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Skelin J, Tomaić V. Comparative Analysis of Alpha and Beta HPV E6 Oncoproteins: Insights into Functional Distinctions and Divergent Mechanisms of Pathogenesis. Viruses 2023; 15:2253. [PMID: 38005929 PMCID: PMC10674601 DOI: 10.3390/v15112253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Human papillomaviruses (HPVs) represent a diverse group of DNA viruses that infect epithelial cells of mucosal and cutaneous tissues, leading to a wide spectrum of clinical outcomes. Among various HPVs, alpha (α) and beta (β) types have garnered significant attention due to their associations with human health. α-HPVs are primarily linked to infections of the mucosa, with high-risk subtypes, such as HPV16 and HPV18, being the major etiological agents of cervical and oropharyngeal cancers. In contrast, β-HPVs are predominantly associated with cutaneous infections and are commonly found on healthy skin. However, certain β-types, notably HPV5 and HPV8, have been implicated in the development of non-melanoma skin cancers in immunocompromised individuals, highlighting their potential role in pathogenicity. In this review, we comprehensively analyze the similarities and differences between α- and β-HPV E6 oncoproteins, one of the major drivers of viral replication and cellular transformation, and how these impact viral fitness and the capacity to induce malignancy. In particular, we compare the mechanisms these oncoproteins use to modulate common cellular processes-apoptosis, DNA damage repair, cell differentiation, and the immune response-further shedding light on their shared and distinct features, which enable them to replicate at divergent locations of the human body and cause different types of cancer.
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Affiliation(s)
| | - Vjekoslav Tomaić
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia;
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2
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Gelbard MK, Munger K. Human papillomaviruses: Knowns, mysteries, and unchartered territories. J Med Virol 2023; 95:e29191. [PMID: 37861365 PMCID: PMC10608791 DOI: 10.1002/jmv.29191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 10/21/2023]
Abstract
There has been an explosion in the number of papillomaviruses that have been identified and fully sequenced. Yet only a minute fraction of these has been studied in any detail. Most of our molecular research efforts have focused on the E6 and E7 proteins of "high-risk," cancer-associated human papillomaviruses (HPVs). Interactions of the high-risk HPV E6 and E7 proteins with their respective cellular targets, the p53 and the retinoblastoma tumor suppressors, have been investigated in minute detail. Some have thus questioned if research on papillomaviruses remains an exciting and worthwhile area of investigation. However, fundamentally new insights on the biological activities and cellular targets of the high-risk HPV E6 and E7 proteins have been discovered and previously unstudied HPVs have been newly associated with human diseases. HPV infections continue to be an important cause of human morbidity and mortality and since there are no antivirals to combat HPV infections, research on HPVs should remain attractive to new investigators and biomedical funding agencies, alike.
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Affiliation(s)
- Maya K. Gelbard
- Genetics, Molecular and Cellular Biology Program, Graduate School of Biomedical Sciences
- Department of Developmental, Molecular and Cellular Biology, Tufts University School of Medicine, Boston, MA 02111
| | - Karl Munger
- Genetics, Molecular and Cellular Biology Program, Graduate School of Biomedical Sciences
- Department of Developmental, Molecular and Cellular Biology, Tufts University School of Medicine, Boston, MA 02111
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3
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Happel AU, Balle C, Havyarimana E, Brown B, Maust BS, Feng C, Yi BH, Gill K, Bekker LG, Passmore JAS, Jaspan HB, Varsani A. Cervicovaginal Human Papillomavirus Genomes, Microbiota Composition and Cytokine Concentrations in South African Adolescents. Viruses 2023; 15:758. [PMID: 36992467 PMCID: PMC10054107 DOI: 10.3390/v15030758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
The interaction between cervicovaginal virome, bacteriome and genital inflammation has not been extensively investigated. We assessed the vaginal DNA virome from 33 South African adolescents (15-19 years old) using shotgun DNA sequencing of purified virions. We present analyses of eukaryote-infecting DNA viruses, with a focus on human papillomavirus (HPV) genomes and relate these to the vaginal bacterial microbiota (assessed by 16S rRNA gene sequencing) and cytokines (assessed by Luminex). The DNA virome included single-stranded (Anelloviridae, Genomoviridae) and double-stranded DNA viruses (Adenoviridae, Alloherpesviridae, Herpesviridae, Marseilleviridae, Mimiviridae, Polyomaviridae, Poxviridae). We identified 110 unique, complete HPV genomes within two genera (Alphapapillomavirus and Gammapapillomavirus) representing 40 HPV types and 12 species. Of the 40 HPV types identified, 35 showed positive co-infection patterns with at least one other type, mainly HPV-16. HPV-35, a high-risk genotype currently not targeted by available vaccines, was the most prevalent HPV type identified in this cohort. Bacterial taxa commonly associated with bacterial vaginosis also correlated with the presence of HPV. Bacterial vaginosis, rather than HPV, was associated with increased genital inflammation. This study lays the foundation for future work characterizing the vaginal virome and its role in women's health.
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Affiliation(s)
- Anna-Ursula Happel
- Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
| | - Christina Balle
- Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
| | - Enock Havyarimana
- Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
| | - Bryan Brown
- Seattle Children’s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109, USA
- Department of Pediatrics, University of Washington, 1510 San Juan Road NE, Seattle, WA 98195, USA
| | - Brandon S. Maust
- Seattle Children’s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109, USA
- Department of Pediatrics, University of Washington, 1510 San Juan Road NE, Seattle, WA 98195, USA
| | - Colin Feng
- Seattle Children’s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109, USA
| | - Byung H. Yi
- Seattle Children’s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109, USA
| | - Katherine Gill
- Desmond Tutu Health Foundation, 3 Woodlands Rd, Woodstock, Cape Town 7915, South Africa
| | - Linda-Gail Bekker
- Desmond Tutu Health Foundation, 3 Woodlands Rd, Woodstock, Cape Town 7915, South Africa
| | - Jo-Ann S. Passmore
- Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
- National Health Laboratory Service, Observatory, Cape Town 7925, South Africa
- NRF-DST Center of Excellence in HIV Prevention, Centre for the AIDS Programme of Research in South Africa, 719 Umbilo Road, Congella, Durban 4013, South Africa
| | - Heather B. Jaspan
- Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
- Seattle Children’s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109, USA
- Department of Pediatrics, University of Washington, 1510 San Juan Road NE, Seattle, WA 98195, USA
- Department of Global Health, University of Washington, 1959 NE Pacific St., Seattle, WA 98195, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town 7925, South Africa
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4
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Gong Y, Sui L, Li Y. Recombination in Papillomavirus: Controversy and Possibility. Virus Res 2022. [DOI: 10.1016/j.virusres.2022.198756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 03/20/2022] [Accepted: 03/23/2022] [Indexed: 10/18/2022]
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Thomas M, Banks L. The biology of papillomavirus PDZ associations: what do they offer papillomaviruses? Curr Opin Virol 2021; 51:119-126. [PMID: 34655911 DOI: 10.1016/j.coviro.2021.09.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/10/2021] [Accepted: 09/21/2021] [Indexed: 01/05/2023]
Abstract
The high-risk α-type papillomaviruses have a C-terminal PDZ-binding motif (PBM) on one of the two major oncoproteins E6 or E7; the vast majority on E6. The PBM is essential for the high-risk HPV life cycle, for episomal maintenance of the virus genome, and for maintaining the mitotic stability of the infected cell. The question is why only these viruses have PBMs - are there specific constraints imposed by the mucosal epithelium in which these viruses replicate? However the low-risk α-HPVs, such as HPV-6 and HPV-11 replicate extremely efficiently without a PBM, while viruses of the alpha8 group, such as HPV-40, replicate well with a very primitive PBM. So what does PDZ-binding capacity contribute to the fitness of the virus?
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Affiliation(s)
- Miranda Thomas
- ICGEB, AREA Science Park, Padriciano 99, 34149, Trieste, Italy.
| | - Lawrence Banks
- ICGEB, AREA Science Park, Padriciano 99, 34149, Trieste, Italy
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Latsuzbaia A, Wienecke-Baldacchino A, Tapp J, Arbyn M, Karabegović I, Chen Z, Fischer M, Mühlschlegel F, Weyers S, Pesch P, Mossong J. Characterization and Diversity of 243 Complete Human Papillomavirus Genomes in Cervical Swabs Using Next Generation Sequencing. Viruses 2020; 12:E1437. [PMID: 33327447 DOI: 10.3390/v12121437] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/04/2020] [Accepted: 12/10/2020] [Indexed: 12/21/2022] Open
Abstract
In recent years, next generation sequencing (NGS) technology has been widely used for the discovery of novel human papillomavirus (HPV) genotypes, variant characterization and genotyping. Here, we compared the analytical performance of NGS with a commercial PCR-based assay (Anyplex II HPV28) in cervical samples of 744 women. Overall, HPV positivity was 50.2% by the Anyplex and 45.5% by the NGS. With the NGS, we detected 25 genotypes covered by Anyplex and 41 additional genotypes. Agreement between the two methods for HPV positivity was 80.8% (kappa = 0.616) and 84.8% (kappa = 0.652) for 28 HPV genotypes and 14 high-risk genotypes, respectively. We recovered and characterized 243 complete HPV genomes from 153 samples spanning 40 different genotypes. According to phylogenetic analysis and pairwise distance, we identified novel lineages and sublineages of four high-risk and 16 low-risk genotypes. In total, 17 novel lineages and 14 novel sublineages were proposed, including novel lineages of HPV45, HPV52, HPV66 and a novel sublineage of HPV59. Our study provides important genomic insights on HPV types and lineages, where few complete genomes were publicly available.
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Flores-Miramontes MG, Olszewski D, Artaza-Irigaray C, Willemsen A, Bravo IG, Vallejo-Ruiz V, Leal-Herrera YA, Piña-Sánchez P, Molina-Pineda A, Cantón-Romero JC, Martínez-Silva MG, Jave-Suárez LF, Aguilar-Lemarroy A. Detection of Alpha, Beta, Gamma, and Unclassified Human Papillomaviruses in Cervical Cancer Samples From Mexican Women. Front Cell Infect Microbiol 2020; 10:234. [PMID: 32582561 PMCID: PMC7296070 DOI: 10.3389/fcimb.2020.00234] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/23/2020] [Indexed: 11/13/2022] Open
Abstract
Background: Cervical cancer (CC) is associated to high-risk human papillomavirus (HPV) infections, for this reason it is crucial to have sensitive and accurate HPV diagnostic tests. To date, most research is focused on HPVs within the Alphapapillomavirus (α-PVs) genus and little attention has been paid to cervical infections with other HPV genotypes, like those of the Betapapillomavirus (β-PVs) and Gammapapillomavirus (γ-PVs) genera. The aim of this study was to determine the HPV genotypes from different genera in women with CC using Next-Generation Sequencing (NGS). Methods: The study comprised 48 HPV positive CC samples evaluated with the Linear Array HPV Genotyping test and individually sequenced by 454 NGS using PGMY09/11 and FAP primers. To determine the HPV genotypes present in each sample, the obtained sequences were compared with all HPV L1 gene reference sequences from the Papillomavirus Episteme database (PaVE). Moreover, 50 HPV positive low-grade cervical lesion samples individually genotyped with NGS were also included to determine the genotypes present preferentially in CC patients. Results: Among the 48 CC samples, 68.75% consisted of multiple HPV infections, 51 different genotypes were detected, of which 7 are still unclassified, 28 belong to α-PVs (6, 11, 16, 18, 26, 30, 33, 35, 39, 42, 43, 44, 45, 51, 52, 53, 54, 59, 62, 66, 68, 69, 70, 71, 74, 81, 102, 114), 10 to β-PVs (5, 12, 21, 37, 38b, 47, 80, 107, 118, 122), and 6 to γ-PVs (101, 103, 123, 135, 147, 214). Among them, HPV16 was the most prevalent genotype (54.2%), followed by HPV18 (16.7%), HPV38b (14.6%), and HPVs 52/62/80 (8.3%). Some genotypes were exclusively found in CC when compared with Cervical Intraepithelial Neoplasia grade 1 (CIN1) samples, such as HPVs 5, 18, 38b, 107, 122, FA39, FA116, mSK_120, and mSK_136. Conclusions: This work demonstrates the great diversity of HPV genotypes detected by combining PGMY and FAP primers with NGS in cervical swabs. The relatively high attribution of β- and γ- PVs in CC samples suggest their possible role as carcinogenic cofactors, but deeper studies need to be performed to determine if they have transforming properties and the significance of HPV-coinfections.
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Affiliation(s)
| | - Dominik Olszewski
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Cristina Artaza-Irigaray
- Centro de Investigación Biomédica de Occidente (CIBO)-Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Mexico
| | - Anouk Willemsen
- Centre National de la Recherche Scientifique (CNRS), Laboratory MIVEGEC (UMR CNRS IRD Uni Montpellier), Montpellier, France
| | - Ignacio G Bravo
- Centre National de la Recherche Scientifique (CNRS), Laboratory MIVEGEC (UMR CNRS IRD Uni Montpellier), Montpellier, France
| | - Verónica Vallejo-Ruiz
- Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social (IMSS), Metepec, Mexico
| | - Yelda Aurora Leal-Herrera
- Centro Institucional de Capacitación y Registro de Cáncer (CICyRC), Unidad Médica de Alta Especialidad (UMAE), Instituto Mexicano del Seguro Social (IMSS), Mérida, Mexico
| | - Patricia Piña-Sánchez
- Laboratorio de Oncología Molecular, Unidad de Investigación Médica en Enfermedades Oncológicas (UIMEO), Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Andrea Molina-Pineda
- Centro de Investigación Biomédica de Occidente (CIBO)-Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Juan Carlos Cantón-Romero
- Unidad Médica de Alta Especialidad (UMAE), Hospital de Ginecología y Obstetricia, Centro Médico Nacional de Occidente, Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Mexico
| | - María Guadalupe Martínez-Silva
- Departamento de Anatomía Patológica, Centro Médico Nacional de Occidente, Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Mexico
| | - Luis Felipe Jave-Suárez
- Centro de Investigación Biomédica de Occidente (CIBO)-Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Mexico
| | - Adriana Aguilar-Lemarroy
- Centro de Investigación Biomédica de Occidente (CIBO)-Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Mexico
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8
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Bolatti EM, Hošnjak L, Chouhy D, Casal PE, Re-Louhau MF, Bottai H, Komloš KF, Poljak M, Giri AA. Assessing Gammapapillomavirus infections of mucosal epithelia with two broad-spectrum PCR protocols. BMC Infect Dis 2020; 20:274. [PMID: 32264841 PMCID: PMC7140492 DOI: 10.1186/s12879-020-4893-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 02/17/2020] [Indexed: 12/14/2022] Open
Abstract
Background Human papillomaviruses (HPVs) have been divided into mucosal and cutaneous types according to their primary epithelial tissue tropism. However, recent studies showed the presence of several cutaneous types in mucosal lesions and healthy mucosa from different anatomical sites. Methods Here, the HPV prevalence and type-specific distribution were assessed in a variety of mucosal samples from 435 individuals using a combination of two established broad-spectrum primer systems: Gamma-PV PCR and CUT PCR. Results Overall HPV prevalence in anal canal swabs, cervical cancer biopsies, genital warts and oral swabs was 85, 47, 62 and 4%, respectively. In anal canal swabs, Alpha-PVs were most frequently found (59%), followed by Gamma- (37%) and Beta-PVs (4%). The prevalence and persistence of HPV infection in the anal canal of 226 individuals were further explored. Overall HPV, Gamma-PVs and multiple HPV infections were significantly higher in men vs. women (p = 0.034, p = 0.027 and p = 0.003, respectively); multiple HPV infections were more common in individuals ≤40 years (p = 0.05), and significantly higher prevalence of Gamma-PVs and multiple HPV infections was observed in HIV-1-positive vs. HIV-1-negative individuals (p = 0.003 and p = 0.04, respectively). Out of 21 patients with follow-up anal swabs, only one persistent infection with the same type (HPV58) was detected. Conclusions Our findings suggest that Gamma-PVs (except species Gamma-6) are ubiquitous viruses with dual muco-cutaneous tissue tropism. Anal canal Gamma-PV infections may be associated with sexual behavior and the host immune status. This study expands the knowledge on Gamma-PVs’ tissue tropism, providing valuable data on the characteristics of HPV infection in the anal canal.
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Affiliation(s)
- Elisa M Bolatti
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, 2000, Rosario, Argentina.,Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Lea Hošnjak
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Zaloška 4, 1000, Ljubljana, Slovenia
| | - Diego Chouhy
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, 2000, Rosario, Argentina.,Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Pablo E Casal
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - María F Re-Louhau
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, 2000, Rosario, Argentina
| | - Hebe Bottai
- Área Estadística y Procesamiento de Datos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Kristina Fujs Komloš
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Zaloška 4, 1000, Ljubljana, Slovenia
| | - Mario Poljak
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Zaloška 4, 1000, Ljubljana, Slovenia.
| | - Adriana A Giri
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, 2000, Rosario, Argentina. .,Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
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9
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Ling Y, Wang J, Yin J, Xu J, Wu Y, Zhou R, Lu J, Yang S, Wang X, Shen Q, Zhang W. Genomic organization of a Gamma-6 papillomavirus metagenomic discovered from vaginal swab samples of Chinese pregnant women. Virol J 2020; 17:44. [PMID: 32234038 PMCID: PMC7110641 DOI: 10.1186/s12985-020-01319-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 03/19/2020] [Indexed: 12/17/2022] Open
Abstract
A complete genome sequence of human papillomaviruses (HPV) named as HPV-ujs-21015 was determined by viral metagenomic and PCR methods. The complete genome is 7354 bp in length with GC content of 41.7%, of which the genome was predicted to contain six ORFs (Open Reading Frame, ORF) coding for four early proteins (E7, E1, E4, and E2) and two late proteins (L1 and L2). Phylogenetic analysis based on the complete genome and the L1 protein showed that HPV-ujs-21015 belongs to a type 214 member within genus Gamma-6 papillomavirus. It is the first complete genome of Gamma-6 papillomavirus discovered from pregnant women in China.
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Affiliation(s)
- Yu Ling
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China.,Department of Laboratory Medicine, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, 210004, People's Republic of China
| | - Jianqiang Wang
- Intensive Care Unit, Jintan District Hospital of Traditional Chinese Medicine, 1006 Huixian Road, Changzhou, Jiangsu, 213200, People's Republic of China
| | - Jun Yin
- Zhangjiagang Customs, 28 Renmin Road, Zhangjiagang, Jiangsu, 215699, People's Republic of China
| | - Jianpu Xu
- Zhangjiagang Customs, 28 Renmin Road, Zhangjiagang, Jiangsu, 215699, People's Republic of China
| | - Yufan Wu
- Zhangjiagang Customs, 28 Renmin Road, Zhangjiagang, Jiangsu, 215699, People's Republic of China
| | - Rui Zhou
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China
| | - Juan Lu
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China
| | - Shixing Yang
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China
| | - Xiaochun Wang
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China
| | - Quan Shen
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China.
| | - Wen Zhang
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China.
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10
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Murahwa AT, Nindo F, Onywera H, Meiring TL, Martin DP, Williamson AL. Evolutionary dynamics of ten novel Gamma-PVs: insights from phylogenetic incongruence, recombination and phylodynamic analyses. BMC Genomics 2019; 20:368. [PMID: 31088349 PMCID: PMC6518707 DOI: 10.1186/s12864-019-5735-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 04/25/2019] [Indexed: 02/06/2023] Open
Abstract
Background Human papillomaviruses (HPVs) are genetically diverse, belonging to five distinct genera: Alpha, Beta, Gamma, Mu and Nu. All papillomaviruses have double stranded DNA genomes that are thought to evolve slowly because they co-opt high-fidelity host cellular DNA polymerases for their replication. Despite extensive efforts to catalogue all the HPV species that infect humans, it is likely that many still remain undiscovered. Here we use the sequences of ten novel Gammapapillomaviruses (Gamma-PVs) characterized in previous studies and related HPVs to analyse the evolutionary dynamics of these viruses at the whole genome and individual gene scales. Results We found statistically significant incongruences between the phylogenetic trees of different genes which imply gene-to-gene variation in the evolutionary processes underlying the diversification of Gamma-PVs. We were, however, only able to detect convincing evidence of a single recombination event which, on its own, cannot explain the observed incongruences between gene phylogenies. The divergence times of the last common ancestor (LCA) of the Alpha, Beta, Mu, Nu and Gamma genera was predicted to have existed between 49.7–58.5 million years ago, before splitting into the five main lineages. The LCA of the Gamma-PVs at this time was predicted to have existed between 45.3 and 67.5 million years ago: approximately at the time when the simian and tarsier lineages of the primates diverged. Conclusion Consequently, we report here phylogenetic tree incongruence without strong evidence of recombination.
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Affiliation(s)
- Alltalents T Murahwa
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Fredrick Nindo
- Division of Computational Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Harris Onywera
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Tracy L Meiring
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Darren P Martin
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,Division of Computational Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Anna-Lise Williamson
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa. .,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa. .,SAMRC Gynaecological Cancer Research Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
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