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da Silva-Júnior AHP, de Oliveira Silva RC, Gurgel APAD, Barros-Júnior MR, Nascimento KCG, Santos DL, Pena LJ, Lima RDCP, Batista MVDA, Chagas BS, de Freitas AC. Identification and Functional Implications of the E5 Oncogene Polymorphisms of Human Papillomavirus Type 16. Trop Med Infect Dis 2024; 9:140. [PMID: 39058182 PMCID: PMC11281449 DOI: 10.3390/tropicalmed9070140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/12/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
The persistence of the human papillomavirus type 16 (HPV16) infection on the cervical epithelium contributes to the progression of cervical cancer. Studies have demonstrated that HPV16 genetic variants may be associated with different risks of developing cervical cancer. However, the E5 oncoprotein of HPV16, which is related to several cellular mechanisms in the initial phases of the infection and thus contributes to carcinogenesis, is still little studied. Here we investigate the HPV16 E5 oncogene variants to assess the effects of different mutations on the biological function of the E5 protein. We detected and analyzed the HPV16 E5 oncogene polymorphisms and their phylogenetic relationships. After that, we proposed a tertiary structure analysis of the protein variants, preferential codon usage, and functional activity of the HPV16 E5 protein. Intra-type variants were grouped in the lineages A and D using in silico analysis. The mutations in E5 were located in the T-cell epitopes region. We therefore analyzed the interference of the HPV16 E5 protein in the NF-kB pathway. Our results showed that the variants HPV16E5_49PE and HPV16E5_85PE did not increase the potential of the pathway activation capacity. This study provides additional knowledge about the mechanisms of dispersion of the HPV16 E5 variants, providing evidence that these variants may be relevant to the modulation of the NF-κB signaling pathway.
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Affiliation(s)
- Antônio Humberto P. da Silva-Júnior
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Pernambuco, Brazil; (A.H.P.d.S.-J.); (R.C.d.O.S.); (M.R.B.-J.); (K.C.G.N.); (D.L.S.); (R.d.C.P.L.); (B.S.C.)
| | - Ruany Cristyne de Oliveira Silva
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Pernambuco, Brazil; (A.H.P.d.S.-J.); (R.C.d.O.S.); (M.R.B.-J.); (K.C.G.N.); (D.L.S.); (R.d.C.P.L.); (B.S.C.)
| | - Ana Pavla A. Diniz Gurgel
- Department of Engineering and Environment, Federal University of Paraiba, João Pessoa 58033-455, Paraíba, Brazil;
| | - Marconi Rêgo Barros-Júnior
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Pernambuco, Brazil; (A.H.P.d.S.-J.); (R.C.d.O.S.); (M.R.B.-J.); (K.C.G.N.); (D.L.S.); (R.d.C.P.L.); (B.S.C.)
| | - Kamylla Conceição Gomes Nascimento
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Pernambuco, Brazil; (A.H.P.d.S.-J.); (R.C.d.O.S.); (M.R.B.-J.); (K.C.G.N.); (D.L.S.); (R.d.C.P.L.); (B.S.C.)
| | - Daffany Luana Santos
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Pernambuco, Brazil; (A.H.P.d.S.-J.); (R.C.d.O.S.); (M.R.B.-J.); (K.C.G.N.); (D.L.S.); (R.d.C.P.L.); (B.S.C.)
| | - Lindomar J. Pena
- Laboratory of Virology and Experimental Therapy, Instituto Aggeu Magalhães (IAM), Oswaldo Cruz Foundation, Recife 50670-901, Pernambuco, Brazil;
| | - Rita de Cássia Pereira Lima
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Pernambuco, Brazil; (A.H.P.d.S.-J.); (R.C.d.O.S.); (M.R.B.-J.); (K.C.G.N.); (D.L.S.); (R.d.C.P.L.); (B.S.C.)
| | - Marcus Vinicius de Aragão Batista
- Laboratory of Molecular Genetics and Biotechnology (GMBio), Department of Biology, Federal University of Sergipe, São Cristóvão 49107-230, Sergipe, Brazil
| | - Bárbara Simas Chagas
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Pernambuco, Brazil; (A.H.P.d.S.-J.); (R.C.d.O.S.); (M.R.B.-J.); (K.C.G.N.); (D.L.S.); (R.d.C.P.L.); (B.S.C.)
| | - Antonio Carlos de Freitas
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Pernambuco, Brazil; (A.H.P.d.S.-J.); (R.C.d.O.S.); (M.R.B.-J.); (K.C.G.N.); (D.L.S.); (R.d.C.P.L.); (B.S.C.)
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Sichero L, Picconi MA, Villa LL. The contribution of Latin American research to HPV epidemiology and natural history knowledge. ACTA ACUST UNITED AC 2020; 53:e9560. [PMID: 32022103 PMCID: PMC6993359 DOI: 10.1590/1414-431x20199560] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 11/18/2019] [Indexed: 04/29/2023]
Abstract
Our aim was to review the major contributions of studies conducted in different Latin American (LA) countries to the field of human papillomavirus (HPV) epidemiology, natural history, risk of disease, and prevention strategies, mainly in the uterine cervix. Although cytological screening is established in several countries in LA, incidence and mortality rates from cervical cancer (CC) are still extremely high. Finally, data from large cohort studies conducted in LA countries provided seminal data to propose primary and secondary prevention modalities: the HPV vaccine has been introduced in the national immunization programs of several LA countries and multiple screening experiences using HPV testing are under evaluation in the region.
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Affiliation(s)
- L Sichero
- Centro de Investigação Translacional em Oncologia, Instituto do Câncer do Estado de São Paulo, Hospital das Clinicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
| | - M A Picconi
- Oncogenic Viruses Service, National and Regional HPV Reference Laboratory, National Institute of Infectious Diseases - ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - L L Villa
- Centro de Investigação Translacional em Oncologia, Instituto do Câncer do Estado de São Paulo, Hospital das Clinicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil.,Departamento de Radiologia e Oncologia, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
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3
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Zhao J, Zhu J, Guo J, Zhu T, Zhong J, Liu M, Ruan Y, Liao S, Li F. Genetic variability and functional implication of HPV16 from cervical intraepithelial neoplasia in Shanghai women. J Med Virol 2019; 92:372-381. [PMID: 31670402 DOI: 10.1002/jmv.25618] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/26/2019] [Indexed: 12/23/2022]
Abstract
Human papillomavirus (HPV)16 gene mutation is usually associated with persistent HPV infection and cervical intraepithelial neoplasia (CIN). However, the functional implications of HPV16 mutations remain poorly understood.145 LCR/E6/E7 of the HPV16 isolates were amplified and sequenced, and HPV16 integration status was detected. In total, 89 SNPs (68 in the LCR, 13 in E6, 8 in E7) were discovered, 11 of which were nonsynonymous mutations (8 in E6, 3 in E7). The H85Y and E120D variants in E6 were significantly reduced in the high-grade squamous intraepithelial lesion (HSIL) group compared to the <HSIL group (P = .046 and .005), conversely the N29S in E7(P = .01). Amino acid substitutions (D32N/E, E36Q, H85Y, and E120D in E6 and N29H/S and R77C in E7) were predicted to have an effect on conserved structural and functional residues, and five amino acid substitutions (H85Y, E36Q, I34L, and D32E in E6; R77C in E7) would potentially change the secondary structure. "6329G>T," a potential binding site for TATA-binding protein, is the most common in LCR variants. A4 (Asian) was associated with an increased risk of HSIL compared to A1-3(P = .009). The H85/E120 in E6 and N29 in HPV16 E7 might play a critical role in carcinogenesis by disrupting p53 and Rb degradation due to affecting their interaction, respectively. In a word, the findings in this study provide preventative and therapeutic interventions of HPV16 -related cervical lesions/cancer.
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Affiliation(s)
- Junwei Zhao
- Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jiacheng Zhu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Maternal and Child Health Research Institute, BGI-Shenzhen, Shenzhen, China
| | - Junhan Guo
- Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Tailin Zhu
- School of Physics HH Wills Physics Laboratory, University of Bristol, Bristol, UK
| | - Jixing Zhong
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, China
| | - Min Liu
- Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yetian Ruan
- Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shujie Liao
- Shujie Liao Cancer Biology Research Center, Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fang Li
- Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, Shanghai, China
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Ramas V, Mirazo S, Bonilla S, Ruchansky D, Arbiza J. Analysis of human papillomavirus 16 E6, E7 genes and Long Control Region in cervical samples from Uruguayan women. Gene 2018; 654:103-109. [PMID: 29454092 DOI: 10.1016/j.gene.2018.02.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 01/12/2018] [Accepted: 02/08/2018] [Indexed: 11/20/2022]
Abstract
OBJECTIVE This study aims to investigate the HPV16 variant distribution by sequence analyses of E6, E7 oncogenes and the Long Control Region (LCR), from cervical cells collected from Uruguayan women, and to reconstruct the phylogenetic relationships among variants. METHODS Forty-seven HPV16 variants, obtained from women with HSIL, LSIL, ASCUS and NILM cytological classes were analyzed for LCR and 12 were further studied for E6 and E7. Detailed sequence comparison, genetic heterogeneity analyses and phylogenetic reconstruction were performed. RESULTS A high variability was observed among LCR sequences, which were distributed in 18 different variants. E6 and E7 sequences exhibited novel non-synonymous substitutions. Uruguayan sequences mainly belonged to the European lineage, and only 5 sequences clustered in non-European branches; 3 of them in the Asian-American and North-American linage and 2 in an African branch. Additionally, 6 new variants from European and African clusters were identified. CONCLUSIONS HPV16 isolates mainly belonged to the European lineage, though strains from African and Asian-American lineages were also identified. Herein is reported for the first time the distribution and molecular characterization of HPV16 variants from Uruguay, providing novel insights on the molecular epidemiology of this infectious disease in the South America. SYNOPSIS A high variability among HPV 16 isolates mainly belonged to European lineage, provides an extensive sequence dataset from a country with high burden of cervical cancer.
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Affiliation(s)
- Viviana Ramas
- Sección Virología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Santiago Mirazo
- Sección Virología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Sylvia Bonilla
- Laboratorio de Citología, Servicio de Atención a la Salud, Intendencia Municipal de Montevideo, Martín C. Martínez 1677, 11200 Montevideo, Uruguay
| | - Dora Ruchansky
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Alfredo Navarro 3051, 11600, Universidad de la República, Montevideo, Uruguay
| | - Juan Arbiza
- Sección Virología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
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Bedoya-Pilozo CH, Medina Magües LG, Espinosa-García M, Sánchez M, Parrales Valdiviezo JV, Molina D, Ibarra MA, Quimis-Ponce M, España K, Párraga Macias KE, Cajas Flores NV, Orlando SA, Robalino Penaherrera JA, Chedraui P, Escobar S, Loja Chango RD, Ramirez-Morán C, Espinoza-Caicedo J, Sánchez-Giler S, Limia CM, Alemán Y, Soto Y, Kouri V, Culasso ACA, Badano I. Molecular epidemiology and phylogenetic analysis of human papillomavirus infection in women with cervical lesions and cancer from the coastal region of Ecuador. Rev Argent Microbiol 2017; 50:136-146. [PMID: 29157596 DOI: 10.1016/j.ram.2017.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 05/28/2017] [Accepted: 06/25/2017] [Indexed: 11/26/2022] Open
Abstract
The aim of the present study was to gather information regarding the molecular epidemiology of Human papillomavirus (HPV) and related risk factors in a group of women with low- and high-grade cervical lesions and cancer from the coastal region of Ecuador. In addition, we studied the evolution of HPV variants from the most prevalent types and provided a temporal framework for their emergence, which may help to trace the source of dissemination within the region. We analyzed 166 samples, including 57 CIN1, 95 CIN2/3 and 14 cancer cases. HPV detection and typing was done by PCR-sequencing (MY09/MY11). HPV variants and estimation of the time to most recent common ancestor (tMRCA) was assessed through phylogeny and coalescence analysis. HPV DNA was found in 54.4% of CIN1, 74.7% of CIN2/3 and 78.6% of cancer samples. HPV16 (38.9%) and HPV58 (19.5%) were the most prevalent types. Risk factors for the development of cervical lesions/cancer were the following: three or more pregnancies (OR=4.3), HPV infection (OR=3.7 for high-risk types; OR=3.5 for HPV16), among others. With regard to HPV evolution, HPV16 isolates belonged to lineages A (69%) and D (31%) whereas HPV58 isolates belonged only to lineage A. The period of emergence of HPV16 was in association with human populations (tMRCA=91052 years for HPV16A and 27000 years for HPV16D), whereas HPV58A preceded Homo sapiens evolution (322257 years). This study provides novel data on HPV epidemiology and evolution in Ecuador, which will be fundamental in the vaccine era.
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Affiliation(s)
- Cesar H Bedoya-Pilozo
- Dirección de Investigación, Desarrollo e Innovación, Instituto Nacional de Investigaciones en Salud Pública (INSPI), Av. Julian Coronel 905 y Esmeraldas, 090510 Guayaquil, Ecuador; Escuela Superior Politécnica del Litoral, ESPOL, Laboratorio de Biomedicina - Facultad de Ciencias de la Vida (FCV), Campus Gustavo Galindo, Km 30.5 Vía Perimetral, Guayaquil, Ecuador.
| | - Lex G Medina Magües
- Escuela Superior Politécnica del Litoral, ESPOL, Laboratorio de Biomedicina - Facultad de Ciencias de la Vida (FCV), Campus Gustavo Galindo, Km 30.5 Vía Perimetral, Guayaquil, Ecuador
| | - Maylen Espinosa-García
- Dirección de Investigación, Desarrollo e Innovación, Instituto Nacional de Investigaciones en Salud Pública (INSPI), Av. Julian Coronel 905 y Esmeraldas, 090510 Guayaquil, Ecuador
| | - Martha Sánchez
- Dirección de Investigación, Desarrollo e Innovación, Instituto Nacional de Investigaciones en Salud Pública (INSPI), Av. Julian Coronel 905 y Esmeraldas, 090510 Guayaquil, Ecuador
| | - Johanna V Parrales Valdiviezo
- Dirección de Investigación, Desarrollo e Innovación, Instituto Nacional de Investigaciones en Salud Pública (INSPI), Av. Julian Coronel 905 y Esmeraldas, 090510 Guayaquil, Ecuador
| | - Denisse Molina
- Dirección de Investigación, Desarrollo e Innovación, Instituto Nacional de Investigaciones en Salud Pública (INSPI), Av. Julian Coronel 905 y Esmeraldas, 090510 Guayaquil, Ecuador
| | - María A Ibarra
- Dirección de Investigación, Desarrollo e Innovación, Instituto Nacional de Investigaciones en Salud Pública (INSPI), Av. Julian Coronel 905 y Esmeraldas, 090510 Guayaquil, Ecuador
| | - María Quimis-Ponce
- Dirección de Investigación, Desarrollo e Innovación, Instituto Nacional de Investigaciones en Salud Pública (INSPI), Av. Julian Coronel 905 y Esmeraldas, 090510 Guayaquil, Ecuador
| | - Karool España
- Dirección de Investigación, Desarrollo e Innovación, Instituto Nacional de Investigaciones en Salud Pública (INSPI), Av. Julian Coronel 905 y Esmeraldas, 090510 Guayaquil, Ecuador
| | - Karla E Párraga Macias
- Dirección de Investigación, Desarrollo e Innovación, Instituto Nacional de Investigaciones en Salud Pública (INSPI), Av. Julian Coronel 905 y Esmeraldas, 090510 Guayaquil, Ecuador
| | - Nancy V Cajas Flores
- Dirección de Investigación, Desarrollo e Innovación, Instituto Nacional de Investigaciones en Salud Pública (INSPI), Av. Julian Coronel 905 y Esmeraldas, 090510 Guayaquil, Ecuador
| | - Solon A Orlando
- Dirección de Investigación, Desarrollo e Innovación, Instituto Nacional de Investigaciones en Salud Pública (INSPI), Av. Julian Coronel 905 y Esmeraldas, 090510 Guayaquil, Ecuador; Universidad Agraria del Ecuador, Av. 25 de Julio y Pio Jaramillo, P.O. BOX 09-04-100, Guayaquil, Ecuador
| | - Jorge A Robalino Penaherrera
- Dirección de Investigación, Desarrollo e Innovación, Instituto Nacional de Investigaciones en Salud Pública (INSPI), Av. Julian Coronel 905 y Esmeraldas, 090510 Guayaquil, Ecuador
| | - Peter Chedraui
- Hospital Gineco-Obstétrico Enrique C. Sotomayor, Guayaquil, Ecuador
| | - Saul Escobar
- Institute of Biomedicine, Facultad Ciencias Médicas, Universidad Católica de Guayaquil, PO Box 09-01-4671, Guayaquil, Ecuador
| | - Rita D Loja Chango
- Institute of Biomedicine, Facultad Ciencias Médicas, Universidad Católica de Guayaquil, PO Box 09-01-4671, Guayaquil, Ecuador
| | - Cecibel Ramirez-Morán
- Institute of Biomedicine, Facultad Ciencias Médicas, Universidad Católica de Guayaquil, PO Box 09-01-4671, Guayaquil, Ecuador
| | - Jasson Espinoza-Caicedo
- Institute of Biomedicine, Facultad Ciencias Médicas, Universidad Católica de Guayaquil, PO Box 09-01-4671, Guayaquil, Ecuador
| | - Sunny Sánchez-Giler
- Facultad de Ciencias Médicas, Universidad Especialidades Espíritu Santo, Km 2,5 vía Samborondón, Ecuador
| | - Celia M Limia
- Sexually Transmitted Diseases Laboratory, Department of Virology, Institute of Tropical Medicine "Pedro Kouri", Autopista Novia del Mediodia, Km 6 ½, La Lisa, Marianao 13, PO Box 601, Havana City, Cuba
| | - Yoan Alemán
- Sexually Transmitted Diseases Laboratory, Department of Virology, Institute of Tropical Medicine "Pedro Kouri", Autopista Novia del Mediodia, Km 6 ½, La Lisa, Marianao 13, PO Box 601, Havana City, Cuba
| | - Yudira Soto
- Sexually Transmitted Diseases Laboratory, Department of Virology, Institute of Tropical Medicine "Pedro Kouri", Autopista Novia del Mediodia, Km 6 ½, La Lisa, Marianao 13, PO Box 601, Havana City, Cuba
| | - Vivian Kouri
- Sexually Transmitted Diseases Laboratory, Department of Virology, Institute of Tropical Medicine "Pedro Kouri", Autopista Novia del Mediodia, Km 6 ½, La Lisa, Marianao 13, PO Box 601, Havana City, Cuba
| | - Andrés C A Culasso
- Investigador Asistente CONICET, Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Rivadavia 1917, (C1033AAJ) Caba, Argentina; Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junin 954, 4to piso, Capital Federal, (C1113AAD) Buenos Aires, Argentina
| | - Inés Badano
- Investigador Asistente CONICET, Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Rivadavia 1917, (C1033AAJ) Caba, Argentina; Laboratorio de Biología Molecular Aplicada, FCEQyN, Universidad Nacional de Misiones, Av. Mariano Moreno 1375, 3300 Posadas, Misiones, Argentina; Yachay EP, Secretaría de Educación Superior, Ciencia, Tecnología e Innovación, 9 de Octubre N22-64 y Ramírez Dávalos, Casa Patrimonial, Ecuador
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Awua AK, Adanu RMK, Wiredu EK, Afari EA, Zubuch VA, Asmah RH, Severini A. Unique LCR variations among lineages of HPV16, 18 and 45 isolates from women with normal cervical cytology in Ghana. Virol J 2017; 14:85. [PMID: 28431571 PMCID: PMC5401561 DOI: 10.1186/s12985-017-0755-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 04/19/2017] [Indexed: 01/08/2023] Open
Abstract
Background In addition to being useful for classification, sequence variations of human Papillomavirus (HPV) genotypes have been implicated in differential oncogenic potential and a differential association with the different histological forms of invasive cervical cancer. These associations have also been indicated for HPV genotype lineages and sub-lineages. In order to better understand the potential implications of lineage variation in the occurrence of cervical cancers in Ghana, we studied the lineages of the three most prevalent HPV genotypes among women with normal cytology as baseline to further studies. Methods Of previously collected self- and health personnel-collected cervical specimen, 54, which were positive for HPV16, 18 and 45, were selected and the long control region (LCR) of each HPV genotype was separately amplified by a nested PCR. DNA sequences of 41 isolates obtained with the forward and reverse primers by Sanger sequencing were analysed. Results Nucleotide sequence variations of the HPV16 genotypes were observed at 30 positions within the LCR (7460 – 7840). Of these, 19 were the known variations for the lineages B and C (African lineages), while the other 11 positions had variations unique to the HPV16 isolates of this study. For the HPV18 isolates, the variations were at 35 positions, 22 of which were known variations of Africa lineages and the other 13 were unique variations observed for the isolates obtained in this study (at positions 7799 and 7813). HPV45 isolates had variations at 35 positions and 2 (positions 7114 and 97) were unique to the isolates of this study. Conclusion This study provides the first data on the lineages of HPV 16, 18 and 45 isolates from Ghana. Although the study did not obtain full genome sequence data for a comprehensive comparison with known lineages, these genotypes were predominately of the Africa lineages and had some unique sequence variations at positions that suggest potential oncogenic implications. These data will be useful for comparison with lineages of these genotypes from women with cervical lesion and all the forms of invasive cervical cancers. Electronic supplementary material The online version of this article (doi:10.1186/s12985-017-0755-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adolf K Awua
- Department of Epidemiology and Disease Control, School of Public Health, University of Ghana, Accra, Ghana. .,Cellular and Clinical Research Centre, Radiological and Medical Sciences Research Institute, Ghana Atomic Energy Commission, Accra, Ghana.
| | - Richard M K Adanu
- Population, Family and Reproductive Health, School of Public Health, University of Ghana, Accra, Ghana
| | - Edwin K Wiredu
- Department of Pathology, School of Biomedical and Allied Health Science, University of Ghana, Korle-Bu, Accra, Ghana
| | - Edwin A Afari
- Department of Epidemiology and Disease Control, School of Public Health, University of Ghana, Accra, Ghana
| | - Vanessa A Zubuch
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Richard H Asmah
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Science, University of Ghana, Korle-Bu, Accra, Ghana
| | - Alberto Severini
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.,University of Manitoba, Winnipeg, MB, Canada
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7
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Pimenoff VN, de Oliveira CM, Bravo IG. Transmission between Archaic and Modern Human Ancestors during the Evolution of the Oncogenic Human Papillomavirus 16. Mol Biol Evol 2017; 34:4-19. [PMID: 28025273 PMCID: PMC5854117 DOI: 10.1093/molbev/msw214] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Every human suffers through life a number of papillomaviruses (PVs) infections, most of them asymptomatic. A notable exception are persistent infections by Human papillomavirus 16 (HPV16), the most oncogenic infectious agent for humans and responsible for most infection-driven anogenital cancers. Oncogenic potential is not homogeneous among HPV16 lineages, and genetic variation within HPV16 exhibits some geographic structure. However, an in-depth analysis of the HPV16 evolutionary history was still wanting. We have analyzed extant HPV16 diversity and compared the evolutionary and phylogeographical patterns of humans and of HPV16. We show that codivergence with modern humans explains at most 30% of the present viral geographical distribution. The most explanatory scenario suggests that ancestral HPV16 already infected ancestral human populations and that viral lineages co-diverged with the hosts in parallel with the split between archaic Neanderthal-Denisovans and ancestral modern human populations, generating the ancestral HPV16A and HPV16BCD viral lineages, respectively. We propose that after out-of-Africa migration of modern human ancestors, sexual transmission between human populations introduced HPV16A into modern human ancestor populations. We hypothesize that differential coevolution of HPV16 lineages with different but closely related ancestral human populations and subsequent host-switch events in parallel with introgression of archaic alleles into the genomes of modern human ancestors may be largely responsible for the present-day differential prevalence and association with cancers for HPV16 variants.
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Affiliation(s)
- Ville N Pimenoff
- Infections and Cancer Laboratory, Cancer Epidemiology Research Programme, Catalan Institute of Oncology, Barcelona, Spain
- Unit of Biomarkers and Susceptibility, Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain
| | - Cristina Mendes de Oliveira
- Infections and Cancer Laboratory, Cancer Epidemiology Research Programme, Catalan Institute of Oncology, Barcelona, Spain
- Virology Laboratory, Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil
| | - Ignacio G Bravo
- Infections and Cancer Laboratory, Cancer Epidemiology Research Programme, Catalan Institute of Oncology, Barcelona, Spain
- MIVEGEC (UMR CNRS 5290, IRD 224, UM), National Center for Scientific Research (CNRS), Montpellier, France
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Badano I, Totaro ME, Culasso ACA, Sanabria DJ, Schurr TG, Balette IC, Roisman A, Basiletti J, Picconi MA, Campos RH, Liotta DJ. Genetic characterization and clinical implications of human papillomavirus type 16 (HPV16) variants from northeastern Argentina. INFECTION GENETICS AND EVOLUTION 2014; 29:103-9. [PMID: 25461847 DOI: 10.1016/j.meegid.2014.11.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 11/11/2014] [Accepted: 11/13/2014] [Indexed: 11/27/2022]
Abstract
BACKGROUND Human papillomavirus type 16 (HPV16) plays a central role in the development of cervical cancer. Worldwide studies indicate the existence of HPV16 variants that show different geographic distributions and oncogenic potential. OBJECTIVE Our goal was to describe the genetic variation of HPV16 isolates identified in urban women with different grades of cervical lesions living in northeastern Argentina. STUDY DESIGN We analyzed 116 HPV16-positive cervical samples (16 NLIM, 62 L-SIL, 16 H-SIL and 22 cervical cancer) from patients attending health centers in Misiones (Argentina) during 2006-13. HPV16 isolates were genetically characterized through PCR amplification and direct sequencing of 364 bp within the long control region, and the resulting sequences classified into variants based on phylogenetic analysis (lineages A, B, C and D). A potential association between HPV16 variants and lesion grade was evaluated through an odds ratio (OR) test. A temporal framework for the origin of HPV16 variants was assessed through coalescence analysis (BEAST v 1.7.5). RESULTS Phylogenetic analysis of HPV16 sequences showed that 92.1% of the samples clustered with lineage A, and 6.9% to lineage D. HPV16 variants from lineage D were more frequently associated with high-grade lesions and cancer (HSIL+) than lineage A variants at an OR of 13.8 (1.6-117.0). The time to most common recent ancestor (tMCRA) of all variants was 119,103 years before present (HPD 95%=48,486-197,239), a date consistent with the time frame for modern human evolution. CONCLUSION Our results suggest that HPV16 variants from lineage D may represent an additional risk factor for the development of cervical cancer in women living in northeastern Argentina. This study provides new information about viral isolates present in Argentina that will contribute to the monitoring of HPV16 infection in the vaccine era.
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Affiliation(s)
- Inés Badano
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Quimicas y Naturales, Universidad Nacional de Misiones, Av. Mariano Moreno 1375, Posadas 3300, Misiones, Argentina.
| | - Maria Elina Totaro
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Quimicas y Naturales, Universidad Nacional de Misiones, Av. Mariano Moreno 1375, Posadas 3300, Misiones, Argentina
| | - Andrés Carlos Alberto Culasso
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junin 954, 4to piso, Capital Federal (C1113AAD), Buenos Aires, Argentina
| | - Daiana Jimena Sanabria
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Quimicas y Naturales, Universidad Nacional de Misiones, Av. Mariano Moreno 1375, Posadas 3300, Misiones, Argentina
| | - Theodore G Schurr
- Laboratory of Molecular Anthropology, Department of Anthropology, University of Pennsylvania, 3260 South Street, Philadelphia, PA 19104-6398, USA
| | - Ileana Cristina Balette
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Quimicas y Naturales, Universidad Nacional de Misiones, Av. Mariano Moreno 1375, Posadas 3300, Misiones, Argentina
| | - Alejandro Roisman
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Quimicas y Naturales, Universidad Nacional de Misiones, Av. Mariano Moreno 1375, Posadas 3300, Misiones, Argentina
| | - Jorge Basiletti
- Servicio de Virus Oncogénicos, Departamento de Virología, INEI-ANLIS "Dr. Carlos G. Malbrán", Av. Velez Sarsfield 563, Capital Federal (C1282AFF), Buenos Aires, Argentina
| | - María Alejandra Picconi
- Servicio de Virus Oncogénicos, Departamento de Virología, INEI-ANLIS "Dr. Carlos G. Malbrán", Av. Velez Sarsfield 563, Capital Federal (C1282AFF), Buenos Aires, Argentina
| | - Rodolfo Héctor Campos
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junin 954, 4to piso, Capital Federal (C1113AAD), Buenos Aires, Argentina
| | - Domingo Javier Liotta
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Quimicas y Naturales, Universidad Nacional de Misiones, Av. Mariano Moreno 1375, Posadas 3300, Misiones, Argentina
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Human papillomavirus 16 non-European variants are preferentially associated with high-grade cervical lesions. PLoS One 2014; 9:e100746. [PMID: 24983739 PMCID: PMC4077691 DOI: 10.1371/journal.pone.0100746] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/29/2014] [Indexed: 01/10/2023] Open
Abstract
HPV16 accounts for 50–70% of cervical cancer cases worldwide. Characterization of HPV16 variants previously indicated that they differ in risks for viral persistence, progression to cervical precancer and malignant cancer. The aim of this study was to examine the association of severity of disease with HPV16 variants identified in specimens (n = 281) obtained from a Cervical Pathology and Colposcopy outpatient clinic in the University Hospital of Espírito Santo State, Southeastern Brazil, from April 2010 to November 2011. All cytologic and histologic diagnoses were determined prior to definitive treatment. The DNA was isolated using QIAamp DNA Mini Kit and HPV was detected by amplification with PGMY09/11 primers and positive samples were genotyped by RFLP analyses and reverse line blot. The genomes of the HPV16 positive samples were sequenced, from which variant lineages were determined. Chi2 statistics was performed to test the association of HPV16 variants between case and control groups. The prevalence of HR-HPV types in <CIN1, CIN2 and CIN3+ were 33.7%, 84.4% and 91.6%, respectively. Thirty-eight of 49 (78%) HPV16 positive samples yielded HPV16 sequence information; of which, 32 complete genomes were sequenced and an additional 6 samples were partially sequenced. Phylogenetic analysis and patterns of variations identified 65.8% (n = 25) as HPV16 European (E) and 34.2% (n = 13) as non-European (NE) variants. Classification of disease into CIN3+ vs. <CIN3 indicated that NE types were associated with high-grade disease with an OR = 4.6 (1.07–20.2, p = 0.05). The association of HPV16 NE variants with an increased risk of CIN3+ is consistent with an HPV16 genetically determined enhanced oncogenicity. The prevalence of genetic variants of HPV16 is distributed across different geographical areas and with recent population admixture, only empiric data will provide information on the highest risk HPV16 variants within a given population.
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