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Basiletti JA, Valls J, Poklépovich T, Fellner MD, Rol M, Alonso R, Correa RM, Colucci MC, Rodríguez de la Peña M, Falabella PG, Saíno A, Campos J, Herrero R, Almonte M, Picconi MA. Human papillomavirus genotyping using next generation sequencing (NGS) in cervical lesions: Genotypes by histologic grade and their relative proportion in multiple infections. PLoS One 2022; 17:e0278117. [PMID: 36417453 PMCID: PMC9683586 DOI: 10.1371/journal.pone.0278117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 11/10/2022] [Indexed: 11/27/2022] Open
Abstract
Sensitive and specific genotyping of human papillomaviruses (HPVs) is critical for the surveillance and monitoring of the vaccine effectiveness. Here, HPV genotypes were identified in 137 cervical samples with different histology (79 ≤CIN1 and 58 CIN3+) using Nested-PCR followed by Next-Generation sequencing (NGS) and relative proportions for each genotype in multiple infections were computed. All samples had been previously genotyped by PCR-Reverse Blotting Hybridization (PCR-RBH) thus allowing for a concordance analysis between both techniques. Multiple infections were present in 85% of ≤CIN1 cases compared to only 41% in CIN3+ cases (p<0.001). Among ≤CIN1 cases a towering genotypic diversity was observed, considering both low (LR-) and high risk (HR-) HPV genotypes; while among CIN3+, diversity was lower, HR-HPVs prevailing in most cases, especially HPV16. Furthermore, the predominance of HR-HPV genotypes in the proportions identified in each sample was higher in CIN3+ cases [(HPV16 (62.5%), followed by HPV31 and HPV58 (8.3% each)], than in ≤CIN1 cases [(HPV16 (17.7%), followed by HPV52 (14.7%) and HPV31 (10.3%)]. Agreement between PCR-RBH and NGS was higher than 90% for all genotypes (with an overall Kappa of 0.7), even though NGS identified eighty-nine positive results for HPV genotypes that had not been detected by PCR-RBH, evidencing its greater sensitivity. These results suggest that a reduction in genotypic diversity and/or an increase in the relative proportion of HR-HPVs in multiple infections can be considered as a biomarker for the potential risk of malignant progression.
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Affiliation(s)
- Jorge Alejandro Basiletti
- Servicio Virus Oncogénicos, Laboratorio Nacional y Regional de Referencia de HPV, Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Malbrán”, Buenos Aires, Argentina
| | - Joan Valls
- Early Detection, Prevention & Infection Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Tomás Poklépovich
- Unidad Operativa Centro de Genómica y Bioinformática, ANLIS "Dr. Malbrán", Buenos Aires, Argentina
| | - María Dolores Fellner
- Servicio Virus Oncogénicos, Laboratorio Nacional y Regional de Referencia de HPV, Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Malbrán”, Buenos Aires, Argentina
| | - Maryluz Rol
- Early Detection, Prevention & Infection Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Rafael Alonso
- Departamento de Métodos Cuantitativos, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Rita Mariel Correa
- Servicio Virus Oncogénicos, Laboratorio Nacional y Regional de Referencia de HPV, Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Malbrán”, Buenos Aires, Argentina
| | - María Celeste Colucci
- Servicio Virus Oncogénicos, Laboratorio Nacional y Regional de Referencia de HPV, Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Malbrán”, Buenos Aires, Argentina
| | | | - Paula Gabriela Falabella
- Servicio de Ginecología, Hospital Nacional “Prof. Posadas”, El Palomar, Provincia de Buenos Aires, Argentina
| | - Agustina Saíno
- Servicio de Anatomía Patológica, Hospital Nacional “Prof. Posadas”, El Palomar, Provincia de Buenos Aires, Argentina
| | - Josefina Campos
- Unidad Operativa Centro de Genómica y Bioinformática, ANLIS "Dr. Malbrán", Buenos Aires, Argentina
| | - Rolando Herrero
- Agencia Costarricense de Investigaciones Biomédicas, San José, Costa Rica
| | - Maribel Almonte
- Early Detection, Prevention & Infection Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - María Alejandra Picconi
- Servicio Virus Oncogénicos, Laboratorio Nacional y Regional de Referencia de HPV, Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Malbrán”, Buenos Aires, Argentina
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The Prevalence, Genotype Distribution and Risk Factors of Human Papillomavirus in Tunisia: A National-Based Study. Viruses 2022; 14:v14102175. [PMID: 36298732 PMCID: PMC9611589 DOI: 10.3390/v14102175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/21/2022] [Accepted: 09/29/2022] [Indexed: 11/28/2022] Open
Abstract
There are limited national population-based studies on HPV genotypes distribution in Tunisia, thus making difficult an assessment of the burden of vaccine-preventable cervical cancer. In this context, we conducted a national survey to determine the HPV prevalence and genotypes distribution and the risk factors for HPV infections in Tunisian women. This is a cross-sectional study performed between December 2012 and December 2014. A liquid-based Pap smear sample was obtained from all women and samples' DNAs were extracted. Only women with betaglobin-positive PCR were further analysed for HPV detection and typing by a nested-PCR of the L1 region followed by next-generation sequencing. A multiple logistic regression model was used for the analysis of associations between the variables. A total of 1517 women were enrolled in this study, and 1229 out of the 1517 cervical samples were positive for the betaglobin control PCR and tested for HPV. Overall HPV infection prevalence was measured to be 7.8% (96/1229), with significant differences between the grand regions, ranging from 2% in the North to 13.1% in Grand Tunis. High-risk HPV genotypes accounted for 5% of the infections. The most prevalent genotypes were HPV 31 (1%), 16 (0.9%), 59 (0.7%). HPV18 was detected only in four cases of the study population. Potential risk factors were living in Grand Tunis region (OR: 7.94 [2.74-22.99]), married status (OR: 2.74 [1.23-6.13]), smoking habit (OR: 2.73 [1.35-5.51]), occupation (OR: 1.81 [1.09-3.01]) and women with multiple sexual partners (OR: 1.91 [1.07-3.39]). These findings underscore the need to evaluate the cost effectiveness of HPV vaccine implementation, contribute to the evidence on the burden of HPV infections, the critical role of sexual behaviour and socioeconomic status, and call for increased support to the preventive program of cervical cancer in Tunisia.
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Rikhotso RR, Mitchell EM, Wilson DT, Doede A, Matume ND, Bessong PO. Prevalence and distribution of selected cervical human papillomavirus types in HIV infected and HIV uninfected women in South Africa, 1989-2021: A narrative review. S Afr J Infect Dis 2022; 37:363. [PMID: 35815224 PMCID: PMC9257898 DOI: 10.4102/sajid.v37i1.363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/10/2022] [Indexed: 11/17/2022] Open
Abstract
Background Human papillomavirus infection, a causative agent of cervical cancer, is of great concern, more so in populations with high HIV prevalence, such as South Africa. Aim This review aimed to examine the prevalence and distribution of selected cervical human papillomavirus (HPV) types in HIV infected and HIV uninfected women in South Africa. Methods PubMed and Web of Science databases were searched using key words. For data integrity, data was assessed by two authors independently. The study inclusion criteria comprised records on cervical HPV, HPV genotyping and HPV type distribution among South African women. Statistical analysis was performed using Social Science Statistics. Results Sixty-nine articles met the inclusion criteria for analysis. Data on cervical HPV prevalence and type distribution was available only for five of the nine provinces of South Africa. Only 4/69 studies used sequencing as an approach to identify HPV types. In a general population, HPV type 16 was the most frequent (8.80%), followed by types 35 (4.86%), 18 (4.14%), 58 and 52 with the frequency of 3.65% and 3.62%, respectively. Furthermore, the least frequent type was HPV 70 (0.74%). Both HIV infected and HIV uninfected populations had a higher prevalence of high-risk human papillomavirus (hrHPV) types 16, 18 and 35 than other HPV types; while HPV types 6, 11 and 70 were the least frequent types from these populations. Lastly, HPV 16 was the most predominant type among women with normal (2.03%) and abnormal cervical cytology (6.60%). Conclusion Expanding on HPV genotyping will improve the knowledge in patterns of HPV type distribution in South Africa that will further help in decision making to improve current diagnostics, and future vaccine development and assessment.
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Affiliation(s)
- Rixongile R Rikhotso
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou, South Africa
| | - Emma M Mitchell
- Department of Family, Community and Mental Health Systems, School of Nursing, University of Virginia, Charlottesville, United States of America
| | - Daniel T Wilson
- Claude Moore Health Sciences Library, School of Nursing, University of Virginia, Charlottesville, United States of America
| | - Aubrey Doede
- Department of Family Medicine and Public Health, University of California San Diego, California, United States of America
| | - Nontokozo D Matume
- HIV/AIDS & Global Health Research Programme, University of Venda, Thohoyandou, South Africa
| | - Pascal O Bessong
- HIV/AIDS & Global Health Research Programme, University of Venda, Thohoyandou, South Africa
- Center for Global Health Equity, School of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
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Ma Z, Gharizadeh B, Cai X, Li M, Fellner MD, Basiletti JA, Correa RM, Colucci MC, Baldoni G, Vacchino M, Galarza P, Picconi MA, Wang C. A comprehensive HPV-STI NGS assay for detection of 29 HPV types and 14 non-HPV sexually transmitted infections. Infect Agent Cancer 2022; 17:9. [PMID: 35313939 PMCID: PMC8935747 DOI: 10.1186/s13027-022-00420-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sexually transmitted infections (STIs) are prevalent throughout the world and impose a significant burden on individual health and public health systems. Missed diagnosis and late treatment of STIs can lead to serious complications such as infertility and cervical cancer. Although sexually transmitted co-infections are common, most commercial assays target one or a few STIs. The HPV-STI ChapterDx Next Generation Sequencing (NGS) assay detects and quantifies 29 HPVs and 14 other STIs in a single-tube and single-step PCR reaction and can be applied to tens to thousands of samples in a single sequencing run. METHODS A cohort of 274 samples, previously analyzed by conventional cytology/histology and Roche cobas HPV Test, were analyzed by ChapterDx HPV-STI NGS assay for detection of 43 HPV and STI. A set of 43 synthetic control DNA fragments for 43 HPV and STI were developed to evaluate the limit of detection, specificity, and sensitivity of ChapterDx HPV-STI NGS assay. RESULTS The assay was evaluated in this study, and the limit of detection was 100% at 50 copies for all targets, and 100%, 96%, 88% at 20 copies for 34, 8, and 1 target, respectively. The performance of this assay has been compared to Roche cobas HPV test, showing an overall agreement of 97.5% for hr-HPV, and 98.5% for both, HPV16 and HPV18. The assay also detected all HPV-infected CIN2/3 with 100% agreement with Roche cobas HPV results. Moreover, several co-infections with non-HPV STIs, such as C. trachomatis, T. vaginalis, M. genitalium, and HSV2 were identified. CONCLUSIONS The ChapterDx HPV-STI NGS assay is a user-friendly, easy to automate and cost-efficient assay, which provides accurate and comprehensive results for a wide spectrum of HPVs and STIs.
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Affiliation(s)
- Zhihai Ma
- Chapter Diagnostics Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA
| | - Baback Gharizadeh
- Chapter Diagnostics Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA
| | - Xingsheng Cai
- Maijing Gene Medical Technology, No. 9, Spiral 4th Road, International Biological Island, Guangzhou, China
| | - Mengzhen Li
- Maijing Gene Medical Technology, No. 9, Spiral 4th Road, International Biological Island, Guangzhou, China
| | - María Dolores Fellner
- Oncogenic Viruses Service, National and Regional HPV Reference Laboratory, National Institute of Infectious Diseases-ANLIS "Dr. Malbrán", Av. Velez Sarsfield 563, C1282AFF, Buenos Aires, Argentina
| | - Jorge Alejandro Basiletti
- Oncogenic Viruses Service, National and Regional HPV Reference Laboratory, National Institute of Infectious Diseases-ANLIS "Dr. Malbrán", Av. Velez Sarsfield 563, C1282AFF, Buenos Aires, Argentina
| | - Rita Mariel Correa
- Oncogenic Viruses Service, National and Regional HPV Reference Laboratory, National Institute of Infectious Diseases-ANLIS "Dr. Malbrán", Av. Velez Sarsfield 563, C1282AFF, Buenos Aires, Argentina
| | - María Celeste Colucci
- Oncogenic Viruses Service, National and Regional HPV Reference Laboratory, National Institute of Infectious Diseases-ANLIS "Dr. Malbrán", Av. Velez Sarsfield 563, C1282AFF, Buenos Aires, Argentina
| | - Gabriela Baldoni
- Sexually Transmitted Diseases Service, National Reference Laboratory for STDs, National Institute of Infectious Diseases-ANLIS "Dr. Malbrán", Av. Velez Sarsfield 563, C1282AFF, Buenos Aires, Argentina
| | - Martín Vacchino
- Sexually Transmitted Diseases Service, National Reference Laboratory for STDs, National Institute of Infectious Diseases-ANLIS "Dr. Malbrán", Av. Velez Sarsfield 563, C1282AFF, Buenos Aires, Argentina
| | - Patricia Galarza
- Sexually Transmitted Diseases Service, National Reference Laboratory for STDs, National Institute of Infectious Diseases-ANLIS "Dr. Malbrán", Av. Velez Sarsfield 563, C1282AFF, Buenos Aires, Argentina
| | - María Alejandra Picconi
- Oncogenic Viruses Service, National and Regional HPV Reference Laboratory, National Institute of Infectious Diseases-ANLIS "Dr. Malbrán", Av. Velez Sarsfield 563, C1282AFF, Buenos Aires, Argentina
| | - Chunlin Wang
- Chapter Diagnostics Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA.
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