hernández-Rivas, Lucía Ramírez-González, José Ernesto Escobar-Escamilla, Noé |
| description | Human papillomavirus 31 (HPV31) is the fourth most frequent high-risk HPV (HR-HPV) genotype identified in cervical cancer (CC) worldwide and in Mexico. It has been recently classified into three lineages (A, B, and C) and eight sublineages (A1, A2, B1, B2, and C1 – C4). Here, we report the complete genomic sequences of 14 HPV31 isolates from cervical samples, and these were compared with viral genome sequences from the GenBank database for phylogenetic and genetic distance analysis. The formation of two novel clades within the C lineage (proposed as C5 and C6) was observed, with a well-defined variant-specific mutational pattern. The smallest average pairwise distance was 0.71% for lineages A and B, 0.94% for lineages A and C, and 1.01% for lineages B and C, and between sublineages, these values were 0.21% for clade A, 0.29% for clade B, and 0.24% for clade C. The isolates were grouped into the sublineages A1, B2, C1-C3, and C6. This is the first report on the whole-genome diversity of HPV31 in Mexico. |
| doi_str_mv | 10.1007/s00705-022-05589-2 |
| format | Article |
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It has been recently classified into three lineages (A, B, and C) and eight sublineages (A1, A2, B1, B2, and C1 – C4). Here, we report the complete genomic sequences of 14 HPV31 isolates from cervical samples, and these were compared with viral genome sequences from the GenBank database for phylogenetic and genetic distance analysis. The formation of two novel clades within the C lineage (proposed as C5 and C6) was observed, with a well-defined variant-specific mutational pattern. The smallest average pairwise distance was 0.71% for lineages A and B, 0.94% for lineages A and C, and 1.01% for lineages B and C, and between sublineages, these values were 0.21% for clade A, 0.29% for clade B, and 0.24% for clade C. The isolates were grouped into the sublineages A1, B2, C1-C3, and C6. This is the first report on the whole-genome diversity of HPV31 in Mexico.</description><identifier>ISSN: 0304-8608</identifier><identifier>EISSN: 1432-8798</identifier><identifier>DOI: 10.1007/s00705-022-05589-2</identifier><identifier>PMID: 36085531</identifier><language>eng</language><publisher>Vienna: Springer Vienna</publisher><subject>Annotated Sequence Record ; Biomedical and Life Sciences ; Biomedicine ; Cervical cancer ; Cervix ; Female ; Genetic analysis ; Genetic distance ; Genetic Variation ; Genome, Viral ; Genomes ; Genomic analysis ; Genotype ; Genotypes ; Human papillomavirus ; Human papillomavirus 31 - genetics ; Human Papillomavirus Viruses ; Humans ; Infectious Diseases ; Medical Microbiology ; Papillomavirus Infections ; Phylogeny ; Uterine Cervical Neoplasms ; Virology</subject><ispartof>Archives of virology, 2022-12, Vol.167 (12), p.2795-2800</ispartof><rights>The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature 2022. Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.</rights><rights>2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c375t-bb8e1ef43ab4c2bbce0c6f2256f721d6031d175240aefaa03456828fdabff6743</citedby><cites>FETCH-LOGICAL-c375t-bb8e1ef43ab4c2bbce0c6f2256f721d6031d175240aefaa03456828fdabff6743</cites><orcidid>0000-0001-7950-5172 ; 0000-0002-7344-7757 ; 0000-0001-8929-476X ; 0000-0001-6272-2584 ; 0000-0003-0477-2211 ; 0000-0003-1871-4311 ; 0000-0003-3728-3887</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00705-022-05589-2$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00705-022-05589-2$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/36085531$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Fragoso-Fonseca, David Esaú</creatorcontrib><creatorcontrib>Ruiz-Hernández, Ubaldo Emilio</creatorcontrib><creatorcontrib>Trujillo-Salgado, Brenda Berenice</creatorcontrib><creatorcontrib>Manuell-Barrios, Rita Teresita</creatorcontrib><creatorcontrib>Garcés-Ayala, Fabiola</creatorcontrib><creatorcontrib>del Mazo-López, Juan Carlos</creatorcontrib><creatorcontrib>Méndez-Tenorio, Alfonso</creatorcontrib><creatorcontrib>Hernández-Rivas, Lucía</creatorcontrib><creatorcontrib>Ramírez-González, José Ernesto</creatorcontrib><creatorcontrib>Escobar-Escamilla, Noé</creatorcontrib><title>Analysis of the genomic diversity of human papillomavirus type 31 in cervical samples reveals the presence of novel sublineages in clade C</title><title>Archives of virology</title><addtitle>Arch Virol</addtitle><addtitle>Arch Virol</addtitle><description>Human papillomavirus 31 (HPV31) is the fourth most frequent high-risk HPV (HR-HPV) genotype identified in cervical cancer (CC) worldwide and in Mexico. It has been recently classified into three lineages (A, B, and C) and eight sublineages (A1, A2, B1, B2, and C1 – C4). Here, we report the complete genomic sequences of 14 HPV31 isolates from cervical samples, and these were compared with viral genome sequences from the GenBank database for phylogenetic and genetic distance analysis. The formation of two novel clades within the C lineage (proposed as C5 and C6) was observed, with a well-defined variant-specific mutational pattern. The smallest average pairwise distance was 0.71% for lineages A and B, 0.94% for lineages A and C, and 1.01% for lineages B and C, and between sublineages, these values were 0.21% for clade A, 0.29% for clade B, and 0.24% for clade C. The isolates were grouped into the sublineages A1, B2, C1-C3, and C6. 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genetics</topic><topic>Human Papillomavirus Viruses</topic><topic>Humans</topic><topic>Infectious Diseases</topic><topic>Medical Microbiology</topic><topic>Papillomavirus Infections</topic><topic>Phylogeny</topic><topic>Uterine Cervical Neoplasms</topic><topic>Virology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Fragoso-Fonseca, David Esaú</creatorcontrib><creatorcontrib>Ruiz-Hernández, Ubaldo Emilio</creatorcontrib><creatorcontrib>Trujillo-Salgado, Brenda Berenice</creatorcontrib><creatorcontrib>Manuell-Barrios, Rita Teresita</creatorcontrib><creatorcontrib>Garcés-Ayala, Fabiola</creatorcontrib><creatorcontrib>del Mazo-López, Juan Carlos</creatorcontrib><creatorcontrib>Méndez-Tenorio, Alfonso</creatorcontrib><creatorcontrib>Hernández-Rivas, Lucía</creatorcontrib><creatorcontrib>Ramírez-González, José Ernesto</creatorcontrib><creatorcontrib>Escobar-Escamilla, Noé</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - 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It has been recently classified into three lineages (A, B, and C) and eight sublineages (A1, A2, B1, B2, and C1 – C4). Here, we report the complete genomic sequences of 14 HPV31 isolates from cervical samples, and these were compared with viral genome sequences from the GenBank database for phylogenetic and genetic distance analysis. The formation of two novel clades within the C lineage (proposed as C5 and C6) was observed, with a well-defined variant-specific mutational pattern. The smallest average pairwise distance was 0.71% for lineages A and B, 0.94% for lineages A and C, and 1.01% for lineages B and C, and between sublineages, these values were 0.21% for clade A, 0.29% for clade B, and 0.24% for clade C. The isolates were grouped into the sublineages A1, B2, C1-C3, and C6. This is the first report on the whole-genome diversity of HPV31 in Mexico.</abstract><cop>Vienna</cop><pub>Springer Vienna</pub><pmid>36085531</pmid><doi>10.1007/s00705-022-05589-2</doi><tpages>6</tpages><orcidid>https://orcid.org/0000-0001-7950-5172</orcidid><orcidid>https://orcid.org/0000-0002-7344-7757</orcidid><orcidid>https://orcid.org/0000-0001-8929-476X</orcidid><orcidid>https://orcid.org/0000-0001-6272-2584</orcidid><orcidid>https://orcid.org/0000-0003-0477-2211</orcidid><orcidid>https://orcid.org/0000-0003-1871-4311</orcidid><orcidid>https://orcid.org/0000-0003-3728-3887</orcidid></addata></record> |
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| ispartof | Archives of virology, 2022-12, Vol.167 (12), p.2795-2800 |
| issn | 0304-8608 1432-8798 |
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| source | MEDLINE; SpringerNature Journals |
| subjects | Annotated Sequence Record Biomedical and Life Sciences Biomedicine Cervical cancer Cervix Female Genetic analysis Genetic distance Genetic Variation Genome, Viral Genomes Genomic analysis Genotype Genotypes Human papillomavirus Human papillomavirus 31 - genetics Human Papillomavirus Viruses Humans Infectious Diseases Medical Microbiology Papillomavirus Infections Phylogeny Uterine Cervical Neoplasms Virology |
| title | Analysis of the genomic diversity of human papillomavirus type 31 in cervical samples reveals the presence of novel sublineages in clade C |
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