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Sichero L, Ferreira S, López RVM, Mello BP, Costa V, El-Achkar VNR, Carlos R, Ribeiro-Silva A, Pignatari S, Kaminagakura E, Villa LL. Prevalence of human papillomavirus 6 and 11 variants in recurrent respiratory papillomatosis. J Med Virol 2021; 93:3835-3840. [PMID: 32910471 DOI: 10.1002/jmv.26503] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/03/2020] [Accepted: 09/08/2020] [Indexed: 11/11/2022]
Abstract
Human papillomavirus (HPV) types 6 and 11 are the etiological agents of recurrent respiratory papillomatosis (RRP). We examined the prevalence and distribution of HPVs 6 and 11 genetic variants in juvenile onset (JORRP) and adult onset (AORRP) laryngeal papillomas. Cases of JORRP and AORRP were collected, retrospectively. HPV detection and genotyping were accessed by polymerase chain reaction-sequencing in 67 RRP samples. Overall, the most prevalent HPV-6 variants were from B1 (55.8%) and B3 (27.9%) sublineages, whereas among HPV-11 positive samples A2 (62.5%) variants were predominant. A higher prevalence of HPV-6 B1 was observed in JORRP (83.3% B1 and 16.7% B3), compared with AORRP cases (58.3% B1 and 41.7% B3). HPV-11 A2 variants were more prevalent both in JORRP (57.2%) and in AORRP cases (70.0%). Nevertheless, with the exception that HPV-6 B1 were significantly less likely to recur, there was a lack of association between any particular HPVs 6 or 11 variant and clinicopathological features. Our data do not support an association between HPVs 6 and 11 variability and RRP.
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Affiliation(s)
- Laura Sichero
- Center for Translational Research in Oncology, Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Silvaneide Ferreira
- Center for Translational Research in Oncology, Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Rossana V M López
- Center for Translational Research in Oncology, Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Barbara P Mello
- Center for Translational Research in Oncology, Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Victor Costa
- Department of Bioscience and Oral Diagnosis, São Paulo State University (UNESP), São Paulo, Brazil
| | - Vivian N R El-Achkar
- Department of Bioscience and Oral Diagnosis, São Paulo State University (UNESP), São Paulo, Brazil
| | - Román Carlos
- Centro Clínico de Cabeza y Cuello, Guatemala City, Guatemala
| | - Alfredo Ribeiro-Silva
- Department of Pathology and Forensic Medicine, Ribeirao Preto Medical School, Universidade de São Paulo, Ribeirao, Preto, Brazil
| | - Shirley Pignatari
- Department of Otorhinolaryngology and Head and Neck Surgery, Sao Paulo Federal University, Sao Paulo, Brazil
| | - Estela Kaminagakura
- Department of Bioscience and Oral Diagnosis, São Paulo State University (UNESP), São Paulo, Brazil
| | - Luisa L Villa
- Center for Translational Research in Oncology, Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
- Department of Otorhinolaryngology and Head and Neck Surgery, Sao Paulo Federal University, Sao Paulo, Brazil
- Department of Radiology and Oncology, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
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Hošnjak L, Kocjan BJ, Pirš B, Seme K, Poljak M. The genetic diversity of human papillomavirus types from the species Gammapapillomavirus 15: HPV135, HPV146, and HPV179. PLoS One 2021; 16:e0249829. [PMID: 33956809 PMCID: PMC8101917 DOI: 10.1371/journal.pone.0249829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/25/2021] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES To determine the prevalence, viral load, tissue tropism, and genetic variability of novel human papillomavirus (HPV) type 179, which is etiologically associated with sporadic cases of common warts in immunocompromised patients, and phylogenetically related HPV types 135 and 146. METHODS The representative collection of 850 HPV-associated clinical samples (oral/nasopharyngeal/anal, archival specimens of oral/oropharyngeal/conjunctival/cervical/skin cancer, benign lesions of the larynx/conjunctiva/skin, and eyebrows), obtained from immunocompetent individuals, was tested for the presence of HPV179, HPV135, and HPV146 using type-specific real-time PCRs. To assess the genetic diversity of the HPVs investigated in the non-coding long control region (LCR), several highly sensitive nested PCR protocols were developed for each HPV type. The genetic diversity of HPV179 was additionally determined in 12 HPV179 isolates from different anatomical sites of an only immunocompromised patient included in the study. RESULTS HPV179, HPV135, and HPV146 were detected in 1.4, 2.0, and 1.5% of the samples tested, respectively, with no preference for cutaneous or mucosal epithelial cells. One (with five single nucleotide polymorphisms; SNPs), four (with one to six SNPs), and four (with one to eight SNPs) genetic variants of HPV179, HPV135, and HPV146, respectively, were identified among eligible samples. HPV179 isolates from the immunocompromised patient exhibited the identical LCR nucleotide sequence, suggesting that HPV179 can cause generalized HPV infections. CONCLUSIONS HPV179, HPV135, and HPV146 have a mucocutaneous tissue tropism and are associated with sporadic infections in immunocompromised and immunocompetent individuals. Because the majority of mutations were found outside the major functional domains of the respective LCRs, we assume that HPV179, HPV135, and HPV146 genetic variants pathogenically do not differ from their prototypes. In addition, no association was found between specific HPV179, HPV135, and HPV146 genetic variants and anatomical sites of infection and/or specific neoplasms.
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Affiliation(s)
- Lea Hošnjak
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | - Boštjan J. Kocjan
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | | | - Katja Seme
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | - Mario Poljak
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
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Nejo YT, Olaleye DO, Odaibo GN. Molecular characterisation of genital human papillomavirus among women in Southwestern, Nigeria. PLoS One 2019; 14:e0224748. [PMID: 31682636 PMCID: PMC6827905 DOI: 10.1371/journal.pone.0224748] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 10/21/2019] [Indexed: 12/20/2022] Open
Abstract
Background Persistent infections with high-risk genital Human papillomavirus (HPV) especially types 16 and 18, are associated with cervical cancer. However, distribution of HPV types varies greatly across geographical regions and the available vaccines target only few types. This study was designed to determine the HPV types circulating in Southwestern Nigeria, thereby providing necessary information for effective control of the virus. Methods Endocervical swab samples were collected from a total of 295 consenting women attending routine cervical cancer screening, STI clinics and community-based outreach programme. Viral DNA was extracted from the samples and the consensus region of the HPV DNA was amplified by PCR using GP-E6/E7 primers. Type-specific nested multiplex PCR and Sanger sequencing were used to genotype the HPV isolates. Results In this study, 51 (17.3%) individuals were positive for HPV DNA using consensus primers that target the E6/E7 genes but only 48 (16.3%) were genotyped. A total of 15 HPV types (HPV-6, 16, 18, 31, 33, 35, 42, 43, 44, 52, 58, 66, 74, 81, 86) were detected, with HPV-31 being the most predominant (32.8%), followed by HPV-35 (17.2%) and HPV-16 (15.5%). Two rare HPV types; 74 and 86 were also detected. The HPV-74 isolate had three nucleotide (CCT) insertions at E7 gene that translated into amino acid proline. Highest nucleotide substitutions (n = 32) were found in HPV-44 genotype. Among positive individuals, 20.8% had dual infections and 86.2% had High-risk HPV types. Conclusions Multiple Human papillomavirus types co-circulated in the study. Most of the circulating Human papillomavirus are high-risk type with type 31 being the most predominant. Although the implication of HPV-74 with proline insertion detected for the first time is unknown, it may have effect on the transformation potential of the virus. Polyvalent HPV vaccine will be more effective for the infection control in Nigeria.
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Affiliation(s)
- Yewande T. Nejo
- Department of Biological Sciences, Bowen University, Iwo, Osun State, Nigeria
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - David O. Olaleye
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Georgina N. Odaibo
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- * E-mail:
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Chen Z, Li Q, Huang J, Li J, Yang F, Min X, Chen Z. E6 and E7 gene polymorphisms in human papillomavirus Type-6 identified in Southwest China. Virol J 2019; 16:114. [PMID: 31511025 PMCID: PMC6740006 DOI: 10.1186/s12985-019-1221-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/05/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Human papillomavirus type-6 (HPV6) is the major etiological agent of anogenital warts both men and women. The present study aimed to characterize the genetic diversity among HPV6 in Southwest China, and to investigate the origin of, selective pressure experienced by, and impact of the resultantly identified genetic variants on the HPV6 secondary structure. METHODS Phylogenetic trees were constructed by Maximum-likelihood and the Kimura 2-parameters methods by Molecular Evolutionary Genetics Analysis version 6.0. The diversity of secondary structure was analyzed by PSIPred software. The selection pressures acting on the E6/E7 genes were estimated by Phylogenetic Analyses by Maximum Likelihood version 4.8 software. RESULTS HPV6 was the most prevalent low risk HPV type in southwest China. In total, 143 E6 and E7 gene sequences of HPV6 isolated from patients were sequenced and compared to GenBank HPV6 reference sequence X00203. The results of these analyses revealed that both the HPV6 E6 and E7 were highly conserved within the analyzed patient samples, and comprised only 3 types of variant sequence, respectively. Furthermore, the analysis of HPV6 E6 and E7 sequences revealed seven/five single-nucleotide mutations, two/four and five/one of which were non-synonymous and synonymous, respectively. The phylogenetic analyses of the E6 and E7 sequences indicated that they belonged to sub-lineage A1 and sub-lineage B1, whereas the selective pressure analyses showed that only the E7 mutation sites 4R, 34E, and 52F were positive selection. CONCLUSIONS HPV6 (detection rate = 13.10%) was very prevalent in southwest China, both the HPV6 E6 and E7 sequences were highly conserved within the analyzed patient samples in southwest China, indicating that the low risk HPV6 can adapt to the environment well without much evolution.
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Affiliation(s)
- Zuyi Chen
- Department of Laboratory medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, People's Republic of China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing, Sichuan, People's Republic of China
| | - Qiongyao Li
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing, Sichuan, People's Republic of China.,Department of Information Technology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, People's Republic of China
| | - Jian Huang
- Department of Laboratory medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, People's Republic of China
| | - Jin Li
- Department of Thoracic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, People's Republic of China
| | - Feng Yang
- Department of Information Technology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, People's Republic of China
| | - Xun Min
- Department of Laboratory medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, People's Republic of China.
| | - Zehui Chen
- Department of Laboratory medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, People's Republic of China
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Dias MC, Stuqui B, Provazzi PJS, Bittar C, Candido NM, de Matos RPA, Badial RM, do Bonfim CM, Melli PPDS, Quintana SM, Cordeiro JA, Rahal P, Calmon MDF. Analysis of Nucleotide Alterations in the E6 Genomic Region of Human Papillomavirus Types 6 and 11 in Condyloma Acuminatum Samples from Brazil. Adv Virol 2019; 2019:5697573. [PMID: 31186642 PMCID: PMC6521423 DOI: 10.1155/2019/5697573] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 02/27/2019] [Accepted: 03/17/2019] [Indexed: 11/17/2022] Open
Abstract
Condyloma acuminata (CA), or genital warts, are benign proliferative epidermal or mucous lesions that are caused by infection with human papillomavirus (HPV), mainly the low-risk types 6 and 11. HPV variants are defined as viral sequences that share identity in the nucleotide sequence of the L1 gene greater than 98%. Based on this criterion, HPV6 and 11 variant lineages have been studied, and there are ongoing attempts to correlate these genetic variants with different clinical findings of infection. Therefore, the aims of this study were to detect variants and nucleotide alterations present in the E6 regions of HPV types 6 and 11 found in CA samples, to correlate the HPV presence with the clinical-pathological data of the patients, and to determine phylogenetic relationships with variants from other places in the world. The E6 regions of 25 HPV6 samples and 7 HPV11 samples from CA were amplified using PCR with specific primers. The products were ligated to a cloning vector and five colonies of each sample were sequenced to observe the nucleotide alterations. Twelve samples were identified as the HPV6B3 variant, presenting the mutation (guanine) G474A (adenine), and one of them also showed the mutation (thymine) T369G. The other 13 patients were positive for HPV6B1 without nucleotide alterations. In the analysis of the HPV11 samples, all patients showed the mutations T137C and (cytosine) C380T. One patient also presented the nucleotide alteration T410C. None of the mutations found in the 32 analyzed samples resulted in amino acid changes. Patient age, local occurrence, and HIV infection did not show significant association with HPV infection. Besides, the data found in this study did not show a relationship with the geographical region of isolation when compared to other data from different regions of the world. In this way, despite the nucleotide alterations found, it was not possible to observe amino acid changes and variants grouping according to geographical region.
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Affiliation(s)
- Marina Carrara Dias
- Institute of Biosciences, Letters and Exact Sciences of São Paulo State University, São José do Rio Preto, SP, Brazil
| | - Bruna Stuqui
- Institute of Biosciences, Letters and Exact Sciences of São Paulo State University, São José do Rio Preto, SP, Brazil
| | - Paola Jocelan Scarin Provazzi
- Institute of Biosciences, Letters and Exact Sciences of São Paulo State University, São José do Rio Preto, SP, Brazil
| | - Cíntia Bittar
- Institute of Biosciences, Letters and Exact Sciences of São Paulo State University, São José do Rio Preto, SP, Brazil
| | - Natália Maria Candido
- Institute of Biosciences, Letters and Exact Sciences of São Paulo State University, São José do Rio Preto, SP, Brazil
| | - Renata Prandini Adum de Matos
- Institute of Biosciences, Letters and Exact Sciences of São Paulo State University, São José do Rio Preto, SP, Brazil
| | - Rodolfo Miglioli Badial
- Institute of Biosciences, Letters and Exact Sciences of São Paulo State University, São José do Rio Preto, SP, Brazil
| | - Caroline Measso do Bonfim
- Institute of Biosciences, Letters and Exact Sciences of São Paulo State University, São José do Rio Preto, SP, Brazil
| | | | | | | | - Paula Rahal
- Institute of Biosciences, Letters and Exact Sciences of São Paulo State University, São José do Rio Preto, SP, Brazil
| | - Marilia de Freitas Calmon
- Institute of Biosciences, Letters and Exact Sciences of São Paulo State University, São José do Rio Preto, SP, Brazil
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Flores-Díaz E, Sereday KA, Ferreira S, Sirak B, Sobrinho JS, Baggio ML, Galan L, Silva RC, Lazcano-Ponce E, Giuliano AR, Villa LL, Sichero L. HPV-6 Molecular Variants Association With the Development of Genital Warts in Men: The HIM Study. J Infect Dis 2017; 215:559-565. [PMID: 28011919 PMCID: PMC5388291 DOI: 10.1093/infdis/jiw600] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/01/2016] [Indexed: 11/14/2022] Open
Abstract
Background Human papillomavirus type 6 (HPV-6) and HPV-11 are the etiological agents of approximately 90% of genital warts (GWs). The impact of HPV-6 genetic heterogeneity on persistence and progression to GWs remains undetermined. Methods HPV Infection in Men (HIM) Study participants who had HPV-6 genital swabs and/or GWs preceded by a viable normal genital swab were analyzed. Variants characterization was performed by polymerase chain reaction sequencing and samples classified within lineages (A, B) and sublineages (B1, B2, B3, B4, B5). Country- and age-specific analyses were conducted for individual variants; odds ratios and 95% confidence intervals for the risk of GWs according to HPV-6 variants were calculated. Results B3 variants were most prevalent. HPV-6 variants distribution differed between countries and case status. HPV-6 B1 variants prevalence was increased in GWs and genital swabs of cases compared to controls. There was difference in B1 and B3 variants detection in GW and the preceding genital swab. We observed significant association of HPV-6 B1 variants detection with GW development. Conclusions HPV-6 B1 variants are more prevalent in genital swabs that precede GW development, and confer an increased risk for GW. Further research is warranted to understand the possible involvement of B1 variants in the progression to clinically relevant lesions.
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Affiliation(s)
- Ema Flores-Díaz
- Molecular Biology Laboratory, Center for Translational Research in Oncology, Instituto do Câncer do Estado de São Paulo, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Brazil
| | - Karen A Sereday
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Silvaneide Ferreira
- Molecular Biology Laboratory, Center for Translational Research in Oncology, Instituto do Câncer do Estado de São Paulo, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Brazil
| | - Bradley Sirak
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - João Simão Sobrinho
- Molecular Biology Laboratory, Center for Translational Research in Oncology, Instituto do Câncer do Estado de São Paulo, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Brazil
| | - Maria Luiza Baggio
- Molecular Biology Laboratory, Center for Translational Research in Oncology, Instituto do Câncer do Estado de São Paulo, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Brazil
| | - Lenice Galan
- Ludwig Institute for Cancer Research, São Paulo Branch, São Paulo, Brazil
| | - Roberto C Silva
- Centro de Referência e Treinamento DST/Aids, São Paulo, Brazil
| | - Eduardo Lazcano-Ponce
- Centro de Investigación en Salud Poblacional, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Anna R Giuliano
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Luisa L Villa
- Molecular Biology Laboratory, Center for Translational Research in Oncology, Instituto do Câncer do Estado de São Paulo, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Brazil.,Department of Radiology and Oncology, Faculdade de Medicina, Universidade de São Paulo, Brazil
| | - Laura Sichero
- Molecular Biology Laboratory, Center for Translational Research in Oncology, Instituto do Câncer do Estado de São Paulo, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Brazil
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Oštrbenk A, Kocjan BJ, Hošnjak L, Li J, Deng Q, Šterbenc A, Poljak M. Identification of a Novel Human Papillomavirus, Type HPV199, Isolated from a Nasopharynx and Anal Canal, and Complete Genomic Characterization of Papillomavirus Species Gamma-12. PLoS One 2015; 10:e0138628. [PMID: 26375679 PMCID: PMC4574437 DOI: 10.1371/journal.pone.0138628] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 08/31/2015] [Indexed: 01/04/2023] Open
Abstract
The novel human papillomavirus type 199 (HPV199) was initially identified in a nasopharyngeal swab sample obtained from a 25 year-old immunocompetent male. The complete genome of HPV199 is 7,184 bp in length with a GC content of 36.5%. Comparative genomic characterization of HPV199 and its closest relatives showed the classical genomic organization of Gammapapillomaviruses (Gamma-PVs). HPV199 has seven major open reading frames (ORFs), encoding five early (E1, E2, E4, E6, and E7) and two late (L1 and L2) proteins, while lacking the E5 ORF. The long control region (LCR) of 513 bp is located between the L1 and E6 ORFs. Phylogenetic analysis additionally confirmed that HPV-199 clusters into the Gamma-PV genus, species Gamma-12, additionally containing HPV127, HV132, HPV148, HPV165, and three putative HPV types: KC5, CG2 and CG3. HPV199 is most closely related to HPV127 (nucleotide identity 77%). The complete viral genome sequence of additional HPV199 isolate was determined from anal canal swab sample. Two HPV199 complete viral sequences exhibit 99.4% nucleotide identity. To the best of our knowledge, this is the first member of Gamma-PV with complete nucleotide sequences determined from two independent clinical samples. To evaluate the tissue tropism of the novel HPV type, 916 clinical samples were tested using HPV199 type-specific real-time PCR: HPV199 was detected in 2/76 tissue samples of histologically confirmed common warts, 2/108 samples of eyebrow hair follicles, 2/137 anal canal swabs obtained from individuals with clinically evident anal pathology, 4/184 nasopharyngeal swabs and 3/411 cervical swabs obtained from women with normal cervical cytology. Although HPV199 was found in 1.4% of cutaneous and mucosal samples only, it exhibits dual tissue tropism. According to the results of our study and literature data, dual tropism of all Gamma-12 members is highly possible.
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Affiliation(s)
- Anja Oštrbenk
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Boštjan J. Kocjan
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Lea Hošnjak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Jingjing Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Qiuju Deng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Anja Šterbenc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- * E-mail:
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Measso do Bonfim C, Simão Sobrinho J, Lacerda Nogueira R, Salgado Kupper D, Cardoso Pereira Valera F, Lacerda Nogueira M, Villa LL, Rahal P, Sichero L. Differences in Transcriptional Activity of Human Papillomavirus Type 6 Molecular Variants in Recurrent Respiratory Papillomatosis. PLoS One 2015; 10:e0132325. [PMID: 26151558 PMCID: PMC4494706 DOI: 10.1371/journal.pone.0132325] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/14/2015] [Indexed: 11/19/2022] Open
Abstract
A significant proportion of recurrent respiratory papillomatosis (RRP) is caused by human papillomavirus type 6 (HPV-6). The long control region (LCR) contains cis-elements for regulation of transcription. Our aim was to characterize LCR HPV-6 variants in RRP cases, compare promoter activity of these isolates and search for cellular transcription factors (TFs) that could explain the differences observed. The complete LCR from 13 RRP was analyzed. Transcriptional activity of 5 variants was compared using luciferase assays. Differences in putative TFs binding sites among variants were revealed using the TRANSFAC database. Chromatin immunoprecipation (CHIP) and luciferase assays were used to evaluate TF binding and impact upon transcription, respectively. Juvenile-onset RRP cases harbored exclusively HPV-6vc related variants, whereas among adult-onset cases HPV-6a variants were more prevalent. The HPV-6vc reference was more transcriptionally active than the HPV-6a reference. Active FOXA1, ELF1 and GATA1 binding sites overlap variable nucleotide positions among isolates and influenced LCR activity. Furthermore, our results support a crucial role for ELF1 on transcriptional downregulation. We identified TFs implicated in the regulation of HPV-6 early gene expression. Many of these factors are mutated in cancer or are putative cancer biomarkers, and must be further studied.
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Affiliation(s)
- Caroline Measso do Bonfim
- Laboratory of Genomic Studies, Universidade do Estado de São Paulo, UNESP, São José do Rio Preto, SP, Brazil
| | - João Simão Sobrinho
- Molecular Biology Laboratory, Center of Translational Oncology, Instituto do Câncer do Estado de São Paulo, ICESP, São Paulo, Brazil
| | - Rodrigo Lacerda Nogueira
- Department of Ophthalmology/Otorhinolaryngology and Head/Neck Surgery, Discipline Otorhinolaryngology, Faculty of Medicine of Ribeirão Preto, Universidade de São Paulo, USP, São Paulo, Brazil
| | - Daniel Salgado Kupper
- Department of Ophthalmology/Otorhinolaryngology and Head/Neck Surgery, Discipline Otorhinolaryngology, Faculty of Medicine of Ribeirão Preto, Universidade de São Paulo, USP, São Paulo, Brazil
| | - Fabiana Cardoso Pereira Valera
- Department of Ophthalmology/Otorhinolaryngology and Head/Neck Surgery, Discipline Otorhinolaryngology, Faculty of Medicine of Ribeirão Preto, Universidade de São Paulo, USP, São Paulo, Brazil
| | - Maurício Lacerda Nogueira
- Laboratory of Research in Virology, Faculty of Medicine of São José do Rio Preto, FAMERP, São José do Rio Preto, Brazil
| | - Luisa Lina Villa
- Molecular Biology Laboratory, Center of Translational Oncology, Instituto do Câncer do Estado de São Paulo, ICESP, São Paulo, Brazil
- Department of Radiology and Oncology, School of Medicine, Universidade de São Paulo, USP, São Paulo, Brazil
- School of Medicine, Santa Casa de São Paulo and HPV Institute, São Paulo, Brazil
| | - Paula Rahal
- Laboratory of Genomic Studies, Universidade do Estado de São Paulo, UNESP, São José do Rio Preto, SP, Brazil
| | - Laura Sichero
- Molecular Biology Laboratory, Center of Translational Oncology, Instituto do Câncer do Estado de São Paulo, ICESP, São Paulo, Brazil
- * E-mail:
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Jelen MM, Chen Z, Kocjan BJ, Burt FJ, Chan PKS, Chouhy D, Combrinck CE, Coutlée F, Estrade C, Ferenczy A, Fiander A, Franco EL, Garland SM, Giri AA, González JV, Gröning A, Heidrich K, Hibbitts S, Hošnjak L, Luk TNM, Marinic K, Matsukura T, Neumann A, Oštrbenk A, Picconi MA, Richardson H, Sagadin M, Sahli R, Seedat RY, Seme K, Severini A, Sinchi JL, Smahelova J, Tabrizi SN, Tachezy R, Tohme S, Uloza V, Vitkauskiene A, Wong YW, Zidovec Lepej S, Burk RD, Poljak M. Global genomic diversity of human papillomavirus 6 based on 724 isolates and 190 complete genome sequences. J Virol 2014; 88:7307-16. [PMID: 24741079 PMCID: PMC4054425 DOI: 10.1128/jvi.00621-14] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 04/08/2014] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Human papillomavirus type 6 (HPV6) is the major etiological agent of anogenital warts and laryngeal papillomas and has been included in both the quadrivalent and nonavalent prophylactic HPV vaccines. This study investigated the global genomic diversity of HPV6, using 724 isolates and 190 complete genomes from six continents, and the association of HPV6 genomic variants with geographical location, anatomical site of infection/disease, and gender. Initially, a 2,800-bp E5a-E5b-L1-LCR fragment was sequenced from 492/530 (92.8%) HPV6-positive samples collected for this study. Among them, 130 exhibited at least one single nucleotide polymorphism (SNP), indel, or amino acid change in the E5a-E5b-L1-LCR fragment and were sequenced in full. A global alignment and maximum likelihood tree of 190 complete HPV6 genomes (130 fully sequenced in this study and 60 obtained from sequence repositories) revealed two variant lineages, A and B, and five B sublineages: B1, B2, B3, B4, and B5. HPV6 (sub)lineage-specific SNPs and a 960-bp representative region for whole-genome-based phylogenetic clustering within the L2 open reading frame were identified. Multivariate logistic regression analysis revealed that lineage B predominated globally. Sublineage B3 was more common in Africa and North and South America, and lineage A was more common in Asia. Sublineages B1 and B3 were associated with anogenital infections, indicating a potential lesion-specific predilection of some HPV6 sublineages. Females had higher odds for infection with sublineage B3 than males. In conclusion, a global HPV6 phylogenetic analysis revealed the existence of two variant lineages and five sublineages, showing some degree of ethnogeographic, gender, and/or disease predilection in their distribution. IMPORTANCE This study established the largest database of globally circulating HPV6 genomic variants and contributed a total of 130 new, complete HPV6 genome sequences to available sequence repositories. Two HPV6 variant lineages and five sublineages were identified and showed some degree of association with geographical location, anatomical site of infection/disease, and/or gender. We additionally identified several HPV6 lineage- and sublineage-specific SNPs to facilitate the identification of HPV6 variants and determined a representative region within the L2 gene that is suitable for HPV6 whole-genome-based phylogenetic analysis. This study complements and significantly expands the current knowledge of HPV6 genetic diversity and forms a comprehensive basis for future epidemiological, evolutionary, functional, pathogenicity, vaccination, and molecular assay development studies.
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Affiliation(s)
- Mateja M Jelen
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Zigui Chen
- Department of Pediatrics, Albert Einstein College of Medicine, New York, New York, USA
| | - Boštjan J Kocjan
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Felicity J Burt
- Department of Medical Microbiology and Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Paul K S Chan
- Department of Microbiology, Faculty of Medicine, Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong Special Administrative Region, China
| | - Diego Chouhy
- Human Virology Group, National Council of Scientific and Technical Research, Institute of Molecular and Cell Biology of Rosario, Rosario, Argentina
| | - Catharina E Combrinck
- Department of Medical Microbiology and Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - François Coutlée
- Laboratoire de Virologie Moléculaire, Centre de Recherche, Centre Hospitalier de L'Université de Montréal, Hôpital Notre-Dame-Pavillon Deschamps, Montréal, Québec, Canada
| | - Christine Estrade
- Lausanne University Hospital (CHUV), Institute of Microbiology, Lausanne, Switzerland
| | - Alex Ferenczy
- Department of Pathology, McGill University and Jewish General Hospital, Montréal, Québec, Canada
| | - Alison Fiander
- Department of Obstetrics and Gynaecology, Cardiff University School of Medicine, Institute of Cancer and Genetics, Cardiff, United Kingdom
| | - Eduardo L Franco
- Department of Oncology, Division of Cancer Epidemiology, McGill University, Montréal, Québec, Canada
| | - Suzanne M Garland
- Department of Microbiology and Infectious Diseases, The Royal Women's Hospital, Parkville, Victoria, Australia Department of Obstetrics and Gynaecology, University of Melbourne, Victoria, Australia Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Adriana A Giri
- Human Virology Group, National Council of Scientific and Technical Research, Institute of Molecular and Cell Biology of Rosario, Rosario, Argentina
| | - Joaquín Víctor González
- Oncogenic Viruses Service, National Institute of Infectious Diseases-ANLIS Dr. Carlos G. Malbrán, Buenos Aires, Argentina
| | - Arndt Gröning
- Medizinisches Versorgungszentrum wagnerstibbe für Laboratoriumsmedizin und Pathologie GmbH, Hannover, Germany
| | - Kerstin Heidrich
- Medizinisches Versorgungszentrum wagnerstibbe für Laboratoriumsmedizin und Pathologie GmbH, Hannover, Germany
| | - Sam Hibbitts
- Department of Obstetrics and Gynaecology, Cardiff University School of Medicine, Institute of Cancer and Genetics, Cardiff, United Kingdom
| | - Lea Hošnjak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tommy N M Luk
- Dermatology Research Centre, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong Special Administrative Region, China Department of Health, Social Hygiene Service, Centre for Health Protection, Hong Kong Special Administrative Region, China
| | - Karina Marinic
- Histocompatibility and Molecular Genetics Laboratory, Dr. Julio C. Perrando Hospital, Resistencia, Chaco, Argentina
| | - Toshihiko Matsukura
- Ganshintetsu Memorial Laboratory, Department of Virology II, National Institute of Health, Tokyo, Japan
| | - Anna Neumann
- Medizinisches Versorgungszentrum wagnerstibbe für Laboratoriumsmedizin und Pathologie GmbH, Hannover, Germany
| | - Anja Oštrbenk
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Maria Alejandra Picconi
- Oncogenic Viruses Service, National Institute of Infectious Diseases-ANLIS Dr. Carlos G. Malbrán, Buenos Aires, Argentina
| | - Harriet Richardson
- Queen's Cancer Research Institute, Queen's University, Kingston, Ontario, Canada
| | - Martin Sagadin
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Roland Sahli
- Lausanne University Hospital (CHUV), Institute of Microbiology, Lausanne, Switzerland
| | - Riaz Y Seedat
- Department of Otorhinolaryngology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Katja Seme
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Alberto Severini
- Viral Exanthemata and STD Section, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Jessica L Sinchi
- Histocompatibility and Molecular Genetics Laboratory, Dr. Julio C. Perrando Hospital, Resistencia, Chaco, Argentina
| | - Jana Smahelova
- Department of Experimental Virology, National Reference Laboratory for Papillomaviruses, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Sepehr N Tabrizi
- Department of Microbiology and Infectious Diseases, The Royal Women's Hospital, Parkville, Victoria, Australia Department of Obstetrics and Gynaecology, University of Melbourne, Victoria, Australia Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Ruth Tachezy
- Department of Experimental Virology, National Reference Laboratory for Papillomaviruses, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Sarah Tohme
- Viral Exanthemata and STD Section, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Virgilijus Uloza
- Department of Otolaryngology, Lithuanian University of Health Sciences, Medical Academy, Kaunas, Lithuania
| | - Astra Vitkauskiene
- Department of Laboratory Medicine, Lithuanian University of Health Sciences, Medical Academy, Kaunas, Lithuania
| | - Yong Wee Wong
- DNA Laboratories Sdn. Bhd., UKM-MTDC Technology Centre, Universti Kebangsaan Malaysia, Bangi, Malaysia
| | - Snježana Zidovec Lepej
- Department of Molecular Diagnostics, University Hospital for Infectious Diseases Dr. Fran Mihaljević, Zagreb, Croatia
| | - Robert D Burk
- Departments of Microbiology and Immunology, Epidemiology and Population Health, Obstetrics and Gynecology and Women's Health, Albert Einstein College of Medicine, New York, New York, USA Department of Pediatrics, Albert Einstein College of Medicine, New York, New York, USA
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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Godínez J, Nicolás-Párraga S, Pimenoff V, Mengual-Chuliá B, Muñoz N, Bosch F, Sánchez G, McCloskey J, Bravo I. Phylogenetically related, clinically different: human papillomaviruses 6 and 11 variants distribution in genital warts and in laryngeal papillomatosis. Clin Microbiol Infect 2014; 20:O406-13. [DOI: 10.1111/1469-0691.12420] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 09/02/2013] [Accepted: 09/30/2013] [Indexed: 12/30/2022]
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11
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Maver PJ, Kocjan BJ, Seme K, Poljak M. Genomic diversity of low-risk human papillomavirus genotypes HPV 40, HPV 42, HPV 43, and HPV 44. J Med Virol 2013; 86:272-82. [PMID: 24155245 DOI: 10.1002/jmv.23822] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2013] [Indexed: 11/11/2022]
Abstract
In order to investigate the genomic diversity of low-risk human papillomavirus (HPV) genotypes, a total of 108 isolates of HPV 40, HPV 42, HPV 43, or HPV 44, obtained from anal swabs or tissue specimens of patients with anogenital warts, and cervical swabs of women with cervical intraepithelial neoplasia of different grades, were analyzed. The characterization of genomic variants was established by sequencing one third of the viral genome and analysis of three different genomic regions: L1, LCR, and E6. Maximum variant divergence accounted for 0.4-1.1% of the investigated genomic segments. Several novel, potentially important nucleotide substitutions, deletions, and insertions are described. Altogether, among 14 HPV 40 isolates, a total of nine different genomic variants were identified, composed of eight L1, five LCR, and four E6 genomic variants. Among 49 HPV 42 isolates, a total of 30 genomic variants were identified, composed of 20 L1, 18 LCR, and four E6 genomic variants. Among 10 HPV 43 isolates, distributed into two major genomic variant lineages with clearly defined nucleotide signatures, three genomic variants were identified, composed of three L1, two LCR, and two E6 genomic variants. Among 35 HPV 44 isolates, a total of eight HPV 44 and 11 subtype HPV 44 genomic variants were identified, composed of 13 L1, 14 LCR, and 6 E6 genomic variants. A similar level of genomic diversity of HPV 44 and its subtype was identified in our geographic region as has been reported previously on isolates collected worldwide.
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Affiliation(s)
- Polona J Maver
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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12
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Danielewski JA, Garland SM, McCloskey J, Hillman RJ, Tabrizi SN. Human papillomavirus type 6 and 11 genetic variants found in 71 oral and anogenital epithelial samples from Australia. PLoS One 2013; 8:e63892. [PMID: 23691108 PMCID: PMC3656832 DOI: 10.1371/journal.pone.0063892] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 04/07/2013] [Indexed: 11/18/2022] Open
Abstract
Genetic variation of 49 human papillomavirus (HPV) 6 and 22 HPV11 isolates from recurrent respiratory papillomatosis (RRP) (n = 17), genital warts (n = 43), anal cancer (n = 6) and cervical neoplasia cells (n = 5), was determined by sequencing the long control region (LCR) and the E6 and E7 genes. Comparative analysis of genetic variability was examined to determine whether different disease states resulting from HPV6 or HPV11 infection cluster into distinct variant groups. Sequence variation analysis of HPV6 revealed that isolates cluster into variants within previously described HPV6 lineages, with the majority (65%) clustering to HPV6 sublineage B1 across the three genomic regions examined. Overall 72 HPV6 and 25 HPV11 single nucleotide variations, insertions and deletions were observed within samples examined. In addition, missense alterations were observed in the E6/E7 genes for 6 HPV6 and 5 HPV11 variants. No nucleotide variations were identified in any isolates at the four E2 binding sites for HPV6 or HPV11, nor were any isolates found to be identical to the HPV6 lineage A or HPV11 sublineage A1 reference genomes. Overall, a high degree of sequence conservation was observed between isolates across each of the regions investigated for both HPV6 and HPV11. Genetic variants identified a slight association with HPV6 and anogenital lesions (p = 0.04). This study provides important information on the genetic diversity of circulating HPV 6 and HPV11 variants within the Australian population and supports the observation that the majority of HPV6 isolates cluster to the HPV6 sublineage B1 with anogenital lesions demonstrating an association with this sublineage (p = 0.02). Comparative analysis of Australian isolates for both HPV6 and HPV11 to those from other geographical regions based on the LCR revealed a high degree of sequence similarity throughout the world, confirming previous observations that there are no geographically specific variants for these HPV types.
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Affiliation(s)
- Jennifer A. Danielewski
- Department of Microbiology and Infectious Diseases, Royal Women’s Hospital, Melbourne, Australia
- Murdoch Childrens Research Institute, Melbourne, Australia
| | - Suzanne M. Garland
- Department of Microbiology and Infectious Diseases, Royal Women’s Hospital, Melbourne, Australia
- Murdoch Childrens Research Institute, Melbourne, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Australia
| | - Jenny McCloskey
- Sexual Health Services, Royal Perth Hospital, Perth, Australia
- School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Australia
| | - Richard J. Hillman
- Western Sydney Sexual Health Centre, University of Sydney, Sydney, Australia
| | - Sepehr N. Tabrizi
- Department of Microbiology and Infectious Diseases, Royal Women’s Hospital, Melbourne, Australia
- Murdoch Childrens Research Institute, Melbourne, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Australia
- * E-mail:
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13
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Seedat RY, Combrinck CE, Burt FJ. HPV associated with recurrent respiratory papillomatosis. Future Virol 2013. [DOI: 10.2217/fvl.13.31] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Papillomaviruses are members of the Papillomaviridae family. Over 150 HPV types have been identified. Recurrent respiratory papillomatosis (RRP) is a chronic condition caused by HPV characterized by recurrent papillomas of the respiratory tract, mainly the larynx. During the early stages, the condition presents with hoarseness, while more advanced disease presents with stridor and respiratory distress. There is no specific cure and treatment consists of repeated surgical procedures to remove the papillomas. Most patients eventually go into remission, but some suffer for many years with this condition, which may be fatal. HPV-6 and HPV-11 are the HPV types most commonly associated with RRP. Although most studies have found RRP due to HPV-11 to be more aggressive than disease due to HPV-6, the variability in disease aggressiveness is probably multifactorial. Information regarding the current epidemiology, molecular diversity and host immune responses is important for strategizing ways to reduce disease. Data on HPV genotypes associated with RRP would provide valuable information for vaccination programs to reduce the incidence of these genotypes in mothers and, in the long term, reduce the incidence of RRP in children. This review focuses on HPV-6 and HPV-11 as the HPV types that cause RRP, and discusses the viral genome and replication, clinical presentation of RRP, current techniques of diagnosis and genotyping, and the molecular diversity of HPV-6 and HPV-11.
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Affiliation(s)
- Riaz Y Seedat
- Department of Otorhinolaryngology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
- Department of Otorhinolaryngology, Universitas Academic Hospital, Bloemfontein, South Africa
| | - Catharina E Combrinck
- Department of Medical Microbiology & Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Felicity J Burt
- Department of Medical Microbiology & Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
- Department of Medical Microbiology & Virology, National Health Laboratory Service Universitas, Bloemfontein, South Africa
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14
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FRET-based detection and genotyping of HPV-6 and HPV-11 causing recurrent respiratory papillomatosis. J Virol Methods 2013; 189:271-6. [PMID: 23473839 DOI: 10.1016/j.jviromet.2013.01.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 01/24/2013] [Accepted: 01/30/2013] [Indexed: 11/20/2022]
Abstract
Recurrent respiratory papillomatosis (RRP) is a potentially life-threatening disease caused by human papillomavirus (HPV), usually HPV types 6 and 11. The conventional method used for detection and typing the RRP isolates in our laboratory is the polymerase chain reaction (PCR) and DNA sequencing method. A real-time PCR assay based on fluorescence resonance energy transfer (FRET) probe technology was developed for the detection and rapid genotyping of HPV-6 and-11 isolates from biopsy material. The primers and probes were designed using multiple alignments of HPV-6 and HPV-11 partial E6 and E7 sequences that included prototypic and non-prototypic variants. Real-time PCR followed by probe-specific melting-curve analysis allowed differentiation of HPV-6 and HPV-11. HPV-6 and HPV-11 amplicons were used to determine detection limits and inter- and intra-assay variability. The detection limit of the assay was 12.8 DNA copies for HPV-6 and 22.5 DNA copies for HPV-11. A total of 60 isolates were genotyped using the FRET real-time PCR assay and a 100% concordance was obtained when results were compared with genotyping based on conventional DNA sequencing. The real-time PCR assay based on FRET technology was able to detect and rapidly genotype HPV from tissue biopsy obtained from patients with RRP. The assay reduces the time required for genotyping from three working days to less than a day.
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15
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de Matos RPA, Sichero L, Mansur IM, do Bonfim CM, Bittar C, Nogueira RL, Küpper DS, Valera FCP, Nogueira ML, Villa LL, Calmon MF, Rahal P. Nucleotide and phylogenetic analysis of human papillomavirus types 6 and 11 isolated from recurrent respiratory papillomatosis in Brazil. INFECTION GENETICS AND EVOLUTION 2013; 16:282-9. [PMID: 23466889 DOI: 10.1016/j.meegid.2012.12.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 12/28/2012] [Accepted: 12/29/2012] [Indexed: 01/21/2023]
Abstract
There are few studies about the distribution of natural molecular variants of low-risk HPVs. Our aim was to evaluate the E6 early gene variability among HPV-6 and HPV-11 isolates detected in recurrent respiratory papillomatosis (RRP) samples obtained in a cohort of Brazilian patients. We also performed a phylogenetic analysis in order to compare nucleotide sequences identified in our study with previously reported isolates from different anatomic sites (laryngeal papillomas, genital warts, cervical cancer and anal swabs) obtained from other parts of the world to determine the phylogenetic relationships of variants detected in Brazil. The complete coding region of the E6 gene of 25 samples was cloned and sequenced: 18 isolates of HPV-6 (72%) and 7 isolates of HPV-11 (28%). A total of four different HPV-6 genomic variants and two HPV-11 genomic variants was identified. It was not possible to correlate specific variants with disease severity. Phylogenetic trees for both HPV types were constructed enclosing both E6 sequences detected in our study and formerly published sequences. In both phylogenetic trees, the sequences from Brazil did not group together. We could not establish a geographical association between HPV-6 or HPV-11 variants, unlike HPV-16 and HPV-18.
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Affiliation(s)
- Renata Prandini Adum de Matos
- UNESP - São Paulo State University, IBILCE, Institute of Bioscience, Language & Literature and Exact Science, Department of Biology, Rua Cristóvão Colombo 2265, Bairro Jardim Nazareth, CEP 15054-010, São José do Rio Preto, São Paulo, Brazil.
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16
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Lack of methylation in the upstream region of human papillomavirus type 6 from aerodigestive tract papillomas. J Virol 2012; 86:13790-4. [PMID: 23035223 DOI: 10.1128/jvi.01938-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methylation of the high-risk human papillomavirus type 16 (HPV16) upstream regulatory region (URR) has been described, but whether methylation is present among low-risk HPVs is unknown. The methylation status of the HPV6 URR was analyzed in papillomas from the upper aerodigestive tract of six adult patients. All CpGs in the URR were unmethylated, from both basal/intermediate and superficial cells, suggesting that methylation is not involved in the regulation of transcription from the HPV6 URR, regardless of epithelial differentiation.
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17
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Kocjan BJ, Jelen MM, Maver PJ, Seme K, Poljak M. Pre-vaccination genomic diversity of human papillomavirus genotype 6 (HPV 6): A comparative analysis of 21 full-length genome sequences. INFECTION GENETICS AND EVOLUTION 2011; 11:1805-10. [DOI: 10.1016/j.meegid.2011.06.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 06/08/2011] [Accepted: 06/27/2011] [Indexed: 11/26/2022]
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18
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Novel HPV-6 variants of human papillomavirus causing recurrent respiratory papillomatosis in southern Africa. Epidemiol Infect 2011; 140:1095-101. [DOI: 10.1017/s0950268811001580] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
SUMMARYThere is currently no information regarding the genetic diversity of HPV-6 variants circulating in South Africa. The aim of this study was to determine the HPV-6 variants affecting patients with recurrent respiratory papillomatosis, to determine whether mutations correlate with disease severity and identify molecular determinants of virulence with prognostic relevance. HPV-6 variants were identified based on genome changes within the 712-991 bp region encompassing the non-coding region (URR) of the genome, with variations in length resulting from insertions and duplications, and the 453-bp gene encoding the E6 protein. Based on manual comparison of sequence data from the URR, the isolates were identified as HPV-6a and HPV-6vc variants. Three novel HPV-6 variants were identified: one based on a mutation in the E6 region; two based on changes in the URR including a unique substitution detected in three isolates and an insertion and 170-bp duplication in the URR genome in one patient, who had clinical features of severe disease.
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Kovanda A, Kocjan BJ, Luzar B, Bravo IG, Poljak M. Characterization of novel cutaneous human papillomavirus genotypes HPV-150 and HPV-151. PLoS One 2011; 6:e22529. [PMID: 21799888 PMCID: PMC3143161 DOI: 10.1371/journal.pone.0022529] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 06/23/2011] [Indexed: 11/19/2022] Open
Abstract
DNA from two novel HPV genotypes, HPV-150 and HPV-151, isolated from hair follicles of immuno-competent individuals, was fully cloned, sequenced and characterized. The complete genomes of HPV-150 and HPV-151 are 7,436-bp and 7,386-bp in length, respectively. Both contain genes for at least six proteins, namely E6, E7, E1, E2, L2, L1, as well as a non-coding upstream regulatory region located between the L1 and E6 genes: spanning 416-bp in HPV-150 (genomic positions 7,371 to 350) and 322-bp in HPV-151 (genomic positions 7,213 to 148). HPV-150 and HPV-151 are phylogenetically placed within the Betapapillomavirus genus and are most closely related to HPV-96 and HPV-22, respectively. As in other members of this genus, the intergenic E2-L2 region is very short and does not encode for an E5 gene. Both genotypes contain typical zinc binding domains in their E6 and E7 proteins, but HPV-151 lacks the regular pRb-binding core sequence within its E7 protein. In order to assess the tissue predilection and clinical significance of the novel genotypes, quantitative type-specific real-time PCR assays were developed. The 95% detection limits of the HPV-150 and HPV-151 assays were 7.3 copies/reaction (range 5.6 to 11.4) and 3.4 copies/reaction (range 2.5 to 6.0), respectively. Testing of a representative collection of HPV-associated mucosal and cutaneous benign and malignant neoplasms and hair follicles (total of 540 samples) revealed that HPV-150 and HPV-151 are relatively rare genotypes with a cutaneous tropism. Both genotypes were found in sporadic cases of common warts and SCC and BCC of the skin as single or multiple infections usually with low viral loads. HPV-150 can establish persistent infection of hair follicles in immuno-competent individuals. A partial L1 sequence of a putative novel HPV genotype, related to HPV-150, was identified in a squamous cell carcinoma of the skin obtained from a 64-year old immuno-compromised male patient.
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Affiliation(s)
- Anja Kovanda
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Boštjan J. Kocjan
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Boštjan Luzar
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Ignacio G. Bravo
- Unit of Infections and Cancer, Catalan Institute of Oncology (ICO), L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER Epidemiology and Public Health (CIBERESP), Barcelona, Spain
- Genomics and Health Centre for Public Health Research (CSISP), Valencia, Spain
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- * E-mail:
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Maver PJ, Kocjan BJ, Seme K, Potočnik M, Gale N, Poljak M. Prevaccination genomic diversity of human papillomavirus genotype 11: A study on 63 clinical isolates and 10 full-length genome sequences. J Med Virol 2011; 83:461-70. [DOI: 10.1002/jmv.21994] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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21
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Vrtačnik Bokal E, Kocjan BJ, Poljak M, Bogovac Ž, Jančar N. Genomic variants of human papillomavirus genotypes 16, 18, and 33 in women with cervical cancer in Slovenia. J Obstet Gynaecol Res 2010; 36:1204-13. [DOI: 10.1111/j.1447-0756.2010.01316.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Maver PJ, Poljak M, Seme K, Kocjan BJ. Detection and typing of low-risk human papillomavirus genotypes HPV 6, HPV 11, HPV 42, HPV 43 and HPV 44 by polymerase chain reaction and restriction fragment length polymorphism. J Virol Methods 2010; 169:215-8. [PMID: 20637805 DOI: 10.1016/j.jviromet.2010.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Revised: 07/02/2010] [Accepted: 07/07/2010] [Indexed: 11/27/2022]
Abstract
A novel PCR-restriction fragment length polymorphism assay (PCR-RFLP) was developed for sensitive detection and reliable differentiation of five low-risk human papillomavirus (lr-HPV) genotypes: HPV 6, HPV 11, HPV 42, HPV 43 and HPV 44, as well as differentiation of prototypic and non-prototypic HPV 6 genomic variants. The assay is based on the amplification of a 320-bp fragment of the HPV E1 gene and subsequent analysis of PCR-products with BsaJI and HinFI. Testing on plasmid standards showed that PCR-RFLP enabled simple and reliable identification and differentiation of five targeted lr-HPV genotypes and could detect reproducibly down to 10 copies of viral genome equivalents per PCR. The PCR-RFLP showed almost complete agreement with previously obtained genotyping results on 42 HPV-DNA negative samples and 223 HPV-DNA positive samples (45 HPV 6, 34 HPV 11, 35 HPV 42, 10 HPV 43, 24 HPV 44 positive samples and 75 samples containing 28 non-targeted HPV genotypes). The novel assay is simple and robust, does not require any sophisticated equipment and can be of great value for epidemiological studies, particularly in settings in which financial resources are limited.
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Affiliation(s)
- Polona J Maver
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloska 4, 1105 Ljubljana, Slovenia
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