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Zhang C, Kou Z, Li R, Ji F, Lin X, Xu A, Song Y, Tao Z. Genomic diversity of human papillomavirus type 6 from patients with condyloma acuminatum in Eastern China. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 96:105146. [PMID: 34800713 DOI: 10.1016/j.meegid.2021.105146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 06/13/2023]
Abstract
OBJECTIVE Human papillomavirus type 6 (HPV6) is the major etiological agent of anogenital warts both men and women. However, there is limited data on its genomic characterization in mainland China. The aim of this study was to understand the complete genomic diversity of HPV6 from patients with condyloma acuminatum (CA) and to explore the prevalence of different variant lineages/sublineages in eastern China. METHODS CA samples were collected in 3 hospitals in Shandong Province, China from January 2020 to March 2021. DNA extraction, PCR amplification, Sanger sequencing and sequence assembly were performed on HPV6-positive samples. The complete genomes obtained in this study were analyzed phylogenetically with global HPV6 sequences in GenBank database using MEGA 11. RESULTS A total of 55 complete genomic sequences of HPV6 were obtained in this study. They were classified as HPV6 variant lineage A (n = 20), sublineage B1 (n = 34) and sublineage B3 (n = 1) by phylogenetic analysis. Sequence alignment showed E1, E5A, E5B, L1, L2, LCR were relatively highly variable regions for sublineage B1 whereas E1, E5A, L2 for lineage A. Both phylogenetic trees of lineage A and sublineage B1 composed of two main branches. Chinese sequences of lineage A segregated into the major branch while those in sublineage B1 belonged to both branches. Genomic divergence between sequences from China and other countries was 0.00% - 0.33% in lineage A and 0.00% - 0.40% in sublineage B1. CONCLUSIONS This is the first study on HPV variant lineages circulating in mainland China. The results revealed that lineage A and sublineage B1 were prevalent and they had different highly variable regions. Further surveillance is needed to understand the dynamic change of different variants in the population.
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Affiliation(s)
- Cui Zhang
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, No. 44 Wenhuaxi Road, Jinan 250012, PR China
| | - Zengqiang Kou
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan 250014, PR China
| | - Renpeng Li
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan 250014, PR China
| | - Feng Ji
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan 250014, PR China
| | - Xiaojuan Lin
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan 250014, PR China
| | - Aiqiang Xu
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, No. 44 Wenhuaxi Road, Jinan 250012, PR China; Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan 250014, PR China
| | - Yanyan Song
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, No. 44 Wenhuaxi Road, Jinan 250012, PR China.
| | - Zexin Tao
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan 250014, PR China.
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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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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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Comparative analysis of human papillomavirus type 6 complete genomes originated from head and neck and anogenital disorders. INFECTION GENETICS AND EVOLUTION 2019; 71:140-150. [PMID: 30905772 DOI: 10.1016/j.meegid.2019.03.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 01/20/2019] [Accepted: 03/20/2019] [Indexed: 01/12/2023]
Abstract
It is increasingly recognized that fundamental differences exist between high-risk and low-risk human papillomavirus (HPV) genotypes regarding interactions with the host. This study aims to join the recently emerging efforts to uncover these differences at the complete genome level and to study how they may influence the disease caused. Sixteen samples of thirteen patients with various HPV6-mediated benign mucosal disorders (nine recurrent respiratory papillomatoses with 2-8 recurrences, one condyloma acuminatum and three premalignant lesions of the genital mucosa) were sampled to determine the complete virus genomes. We collected the 197 HPV6 complete genomes deposited in the GenBank for cluster analysis to determine (sub)lineages. Genome polymorphisms were determined against the reference sequences of the (sub)lineages. Genome polymorphisms of the long control region (LCR) were tested for putative transcription factor binding sites; their functional analysis was performed by transient transfection of cloned whole LCRs into HEp-2 cells using a luciferase reporter system. Genomes from the same patients were always identical. Three, nine and one patients carried HPV6 lineage A, sublineage B1 and B2 variants, respectively. The three lineage A sequences were highly similar to each other, but distinct from the reference genome. A unique non-synonymous single nucleotide polymorphism (SNP) was found in the E5a open reading frame (ORF). Sublineage B1 genomes were more diverse, exhibited unique non-synonymous SNPs in the LCR and the E2/E4, L1, L2 ORFs. LCR activity of lineage A and sublineage B1 differed significantly; activity of one sublineage B1 LCR exhibiting two unique SNPs was significantly higher than that of other B1 LCR variants, close to the mean of LCR activities of lineage A variants. Different HPV6 lineages showed marked differences in variability patterns of the different genome regions. This may be involved in the differences in their distribution in different diseases or patient populations.
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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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Determination of the complete genome and functional analysis of HPV6 isolate VBD19/10 from a patient with aggressive recurrent respiratory papillomatosis. Epidemiol Infect 2016; 144:2128-35. [DOI: 10.1017/s0950268816000388] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
SUMMARYHuman papillomavirus (HPV) types 6 and 11 are the aetiological agent of recurrent respiratory papillomatosis (RRP). The complete genome of an HPV6 isolate with a 170 base pair (bp) duplication identified within the long control region (LCR) from a patient with aggressive recurrent respiratory papillomatosis was determined. The promoter sequence from the HPV LCR including the 170 bp duplication was placed upstream of a heterologous reporter gene and the activity of the reporter gene product determined using transfected cells. In total, mutations were observed at 157 nucleotide positions of the complete genome and included nucleotide substitutions, deletions and insertions, resulting in amino acid changes at 43 residue positions. Reporter gene activity using an HPV-derived LCR region with a 170 bp duplication was significantly higher than that using an HPV-derived LCR region with no duplication within this region. The results suggest that novel HPV variants warrant further investigation for potential biomarkers of aggressive disease.
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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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9
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Mammas IN, Spandidos DA, Sourvinos G. Genomic diversity of human papillomaviruses (HPV) and clinical implications: an overview in adulthood and childhood. INFECTION GENETICS AND EVOLUTION 2013; 21:220-6. [PMID: 24291228 DOI: 10.1016/j.meegid.2013.11.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 11/01/2013] [Accepted: 11/06/2013] [Indexed: 11/18/2022]
Abstract
During the last years, several researchers have highlighted the importance of characterizing more than one genomic region in order to detect recombination and classify variants of human papillomaviruses (HPVs) properly. HPVs variants differ in their biological, molecular and chemical properties. Therefore, this genomic diversity can present differences in the natural history and pathogenicity of HPVs. Different 'high-risk' HPVs variants of the genotypes HPV 16 and 18 can confer varied risks of viral persistence in the human cervix and influence HPVs progression to cervical cancer. Moreover, different 'low-risk' HPVs variants of the genotypes HPV 6 and 11 can play a unique role in the development of anogenital and cutaneous warts, recurrent respiratory papillomatosis (RRP) and ophthalmic pterygium. In future, the precise impact of genomic HPVs diversity to the clinical course of HPVs-associated diseases as well as to the efficacy of the current HPVs vaccines remains to be elucidated.
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Affiliation(s)
- Ioannis N Mammas
- Department of Clinical Virology, University of Crete, Medical School, Heraklion, Crete, Greece
| | - Demetrios A Spandidos
- Department of Clinical Virology, University of Crete, Medical School, Heraklion, Crete, Greece
| | - George Sourvinos
- Department of Clinical Virology, University of Crete, Medical School, Heraklion, Crete, Greece.
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10
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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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11
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Chouhy D, Bolatti EM, Pérez GR, Giri AA. Analysis of the genetic diversity and phylogenetic relationships of putative human papillomavirus types. J Gen Virol 2013; 94:2480-2488. [PMID: 23997181 DOI: 10.1099/vir.0.055137-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
More than 170 human papillomavirus (HPV) types have been completely sequenced, curated and divided into five genera: Alphapapillomavirus, Betapapillomavirus, Gammapapillomavirus, Mupapillomavirus and Nupapillomavirus. With the application of PCR methods, hundreds of putative novel HPV types have been identified as PCR amplicons in mucosa and skin. However, at present there are no studies reporting a systematic search of the currently known L1 amplicons and their phylogenetic relationships. This survey revealed the existence of at least 202 different putative HPV types that are pending for full-genome characterization: five alphapapillomaviruses, 37 betapapillomaviruses, 159 gammapapillomaviruses and one mupapillomavirus. All potential viruses of the genera Alphapapillomavirus and Betapapillomavirus were grouped in the defined species, while 59 putative gammapapillomaviruses types were segregated in 21 unidentified putative species. These data highlight the need for progress in the identification of additional taxa of the family Papillomaviridae in order to elucidate the diversity, evolution and medical implications of these viruses.
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Affiliation(s)
- Diego Chouhy
- Instituto de Biología Molecular y Celular de Rosario (CONICET), Rosario, Argentina.,Area Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Elisa M Bolatti
- Instituto de Biología Molecular y Celular de Rosario (CONICET), Rosario, Argentina
| | - Germán R Pérez
- Instituto de Biología Molecular y Celular de Rosario (CONICET), Rosario, Argentina.,Area Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Adriana A Giri
- Instituto de Biología Molecular y Celular de Rosario (CONICET), Rosario, Argentina.,Area Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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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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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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Kocjan BJ, Gale N, Hočevar Boltežar I, Seme K, Fujs Komloš K, Hošnjak L, Maver PJ, Jelen MM, Zupanič Pajnič I, Balažic J, Poljak M. Identical human papillomavirus (HPV) genomic variants persist in recurrent respiratory papillomatosis for up to 22 years. J Infect Dis 2012. [PMID: 23204170 DOI: 10.1093/infdis/jis733] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Seventy initial and 125 follow-up tissue specimens of laryngeal papillomas, obtained from 70 patients who had had recurrent respiratory papillomatosis for from 1-22 years, were investigated for the presence of human papillomavirus (HPV) DNA and HPV E5a, LCR and/or full-length genomic variants. HPV-6 was found in 130/195, HPV-11 in 63/195, and HPV-6/HPV-11 in 2/195 samples. Within 67/70 (95.7%) patients, all follow-up HPV isolates genetically matched completely initial HPV isolate over the highly variable parts of the genome or over the entire genome. Frequent recurrence of laryngeal papillomas is a consequence of long-term persistence of the identical initial HPV genomic variant.
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Affiliation(s)
- Boštjan J Kocjan
- Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
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15
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Komloš KF, Kocjan BJ, Košorok P, Luzar B, Meglič L, Potočnik M, Hočevar-Boltežar I, Gale N, Seme K, Poljak M. Tumor-specific and gender-specific pre-vaccination distribution of human papillomavirus types 6 and 11 in anogenital warts and laryngeal papillomas: A study on 574 tissue specimens. J Med Virol 2012; 84:1233-41. [DOI: 10.1002/jmv.23318] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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