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Prétet JL, Arroyo Mühr LS, Cuschieri K, Fellner MD, Correa RM, Picconi MA, Garland SM, Murray GL, Molano M, Peeters M, Van Gucht S, Lambrecht C, Broeck DV, Padalko E, Arbyn M, Lepiller Q, Brunier A, Silling S, Søreng K, Christiansen IK, Poljak M, Lagheden C, Yilmaz E, Eklund C, Thapa HR, Querec TD, Unger ER, Dillner J. Human papillomavirus negative high grade cervical lesions and cancers: Suggested guidance for HPV testing quality assurance. J Clin Virol 2024; 171:105657. [PMID: 38401369 DOI: 10.1016/j.jcv.2024.105657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 02/12/2024] [Accepted: 02/19/2024] [Indexed: 02/26/2024]
Abstract
BACKGROUND Some high-grade cervical lesions and cervical cancers (HSIL+) test negative for human papillomavirus (HPV). The HPV-negative fraction varies between 0.03 % and 15 % between different laboratories. Monitoring and extended re-analysis of HPV-negative HSIL+ could thus be helpful to monitor performance of HPV testing services. We aimed to a) provide a real-life example of a quality assurance (QA) program based on re-analysis of HPV-negative HSIL+ and b) develop international guidance for QA of HPV testing services based on standardized identification of apparently HPV-negative HSIL+ and extended re-analysis, either by the primary laboratory or by a national HPV reference laboratory (NRL). METHODS There were 116 initially HPV-negative cervical specimens (31 histopathology specimens and 85 liquid-based cytology samples) sent to the Swedish HPV Reference Laboratory for re-testing. Based on the results, an international QA guidance was developed through an iterative consensus process. RESULT Standard PCR testing detected HPV in 55.2 % (64/116) of initially "HPV-negative" samples. Whole genome sequencing of PCR-negative samples identified HPV in an additional 7 samples (overall 61.2 % HPV positivity). Reasons for failure to detect HPV in an HSIL+ lesion are listed and guidance to identify cases for extended re-testing, including which information should be included when referring samples to an NRL are presented. CONCLUSION Monitoring the proportion of and reasons for failure to detect HPV in HSIL+ will help support high performance and quality improvement of HPV testing services. We encourage implementation of QA strategies based on re-analysis of "HPV negative" HSIL+ samples.
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Affiliation(s)
- Jean Luc Prétet
- French National Papillomavirus Reference Center, CHU de Besançon, EA3181, Université of Franche-Comté, F-25000 Besançon, France
| | - Laila Sara Arroyo Mühr
- Swedish National HPV Reference Laboratory, Center for Cervical Cancer Elimination, Karolinska Institutet and Karolinska University Hospital F56, 141 86 Stockholm, Sweden
| | - Kate Cuschieri
- Scottish HPV Reference Laboratory, Deptartment of Lab Medicine, Royal Infirmary of Edinburgh, Edinburgh, EH16 4SA, UK
| | - María Dolores Fellner
- Laboratorio Nacional y Regional de Referencia de Papilomavirus Humanos, Instituto Nacional de Enfermedades Infecciosas-ANLIS "Dr Malbrán", C1282AFF Buenos Aires, Argentina
| | - Rita Mariel Correa
- Laboratorio Nacional y Regional de Referencia de Papilomavirus Humanos, Instituto Nacional de Enfermedades Infecciosas-ANLIS "Dr Malbrán", C1282AFF Buenos Aires, Argentina
| | - María Alejandra Picconi
- Laboratorio Nacional y Regional de Referencia de Papilomavirus Humanos, Instituto Nacional de Enfermedades Infecciosas-ANLIS "Dr Malbrán", C1282AFF Buenos Aires, Argentina
| | - Suzanne M Garland
- Royal Women's Hospital, Parkville 3052 VIC, Australia; Department of Obstetrics and Gynaecology, University of Melbourne, Parkville 3052 VIC, Australia
| | - Gerald L Murray
- Royal Women's Hospital, Parkville 3052 VIC, Australia; Department of Obstetrics and Gynaecology, University of Melbourne, Parkville 3052 VIC, Australia
| | - Monica Molano
- Royal Women's Hospital, Parkville 3052 VIC, Australia
| | - Michael Peeters
- National Reference Centre for Human Papillomaviruses, Viral Diseases, Infectious Diseases in Humans, Sciensano. Rue Juliette Wytsman 14, 1050 Brussels, Belgium
| | - Steven Van Gucht
- National Reference Centre for Human Papillomaviruses, Viral Diseases, Infectious Diseases in Humans, Sciensano. Rue Juliette Wytsman 14, 1050 Brussels, Belgium
| | - Charlotte Lambrecht
- National Reference Centre for Human Papillomaviruses, Algemeen Medisch Laboratorium. Emiel Vloorsstraat 9, 2020 Antwerp, Belgium
| | - Davy Vanden Broeck
- National Reference Centre for Human Papillomaviruses, Algemeen Medisch Laboratorium. Emiel Vloorsstraat 9, 2020 Antwerp, Belgium
| | - Elizaveta Padalko
- National Reference Centre for Human Papillomaviruses, Laboratory of Medical Microbiology, University Hospital Ghent. C. Heymanslaan 10, 9000 Ghent, Belgium
| | - Marc Arbyn
- Unit Cancer Epidemiology, Cancer centre, Sciensano. Rue Juliette Wytsman 14, 1050 Brussels, Belgium
| | - Quentin Lepiller
- French National Papillomavirus Reference Center, CHU de Besançon, EA3181, Université of Franche-Comté, F-25000 Besançon, France
| | - Alice Brunier
- French National Papillomavirus Reference Center, CHU de Besançon, EA3181, Université of Franche-Comté, F-25000 Besançon, France
| | - Steffi Silling
- Institute of Virology, National Reference Center for Papilloma- and Polyomaviruses, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50935 Cologne, Germany
| | - Kristiane Søreng
- Norwegian HPV Reference Laboratory, Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - Irene Kraus Christiansen
- Norwegian HPV Reference Laboratory, Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia
| | - Camilla Lagheden
- Swedish National HPV Reference Laboratory, Center for Cervical Cancer Elimination, Karolinska Institutet and Karolinska University Hospital F56, 141 86 Stockholm, Sweden
| | - Emel Yilmaz
- Swedish National HPV Reference Laboratory, Center for Cervical Cancer Elimination, Karolinska Institutet and Karolinska University Hospital F56, 141 86 Stockholm, Sweden
| | - Carina Eklund
- Swedish National HPV Reference Laboratory, Center for Cervical Cancer Elimination, Karolinska Institutet and Karolinska University Hospital F56, 141 86 Stockholm, Sweden
| | - Hem R Thapa
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Troy D Querec
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Elizabeth R Unger
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Joakim Dillner
- Swedish National HPV Reference Laboratory, Center for Cervical Cancer Elimination, Karolinska Institutet and Karolinska University Hospital F56, 141 86 Stockholm, Sweden.
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Dube Mandishora RS, Rounge TB, Fitzpatrick M, Christiansen IK, Ambur OH, Lagström S, Stray-Pedersen B, Tommasino M, Palefsky J, Chirenje ZM. Correction: Self-collected and clinician-collected anal swabs show modest agreement for HPV genotyping. PLoS One 2023; 18:e0288418. [PMID: 37418482 DOI: 10.1371/journal.pone.0288418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2023] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0250426.].
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Hesselberg Løvestad A, Stosic MS, Costanzi JM, Christiansen IK, Aamot HV, Ambur OH, Rounge TB. TaME-seq2: tagmentation-assisted multiplex PCR enrichment sequencing for viral genomic profiling. Virol J 2023; 20:44. [PMID: 36890572 PMCID: PMC9993372 DOI: 10.1186/s12985-023-02002-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/27/2023] [Indexed: 03/10/2023] Open
Abstract
BACKGROUND Previously developed TaME-seq method for deep sequencing of HPV, allowed simultaneous identification of the human papillomavirus (HPV) DNA consensus sequence, low-frequency variable sites, and chromosomal integration events. The method has been successfully validated and applied to the study of five carcinogenic high-risk (HR) HPV types (HPV16, 18, 31, 33, and 45). Here, we present TaME-seq2 with an updated laboratory workflow and bioinformatics pipeline. The HR-HPV type repertoire was expanded with HPV51, 52, and 59. As a proof-of-concept, TaME-seq2 was applied on SARS-CoV-2 positive samples showing the method's flexibility to a broader range of viruses, both DNA and RNA. RESULTS Compared to TaME-seq version 1, the bioinformatics pipeline of TaME-seq2 is approximately 40× faster. In total, 23 HPV-positive samples and seven SARS-CoV-2 clinical samples passed the threshold of 300× mean depth and were submitted to further analysis. The mean number of variable sites per 1 kb was ~ 1.5× higher in SARS-CoV-2 than in HPV-positive samples. Reproducibility and repeatability of the method were tested on a subset of samples. A viral integration breakpoint followed by a partial genomic deletion was found in within-run replicates of HPV59-positive sample. Identified viral consensus sequence in two separate runs was > 99.9% identical between replicates, differing by a couple of nucleotides identified in only one of the replicates. Conversely, the number of identical minor nucleotide variants (MNVs) differed greatly between replicates, probably caused by PCR-introduced bias. The total number of detected MNVs, calculated gene variability and mutational signature analysis, were unaffected by the sequencing run. CONCLUSION TaME-seq2 proved well suited for consensus sequence identification, and the detection of low-frequency viral genome variation and viral-chromosomal integrations. The repertoire of TaME-seq2 now encompasses seven HR-HPV types. Our goal is to further include all HR-HPV types in the TaME-seq2 repertoire. Moreover, with a minor modification of previously developed primers, the same method was successfully applied for the analysis of SARS-CoV-2 positive samples, implying the ease of adapting TaME-seq2 to other viruses.
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Affiliation(s)
- Alexander Hesselberg Løvestad
- Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway.,Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - Milan S Stosic
- Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway
| | - Jean-Marc Costanzi
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - Irene Kraus Christiansen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway.,Division of Medicine, Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital and University of Oslo, Lørenskog, Norway
| | - Hege Vangstein Aamot
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - Ole Herman Ambur
- Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway.
| | - Trine B Rounge
- Department of Research, Cancer Registry of Norway, Oslo, Norway. .,Department of Pharmacy, Centre for Bioinformatics, University of Oslo, Oslo, Norway.
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Løvestad AH, Repesa A, Costanzi JM, Lagström S, Christiansen IK, Rounge TB, Ambur OH. Differences in integration frequencies and APOBEC3 profiles of five high-risk HPV types adheres to phylogeny. Tumour Virus Res 2022; 14:200247. [PMID: 36100161 PMCID: PMC9485212 DOI: 10.1016/j.tvr.2022.200247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 02/06/2023] Open
Abstract
Persistent infection with Human Papillomavirus (HPV) is responsible for almost all cases of cervical cancers, and HPV16 and HPV18 associated with the majority of these. These types differ in the proportion of viral minor nucleotide variants (MNVs) caused by APOBEC3 mutagenesis as well as integration frequencies. Whether these traits extend to other types remains uncertain. This study aimed to investigate and compare genomic variability and chromosomal integration in the two phylogenetically distinct Alpha-7 and Alpha-9 clades of carcinogenic HPV types. The TaME-seq protocol was employed to sequence cervical cell samples positive for HPV31, HPV33 or HPV45 and combine these with data from a previous study on HPV16 and HPV18. APOBEC3 mutation signatures were found in Alpha-9 (HPV16/31/33) but not in Alpha-7 (HPV18/45). HPV45 had significantly more MNVs compared to the other types. Alpha-7 had higher integration frequency compared to Alpha-9. An increase in integration frequency with increased diagnostic severity was found for Alpha-7. The results highlight important differences and broaden our understanding of the molecular mechanisms behind cervical cancer induced by high-risk HPV types from the Alpha-7 and Alpha-9 clades.
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Affiliation(s)
- Alexander Hesselberg Løvestad
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway
| | - Adina Repesa
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway
| | - Jean-Marc Costanzi
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - Sonja Lagström
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway,Department of Research, Cancer Registry of Norway, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Irene Kraus Christiansen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway,Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital and University of Oslo, Lørenskog, Norway
| | - Trine B. Rounge
- Department of Research, Cancer Registry of Norway, Oslo, Norway,Centre for Bioinformatics, Department of Pharmacy, University of Oslo, Oslo, Norway,Corresponding author. Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Ole Herman Ambur
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway,Corresponding authors.
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Nygård M, Engesæter B, Castle PE, Berland JM, Eide ML, Iversen OE, Jonassen CM, Christiansen IK, Vintermyr OK, Tropé A. Randomized Implementation of a Primary Human Papillomavirus Testing-based Cervical Cancer Screening Protocol for Women 34 to 69 Years in Norway. Cancer Epidemiol Biomarkers Prev 2022; 31:1812-1822. [PMID: 35793700 PMCID: PMC9437559 DOI: 10.1158/1055-9965.epi-22-0340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/30/2022] [Accepted: 07/01/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Cervical cancer screening programs are facing a programmatic shift where screening protocol based on human papillomavirus testing (HPV-Screening protocol) is replacing the liquid-based cytology (LBC-Screening protocol). For safe technology transfer within the nationwide screening programme in Norway, HPV-Screening protocol was implemented randomized to compare the real-world effectiveness of HPV-Screening protocol and LBC-Screening protocol at the first screening round. METHODS Among 302,295 women ages 34 to 69 years scheduled to attend screening from February 2015 to June 2017, 157,447 attended. A total of 77,207 were randomly allocated to the HPV-Screening protocol and 80,240 were allocated to the LBC-Screening protocol. All women were followed up for 18 months. RESULTS The HPV-Screening protocol resulted in a relative increase of 60% in the detection of cervical intraepithelial neoplasia (CIN) grade 2 or worse [risk ratio (RR) = 1.6, 95% confidence interval (CI) = 1.5-1.7], 40% in CIN grade 3 or worse (RR = 1.4, 95% CI = 1.3-1.6), 40% in cancer (RR = 1.4, 95% CI = 1.0-2.1), and 60% in colposcopy referrals (RR = 1.6, 95% CI = 1.5-1.6) compared with LBC-Screening. The performance of both protocols was age dependent, being more effective in women ages under 50 years. CONCLUSIONS The HPV-Screening protocol was well accepted by women in Norway and detected more CIN2, CIN3, and cancers compared with the LBC-Screening protocol. IMPACT A randomized implementation of the HPV-Screening protocol with real-world assessment enabled a gradual, quality assured, and safe technology transition. HPV-based screening protocol may further be improved by using HPV genotyping and age-specific referral algorithms.
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Affiliation(s)
- Mari Nygård
- The Cancer Registry of Norway, Oslo, Norway.,Corresponding Author: Mari Nygård, Research Department, The Cancer Registry of Norway, Postbox 5313 Majorstuen, Oslo 0304, Norway. Phone: 47-9518-1886; E-mail:
| | | | - Philip E. Castle
- Division of Cancer Prevention, NCI, NIH, Rockville, Maryland.,Division of Cancer Epidemiology and Genetics, NCI, NIH, Rockville, Maryland
| | | | - Maj Liv Eide
- Trondheim University Hospital, Trondheim, Norway
| | - Ole Erik Iversen
- Institute of Clinical Science, University of Bergen, Bergen, Norway.,Haukeland University Hospital, Bergen, Norway
| | | | | | - Olav Karsten Vintermyr
- Haukeland University Hospital, Bergen, Norway.,The Gades Laboratory for Pathology, University of Bergen, Bergen, Norway
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Lagström S, Løvestad AH, Umu SU, Ambur OH, Nygård M, Rounge TB, Christiansen IK. HPV16 and HPV18 type-specific APOBEC3 and integration profiles in different diagnostic categories of cervical samples. Tumour Virus Res 2021; 12:200221. [PMID: 34175494 PMCID: PMC8287217 DOI: 10.1016/j.tvr.2021.200221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 04/09/2021] [Accepted: 06/07/2021] [Indexed: 12/14/2022] Open
Abstract
Human papillomavirus (HPV) 16 and 18 are the most predominant types in cervical cancer. Only a small fraction of HPV infections progress to cancer, indicating that additional factors and genomic events contribute to the carcinogenesis, such as minor nucleotide variation caused by APOBEC3 and chromosomal integration. We analysed intra-host minor nucleotide variants (MNVs) and integration in HPV16 and HPV18 positive cervical samples with different morphology. Samples were sequenced using an HPV whole genome sequencing protocol TaME-seq. A total of 80 HPV16 and 51 HPV18 positive samples passed the sequencing depth criteria of 300× reads, showing the following distribution: non-progressive disease (HPV16 n = 21, HPV18 n = 12); cervical intraepithelial neoplasia (CIN) grade 2 (HPV16 n = 27, HPV18 n = 9); CIN3/adenocarcinoma in situ (AIS) (HPV16 n = 27, HPV18 n = 30); cervical cancer (HPV16 n = 5). Similar numbers of MNVs in HPV16 and HPV18 samples were observed for most viral genes, with the exception of HPV18 E4 with higher numbers across clinical categories. APOBEC3 signatures were observed in HPV16 lesions, while similar mutation patterns were not detected for HPV18. The proportion of samples with integration was 13% for HPV16 and 59% for HPV18 positive samples, with a noticeable portion located within or close to cancer-related genes.
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Affiliation(s)
- Sonja Lagström
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway; Department of Research, Cancer Registry of Norway, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Sinan Uğur Umu
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Ole Herman Ambur
- Faculty of Health Sciences, OsloMet, Oslo Metropolitan University, Oslo, Norway
| | - Mari Nygård
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Trine B Rounge
- Department of Research, Cancer Registry of Norway, Oslo, Norway; Department of Informatics, University of Oslo, Oslo, Norway.
| | - Irene Kraus Christiansen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway; Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital and University of Oslo, Lørenskog, Norway.
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Dube Mandishora RS, Rounge TB, Fitzpatrick M, Christiansen IK, Ambur OH, Lagström S, Stray-Pedersen B, Tommasino M, Palefsky J, Chirenje ZM. Self-collected and clinician-collected anal swabs show modest agreement for HPV genotyping. PLoS One 2021; 16:e0250426. [PMID: 33901223 PMCID: PMC8075200 DOI: 10.1371/journal.pone.0250426] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 04/06/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND & AIM Women with HIV/HPV coinfection and cervical lesions are at increased risk of developing HPV related anal cancer. Self-collection of anal swabs may facilitate HPV molecular testing in anal cancer screening, especially in high-risk groups, and yet it is not adequately studied. We evaluated level of agreement between self-collected anal swabs (SCAS) and clinician-collected anal swabs (CCAS) when used for HPV genotyping. We also described the anal HPV genotype distribution and HIV/HPV coinfection. METHODS We performed a cross sectional study with participants from a visual-inspection-with-acetic-acid and cervicography (VIAC) clinic, in Harare, Zimbabwe. In a clinic setting, the women aged ≥18 years provided anal swabs in duplicate; first CCAS and then SCAS immediately after. HPV detection and genotyping were performed using next generation amplicon sequencing of a 450bp region of the HPV L1 gene. Level of agreement of HPV genotypes between CCAS and SCAS was calculated using the kappa statistic. McNemar tests were used to evaluate agreement in the proportion of genotypes detected by either method. RESULTS Three-hundred women provided 600 samples for HPV genotyping. HPV genotypes were detected in 25% of SCAS and in 22% of CCAS. The most common genotypes with CCAS were HPV52, HPV62 and HPV70 and with SCAS were HPV62, HPV44, HPV52, HPV53 and HPV68. Total HPV genotypes detected in CCAS were more than those detected in SCAS, 32 versus 27. The agreement of HPV genotypes between the two methods was 0.55 in kappa value (k). The test of proportions using McNemar gave a Chi-square value of 0.75 (p = 0.39). Multiple HPV infections were detected in 28/75 and 29/67 women for CCAS and SCAS respectively. CONCLUSIONS SCAS and CCAS anal swabs showed moderate agreement, with no statistically significant difference in the proportion of genotypes detected by either methods. Although the differences between the two methods were not statistically significant, CCAS detected more HPV genotypes than SCAS and more HPV infections were detected in SCAS than in CCAS. Our data suggest that self-collected anal swabs can be used as an alternative to clinician-collected anal swabs for HPV genotyping.
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Affiliation(s)
- Racheal S. Dube Mandishora
- Department of Medical Microbiology, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
- Infections and Cancer Biology Group, International Agency for Research on Cancer, Lyon, France
| | - Trine B. Rounge
- Department of Research, Cancer Registry of Norway, Oslo, Norway
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Megan Fitzpatrick
- Department of Pathology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Irene Kraus Christiansen
- Department of Microbiology and Infection Control, The Norwegian HPV Reference Laboratory, Akershus University Hospital, Lørenskog, Norway
- Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital and University of Oslo, Lørenskog, Norway
| | - Ole Herman Ambur
- Faculty of Health Sciences, OsloMet—Oslo Metropolitan University, Oslo, Norway
| | - Sonja Lagström
- Department of Research, Cancer Registry of Norway, Oslo, Norway
- Department of Microbiology and Infection Control, The Norwegian HPV Reference Laboratory, Akershus University Hospital, Lørenskog, Norway
| | - Babill Stray-Pedersen
- Women’s Clinic, Rikshospitalet, Oslo University Hospital and Institute of Clinical Medicine, Oslo, Norway
| | - Massimo Tommasino
- Infections and Cancer Biology Group, International Agency for Research on Cancer, Lyon, France
| | - Joel Palefsky
- Department of Medicine, UCSF School of Medicine, San Francisco, CA, United States of America
| | - Zvavahera M. Chirenje
- Department of Obstetrics and Gynaecology, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
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Bhatia R, Boada EA, Bonde J, Quint W, Christiansen IK, Xu L, Ejegod DM, Moncur S, Cuschieri K, Arbyn M. Evaluation of HarmoniaHPV test for detection of clinically significant Human Papillomavirus infection using the VALGENT framework. J Virol Methods 2021; 294:114161. [PMID: 33895238 DOI: 10.1016/j.jviromet.2021.114161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/29/2021] [Accepted: 04/09/2021] [Indexed: 11/29/2022]
Abstract
AIM The VALidation of HPV GENotyping Tests (VALGENT) is a framework for comparison and validation of HPV tests with genotyping capabilities. In this study, the clinical performance of a single tube HPV test -HarmoniaHPV- was assessed in SurePath™ samples and compared to a clinically validated reference test, the GP5+/6+ Enzyme ImmunoAssay (GP5+/6 + EIA). METHODS HarmoniaHPV test is a real-time, PCR based, limited genotyping HPV test which detects 14 high-risk HPV types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68 with HPV16, and HPV 18 reported individually. Clinical performance was assessed using 998 unselected, cervical screening samples enriched with 297 cytologically abnormal specimens (100 atypical squamous cells of unspecified significance, 100 low-grade squamous intraepithelial lesions, 97 high-grade squamous intraepithelial lesions). Cases were defined as women diagnosed with histologically confirmed cervical intraepithelial neoplasia 2 or more (≥CIN2, N = 122). RESULTS Using the manufacturer recommended (un-adjusted) cut-offs, HarmoniaHPV had non-inferior sensitivity for detection of ≥ CIN2 but showed inferior specificity. A cut-off optimisation exercise was therefore carried out and optimised cut-offs for each individual channel rendered a sensitivity and specificity of HarmoniaHPV that was non-inferior to GP5+/6 + EIA. Analytically, the test showed excellent intra- and inter-laboratory reproducibility, which improved further with the use of the optimised cut-offs. CONCLUSION HarmoniaHPV when operated with optimised cut-offs fulfils the international clinical criteria for use in cervical cancer screening on SurePath samples. The optimised cut-offs warrant additional testing and independent validation.
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Affiliation(s)
- Ramya Bhatia
- HPV Research Group, University of Edinburgh, EH16 4TJ, Edinburgh, Scotland, United Kingdom; Scottish HPV Reference Laboratory, Royal Infirmary of Edinburgh, EH16 4SA, Edinburgh, Scotland, United Kingdom.
| | - Elia Alcañiz Boada
- HPV Research Group, University of Edinburgh, EH16 4TJ, Edinburgh, Scotland, United Kingdom
| | - Jesper Bonde
- Molecular Pathology Laboratory, Department of Pathology, Copenhagen University Hospital, Kettegårds Alle 30, 2650, Hvidovre, Denmark
| | - Wim Quint
- DDL Diagnostic Laboratory, Rijswijk, the Netherlands
| | - Irene Kraus Christiansen
- Norwegian HPV Reference Laboratory, Department of Microbiology and Infection Control, Akershus University Hospital, 1478, Lørenskog, Norway
| | - Lan Xu
- Unit of Cancer Epidemiology, Belgian Cancer Centre, Sciensano, Juliette Wytsmanstreet 14, B1050, Brussels, Belgium
| | - Ditte Møller Ejegod
- Molecular Pathology Laboratory, Department of Pathology, Copenhagen University Hospital, Kettegårds Alle 30, 2650, Hvidovre, Denmark
| | - Sharon Moncur
- Scottish HPV Reference Laboratory, Royal Infirmary of Edinburgh, EH16 4SA, Edinburgh, Scotland, United Kingdom
| | - Kate Cuschieri
- Scottish HPV Reference Laboratory, Royal Infirmary of Edinburgh, EH16 4SA, Edinburgh, Scotland, United Kingdom
| | - Marc Arbyn
- Unit of Cancer Epidemiology, Belgian Cancer Centre, Sciensano, Juliette Wytsmanstreet 14, B1050, Brussels, Belgium; Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, University Ghent, Ghent, Belgium
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Ejegod DM, Hansen M, Christiansen IK, Pedersen H, Quint W, Xu L, Arbyn M, Bonde J. Clinical validation of the Cobas 4800 HPV assay using cervical samples in SurePath medium under the VALGENT4 framework. J Clin Virol 2020; 128:104336. [PMID: 32446166 DOI: 10.1016/j.jcv.2020.104336] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/05/2020] [Accepted: 03/23/2020] [Indexed: 10/24/2022]
Abstract
BACKGROUND The VALidation of HPV Genotyping Tests (VALGENT) framework is an international cooperation designed for comparison and clinical validation of HPV assays with genotyping capabilities. OBJECTIVES Here we addressed the accuracy of the Roche cobas 4800 HPV test using SurePath samples from the Danish cervical cancer screening program under the VALGENT framework. MATERIAL AND METHODS The VALGENT4 panel comprises 998 consecutive SurePath cervical samples from routine screening and 297 SurePath samples enriched for disease (100 ASC-US, 100 LSIL, 97 HSIL). The cobas HPV test is a real-time PCR assay which detects HPV16 and 18 individually and 12 other high-risk (hr) HPV genotypes in one bulk. RESULTS The clinical performance of the cobas test was assessed relative to that of the comparator assay GP5+/6 + PCR Enzyme ImmunoAssay (GP-EIA) by a non-inferiority test. The relative sensitivity for ≥ CIN2 was 1.00 (95% CI: 0.97-1.04) and relative specificity for the control group was 1.02 (95% CI: 1.01-1.04). The cobas test was found non-inferior to that of GP-EIA for both sensitivity and specificity (p-0.0006 and p < 0.0001, respectively). The type specific performance of the cobas test was evaluated using the GP5+/6 + PCR with Luminex genotyping (GP-LMNX) as comparator. The cobas test showed excellent to good concordance (Kappa: 0.70 to 0.90) with GP-LMNX for all three genotype groups in the overall VALGENT population but good to moderate concordance in the Screening population (kappa from 0.56 to 0.80). CONCLUSIONS The cobas HPV test demonstrated non-inferiority to the comparator assay on cervical SurePath screening samples using the VALGENT4 panel.
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Affiliation(s)
- Ditte Møller Ejegod
- Molecular Pathology Laboratory, Department of Pathology, Copenhagen University Hospital, Hvidovre, Kettegård Alle 30, 2650 Hvidovre, Denmark.
| | - Mona Hansen
- National HPV Reference Laboratory, Department of Microbiology and Infection Control, Akershus University Hospital, 1478 Lørenskog, Norway
| | - Irene Kraus Christiansen
- National HPV Reference Laboratory, Department of Microbiology and Infection Control, Akershus University Hospital, 1478 Lørenskog, Norway
| | - Helle Pedersen
- Molecular Pathology Laboratory, Department of Pathology, Copenhagen University Hospital, Hvidovre, Kettegård Alle 30, 2650 Hvidovre, Denmark
| | - Wim Quint
- DDL diagnostics Laboratory, Rijswijk, Nederlands
| | - Lan Xu
- Unit Cancer Epidemiology, Belgian Cancer Centre, Juliette Wytsmanstreet 14, 1050 Brussels, Belgium
| | - Marc Arbyn
- Unit Cancer Epidemiology, Belgian Cancer Centre, Juliette Wytsmanstreet 14, 1050 Brussels, Belgium
| | - Jesper Bonde
- Molecular Pathology Laboratory, Department of Pathology, Copenhagen University Hospital, Hvidovre, Kettegård Alle 30, 2650 Hvidovre, Denmark
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10
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Ehrig F, Häfner N, Driesch C, Kraus Christiansen I, Beer K, Schmitz M, Runnebaum IB, Dürst M. Differences in Stability of Viral and Viral-Cellular Fusion Transcripts in HPV-Induced Cervical Cancers. Int J Mol Sci 2019; 21:ijms21010112. [PMID: 31877944 PMCID: PMC6981427 DOI: 10.3390/ijms21010112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 12/14/2022] Open
Abstract
HPV-DNA integration results in dysregulation of viral oncogene expression. Because viral-cellular fusion transcripts inherently lack the viral AU-rich elements of the 3’UTR, they are considered to be more stable than episome-derived transcripts. The aim of this study is to provide formal proof for this assumption by comparing the stability of viral early transcripts derived from episomal and integrated HPV16 DNA, respectively. Full-length cDNA of three fusion transcripts comprising viral and cellular sequences in sense orientation were amplified and cloned into the adeno-viral-vector pAd/CMV/V5-DEST. The most abundant HPV16 oncogene transcript E6*I-E7-E1vE4-E5 with and without 3’UTR, served as reference and control, respectively. Human primary keratinocytes were transduced using high titer virus stocks. qRT-PCR was performed to determine mRNA stability in relation to GAPDH in the presence of actinomycin-D. In four independent transduction experiments, all three viral-cellular fusion transcripts were significantly more stable compared to the episome-derived reference. Among the three viral-cellular fusion transcripts the most stable transcript was devoid of the instability core motif “AUUUA”. Unexpectedly, there was no significant difference in the stability between the episome-derived transcripts either with or without 3’UTR, indicating that the AU-rich elements of the 3’UTR are not contributing to RNA stability. Instead, the three “AUUUA” motifs located in the untranslated region between the viral E4 and E5 genes may be responsible for the instability. This is the first report showing that authentic viral-cellular fusion transcripts are more stable than episome-derived transcripts. The longer half-life of the fusion transcripts may result in increased levels of viral oncoproteins and thereby drive the carcinogenic process.
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Affiliation(s)
- Franziska Ehrig
- Department of Gynecology, Jena University Hospital, Friedrich Schiller University Jena, 07747 Jena, Germany; (F.E.); (N.H.); (C.D.); (K.B.); (I.B.R.)
| | - Norman Häfner
- Department of Gynecology, Jena University Hospital, Friedrich Schiller University Jena, 07747 Jena, Germany; (F.E.); (N.H.); (C.D.); (K.B.); (I.B.R.)
| | - Corina Driesch
- Department of Gynecology, Jena University Hospital, Friedrich Schiller University Jena, 07747 Jena, Germany; (F.E.); (N.H.); (C.D.); (K.B.); (I.B.R.)
| | - Irene Kraus Christiansen
- Department of Microbiology and Infection Control, Akershus University Hospital, 1478 Lørenskog, Norway;
| | - Katrin Beer
- Department of Gynecology, Jena University Hospital, Friedrich Schiller University Jena, 07747 Jena, Germany; (F.E.); (N.H.); (C.D.); (K.B.); (I.B.R.)
| | | | - Ingo B. Runnebaum
- Department of Gynecology, Jena University Hospital, Friedrich Schiller University Jena, 07747 Jena, Germany; (F.E.); (N.H.); (C.D.); (K.B.); (I.B.R.)
| | - Matthias Dürst
- Department of Gynecology, Jena University Hospital, Friedrich Schiller University Jena, 07747 Jena, Germany; (F.E.); (N.H.); (C.D.); (K.B.); (I.B.R.)
- Correspondence: ; Tel.: +49-3641-939-0890
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11
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Enerly E, Flingtorp R, Christiansen IK, Campbell S, Hansen M, Myklebust TÅ, Weiderpass E, Nygård M. An observational study comparing HPV prevalence and type distribution between HPV-vaccinated and -unvaccinated girls after introduction of school-based HPV vaccination in Norway. PLoS One 2019; 14:e0223612. [PMID: 31600341 PMCID: PMC6786612 DOI: 10.1371/journal.pone.0223612] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/24/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Many countries have initiated school-based human papillomavirus (HPV) vaccination programs. The real-life effectiveness of HPV vaccines has become increasingly evident, especially among girls vaccinated before HPV exposure in countries with high vaccine uptake. In 2009, Norway initiated a school-based HPV vaccination program for 12-year-old girls using the quadrivalent HPV vaccine (Gardasil®), which targets HPV6, 11, 16, and 18. Here, we aim to assess type-specific vaginal and oral HPV prevalence in vaccinated compared with unvaccinated girls in the first birth cohort eligible for school-based vaccination (born in 1997). METHODS This observational, cross-sectional study measured the HPV prevalence ratio (PR) between vaccinated and unvaccinated girls in Norway. Facebook advertisement was used to recruit participants and disseminate information about the study. Participants self-sampled vaginal and oral specimens using an Evalyn® Brush and a FLOQSwab™, respectively. Sexual behavior was ascertained through a short questionnaire. RESULTS Among the 312 participants, 239 (76.6%) had received at least one dose of HPV vaccine prior to sexual debut. 39.1% of vaginal samples were positive for any HPV type, with similar prevalence among vaccinated and unvaccinated girls (38.5% vs 41.1%, PR: 0.93, 95% confidence interval [CI]: 0.62-1.41). For vaccine-targeted types there was some evidence of lower prevalence in the vaccinated (0.4%) compared to the unvaccinated (6.8%) group (PR: 0.06, 95%CI: 0.01-0.52). This difference remained after adjusting for sexual behavior (PR: 0.04, 95%CI: 0.00-0.42). Only four oral samples were positive for any HPV type, and all of these participants had received at least one dose of HPV vaccine at least 1 year before oral sexual debut. CONCLUSION There is evidence of a lower prevalence of vaccine-targeted HPV types in the vagina of vaccinated girls from the first birth cohort eligible for school-based HPV vaccination in Norway; this was not the case when considering all HPV types or types not included in the quadrivalent HPV vaccine.
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Affiliation(s)
- Espen Enerly
- Department of Research, Cancer Registry of Norway, Oslo, Norway
- * E-mail:
| | | | - Irene Kraus Christiansen
- Department of Microbiology and Infection Control, National HPV Reference Laboratory, Akershus University Hospital, Lørenskog, Norway
| | | | - Mona Hansen
- Department of Microbiology and Infection Control, National HPV Reference Laboratory, Akershus University Hospital, Lørenskog, Norway
| | - Tor Åge Myklebust
- Department of Registration, Cancer Registry of Norway, Oslo, Norway
- Department of Research and Innovation, Møre and Romsdal Hospital Trust, Ålesund, Norway
| | - Elisabete Weiderpass
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
| | - Mari Nygård
- Department of Research, Cancer Registry of Norway, Oslo, Norway
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12
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Lagström S, van der Weele P, Rounge TB, Christiansen IK, King AJ, Ambur OH. HPV16 whole genome minority variants in persistent infections from young Dutch women. J Clin Virol 2019; 119:24-30. [PMID: 31446251 DOI: 10.1016/j.jcv.2019.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 08/06/2019] [Accepted: 08/09/2019] [Indexed: 11/16/2022]
Abstract
BACKGROUND Chronic infections by one of the oncogenic human papillomaviruses (HPVs) are responsible for near 5% of the global cancer burden and HPV16 is the type most often found in cancers. HPV genomes display unexpected levels of variation when deep-sequenced. Minor nucleotide variations (MNVs) may reveal HPV genomic instability and HPV-related carcinogenic transformation of host cells. OBJECTIVES The objective of this study was to investigate HPV16 genome variation at the minor variant level on persisting HPV16 cervical infections from a population of young Dutch women. STUDY DESIGN 15 HPV16 infections were sequenced using a whole-HPV genome deep sequencing protocol (TaME-seq). One infection was followed over a three-year period, eight were followed over a two-year period, three were followed over a one-year period and three infections had a single sampling point. RESULTS AND CONCLUSIONS Using a 1% variant frequency cutoff, we find on average 48 MNVs per HPV16 genome and 1717 MNVs in total when sequencing coverage was >100 × . We find the transition mutation T > C to be the most common, in contrast to other studies detecting APOBEC-related C > T mutation profiles in pre-cancerous and cancer samples. Our results suggest that the relative mutagenic footprint of HPV16 genomes may differ between the infections in this study and transforming lesions. In addition, we identify a number of MNVs that have previously been associated with higher incidence of high-grade lesions (CIN3+) in a population study. These findings may provide a starting point for future studies exploring causality between emerging HPV minor genomic variants and cancer development.
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Affiliation(s)
- Sonja Lagström
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway; Department of Research, Cancer Registry of Norway, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Pascal van der Weele
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Research, Diagnostics and Screening, Bilthoven, the Netherlands; Vrije Universiteit-University Medical Center (VUmc), Department of Pathology, Amsterdam, the Netherlands
| | | | - Irene Kraus Christiansen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway; Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Audrey J King
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Research, Diagnostics and Screening, Bilthoven, the Netherlands.
| | - Ole Herman Ambur
- Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway.
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13
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Lagström S, Umu SU, Lepistö M, Ellonen P, Meisal R, Christiansen IK, Ambur OH, Rounge TB. TaME-seq: An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration. Sci Rep 2019; 9:524. [PMID: 30679491 PMCID: PMC6345795 DOI: 10.1038/s41598-018-36669-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 11/26/2018] [Indexed: 12/11/2022] Open
Abstract
HPV genomic variability and chromosomal integration are important in the HPV-induced carcinogenic process. To uncover these genomic events in an HPV infection, we have developed an innovative and cost-effective sequencing approach named TaME-seq (tagmentation-assisted multiplex PCR enrichment sequencing). TaME-seq combines tagmentation and multiplex PCR enrichment for simultaneous analysis of HPV variation and chromosomal integration, and it can also be adapted to other viruses. For method validation, cell lines (n = 4), plasmids (n = 3), and HPV16, 18, 31, 33 and 45 positive clinical samples (n = 21) were analysed. Our results showed deep HPV genome-wide sequencing coverage. Chromosomal integration breakpoints and large deletions were identified in HPV positive cell lines and in one clinical sample. HPV genomic variability was observed in all samples allowing identification of low frequency variants. In contrast to other approaches, TaME-seq proved to be highly efficient in HPV target enrichment, leading to reduced sequencing costs. Comprehensive studies on HPV intra-host variability generated during a persistent infection will improve our understanding of viral carcinogenesis. Efficient identification of both HPV variability and integration sites will be important for the study of HPV evolution and adaptability and may be an important tool for use in cervical cancer diagnostics.
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Affiliation(s)
- Sonja Lagström
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway.,Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Sinan Uğur Umu
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Maija Lepistö
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Pekka Ellonen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Roger Meisal
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - Irene Kraus Christiansen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway.,Clinical Molecular Biology (EpiGen), Medical Division, Akershus University Hospital and Institute of Clinical Medicine, University of, Oslo, Norway
| | - Ole Herman Ambur
- Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway
| | - Trine B Rounge
- Department of Research, Cancer Registry of Norway, Oslo, Norway.
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14
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Feiring B, Laake I, Christiansen IK, Hansen M, Stålcrantz J, Ambur OH, Magnus P, Jonassen CM, Trogstad L. Substantial Decline in Prevalence of Vaccine-Type and Nonvaccine-Type Human Papillomavirus (HPV) in Vaccinated and Unvaccinated Girls 5 Years After Implementing HPV Vaccine in Norway. J Infect Dis 2018; 218:1900-1910. [PMID: 30010913 PMCID: PMC6217723 DOI: 10.1093/infdis/jiy432] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/12/2018] [Indexed: 12/12/2022] Open
Abstract
Background In 2009, quadrivalent human papillomavirus (HPV) vaccine was introduced in a school-based single-cohort program targeting 12-year-old girls in Norway. We estimated the impact of the Norwegian HPV immunization program. Methods Three birth cohorts of 17-year-old girls, 2 nonvaccine-eligible cohorts (born 1994 or 1996) and 1 vaccine-eligible cohort (born 1997) were invited to deliver urine samples. The samples were analyzed for 37 HPV genotypes. HPV prevalence was compared between birth cohorts and between vaccinated and unvaccinated girls within and across birth cohorts after linkage to the Norwegian Immunisation Registry. Results In total, 17749 urine samples were analyzed. A 42% (95% confidence interval [CI], 37%-47%) reduction in any HPV type and 81% (95% CI, 76%-85%) reduction in vaccine types (HPV-6/11/16/18) were observed in the vaccine-eligible cohort compared to the 1994 cohort. Vaccine types were reduced by 54% (95% CI, 39%-66%) and 90% (95% CI, 86%-92%) in unvaccinated and vaccinated girls, respectively, from the 1997 cohort, compared with unvaccinated girls born in 1994. A significant reduction was also observed for several nonvaccine types. Vaccine-type prevalence was reduced by 77% (95% CI, 65%-85%) in vaccinated compared with unvaccinated girls from the 1997 cohort. Conclusions In this largely HPV-naive population, we observed a substantial reduction in vaccine and nonvaccine types in vaccinated and unvaccinated girls following introduction of HPV vaccination.
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Affiliation(s)
- Berit Feiring
- Department of Infectious Disease Epidemiology and Modelling, Norwegian Institute of Public Health, Oslo
| | - Ida Laake
- Department of Infectious Disease Epidemiology and Modelling, Norwegian Institute of Public Health, Oslo
| | | | - Mona Hansen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog
| | - Jeanette Stålcrantz
- Department of Vaccine Preventable Diseases, Norwegian Institute of Public Health, Oslo
| | - Ole Herman Ambur
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog
- Department of Natural Sciences and Health, Oslo Metropolitan University, Oslo
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo
| | | | - Lill Trogstad
- Department of Infectious Disease Epidemiology and Modelling, Norwegian Institute of Public Health, Oslo
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15
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Dube Mandishora RS, Gjøtterud KS, Lagström S, Stray-Pedersen B, Duri K, Chin'ombe N, Nygård M, Christiansen IK, Ambur OH, Chirenje MZ, Rounge TB. Intra-host sequence variability in human papillomavirus. Papillomavirus Res 2018; 5:180-191. [PMID: 29723682 PMCID: PMC6047465 DOI: 10.1016/j.pvr.2018.04.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 03/14/2018] [Accepted: 04/27/2018] [Indexed: 11/20/2022]
Abstract
Human papillomaviruses (HPVs) co-evolve slowly with the human host and each HPV genotype displays epithelial tropisms. We assessed the evolution of intra HPV genotype variants within samples, and their association to anogenital site, cervical cytology and HIV status. Variability in the L1 gene of 35 HPV genotypes was characterized phylogenetically using maximum likelihood, and portrayed by phenotype. Up to a thousand unique variants were identified within individual samples. In-depth analyses of the most prevalent genotypes, HPV16, HPV18 and HPV52, revealed that the high diversity was dominated by a few abundant variants. This suggests high intra-host mutation rates. Clades of HPV16, HPV18 and HPV52 were associated to anatomical site and HIV co-infection. Particularly, we observed that one HPV16 clade was specific to vaginal cells and one HPV52 clade was specific to anal cells. One major HPV52 clade, present in several samples, was strongly associated with cervical neoplasia. Overall, our data suggest that tissue tropism and HIV immunosuppression are strong shapers of HPV evolution.
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Affiliation(s)
- Racheal S Dube Mandishora
- Department of Medical Microbiology, University of Zimbabwe College of Health Sciences, P.O Box A178, Avondale, Harare, Zimbabwe
| | - Kristina S Gjøtterud
- Department of Research, Cancer Registry of Norway, P.O. box 5313 Majorstuen, 0304 Oslo, Norway
| | - Sonja Lagström
- Department of Research, Cancer Registry of Norway, P.O. box 5313 Majorstuen, 0304 Oslo, Norway; Department of Microbiology and Infection Control, The Norwegian HPV Reference Laboratory, Akershus University Hospital, Sykehusveien 25, Lørenskog, Norway
| | - Babill Stray-Pedersen
- Women's clinic, Rikshospitalet, Oslo University Hospital and Institute of Clinical Medicine, P.O Box 4950 Nydalen, 0424 Oslo, Norway
| | - Kerina Duri
- Department of Immunology, University of Zimbabwe College of Health Sciences, P.O Box A178, Avondale, Harare, Zimbabwe
| | - Nyasha Chin'ombe
- Department of Medical Microbiology, University of Zimbabwe College of Health Sciences, P.O Box A178, Avondale, Harare, Zimbabwe
| | - Mari Nygård
- Department of Research, Cancer Registry of Norway, P.O. box 5313 Majorstuen, 0304 Oslo, Norway
| | - Irene Kraus Christiansen
- Department of Microbiology and Infection Control, The Norwegian HPV Reference Laboratory, Akershus University Hospital, Sykehusveien 25, Lørenskog, Norway
| | - Ole Herman Ambur
- Department of Microbiology and Infection Control, The Norwegian HPV Reference Laboratory, Akershus University Hospital, Sykehusveien 25, Lørenskog, Norway; Department of Life Sciences and Health, Oslo and Akershus University College of Applied Sciences, P.O Box 4 St. Olavs plass, N-0130 Oslo, Norway
| | - Mike Z Chirenje
- Department of Obstetrics and Gynaecology, University of Zimbabwe College of Health Sciences, Box A178, Avondale, Harare, Zimbabwe
| | - Trine B Rounge
- Department of Research, Cancer Registry of Norway, P.O. box 5313 Majorstuen, 0304 Oslo, Norway.
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16
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Meisal R, Rounge TB, Christiansen IK, Eieland AK, Worren MM, Molden TF, Kommedal Ø, Hovig E, Leegaard TM, Ambur OH. HPV Genotyping of Modified General Primer-Amplicons Is More Analytically Sensitive and Specific by Sequencing than by Hybridization. PLoS One 2017; 12:e0169074. [PMID: 28045981 PMCID: PMC5207713 DOI: 10.1371/journal.pone.0169074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 12/12/2016] [Indexed: 01/11/2023] Open
Abstract
Sensitive and specific genotyping of human papillomaviruses (HPVs) is important for population-based surveillance of carcinogenic HPV types and for monitoring vaccine effectiveness. Here we compare HPV genotyping by Next Generation Sequencing (NGS) to an established DNA hybridization method. In DNA isolated from urine, the overall analytical sensitivity of NGS was found to be 22% higher than that of hybridization. NGS was also found to be the most specific method and expanded the detection repertoire beyond the 37 types of the DNA hybridization assay. Furthermore, NGS provided an increased resolution by identifying genetic variants of individual HPV types. The same Modified General Primers (MGP)-amplicon was used in both methods. The NGS method is described in detail to facilitate implementation in the clinical microbiology laboratory and includes suggestions for new standards for detection and calling of types and variants with improved resolution.
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Affiliation(s)
- Roger Meisal
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | | | - Irene Kraus Christiansen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | | | - Merete Molton Worren
- Bioinformatics Core Facility, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | | | - Øyvind Kommedal
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Eivind Hovig
- Department of Informatics, University of Oslo, Oslo, Norway
- Department of Tumor Biology, Institute of Cancer Research and Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Truls Michael Leegaard
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
- Division of Medicine and Laboratory Sciences, University of Oslo, Oslo Norway
| | - Ole Herman Ambur
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
- Department of Life Sciences and Health, Oslo and Akershus University College of Applied Sciences, Oslo, Norway
- * E-mail:
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17
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Engesæter B, van Diermen Hidle B, Hansen M, Moltu P, Staby KM, Borchgrevink-Persen S, Vintermyr OK, Lönnberg S, Nygård M, Janssen EAM, Castle PE, Christiansen IK. Quality assurance of human papillomavirus (HPV) testing in the implementation of HPV primary screening in Norway: an inter-laboratory reproducibility study. BMC Infect Dis 2016; 16:698. [PMID: 27881082 PMCID: PMC5122146 DOI: 10.1186/s12879-016-2028-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 11/14/2016] [Indexed: 01/09/2023] Open
Abstract
Background Human papillomavirus (HPV) testing as primary screening for cervical cancer is currently being implemented in Norway in a randomized controlled fashion, involving three laboratories. As part of the quality assurance programme of the implementation, an evaluation of the inter-laboratory reproducibility of the HPV test was initiated, to ensure satisfactory HPV test reliability in all three laboratories. Methods The HPV test used is the cobas 4800 HPV Test, detecting 14 high-risk types with individual HPV genotype results for HPV16 and HPV18. In addition to the three laboratories involved in the implementation, the Norwegian HPV reference laboratory was included as a fourth comparative laboratory. A stratified sample of 500 cervical liquid based cytology (LBC) samples was used in the evaluation, with an aim towards a high-risk HPV positivity of ~25%. Samples were collected at one laboratory, anonymized, aliquoted, and distributed to the other laboratories. Results Comparison of the test results of all four laboratories revealed a 95.6% agreement, an 86.3% positive agreement and a kappa value of 0.94 (95% CI 0.92–0.97). For negative cytology specimens, there was a 95.8% overall agreement, a 67.4% positive agreement, and a kappa value of 0.88 (95% CI 0.80–0.93). For abnormal cytology specimens, there was a 95.8% overall agreement, a 95.5% positive agreement, and a kappa value of 0.86 (95% CI 0.71–0.97). Conclusions The study showed a high inter-laboratory reproducibility of HPV testing, implying satisfactory user performance and reliability in the laboratories involved in the implementation project. This is important knowledge and we recommend similar studies always to be performed prior to the introduction of new screening routines. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-2028-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Mona Hansen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - Pia Moltu
- Department of Pathology, Stavanger University Hospital, Stavanger, Norway
| | | | - Siri Borchgrevink-Persen
- Department of Pathology and Medical Genetics, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Olav K Vintermyr
- Department of Pathology, Haukeland University Hospital, Bergen, Norway.,The Gade Laboratory for Pathology, Department of Clinical Medicine (K1), University of Bergen, Bergen, Norway
| | | | | | - Emiel A M Janssen
- Department of Pathology, Stavanger University Hospital, Stavanger, Norway.,Department of Mathematics and Natural Sciences, University of Stavanger, Stavanger, Norway
| | | | - Irene Kraus Christiansen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway.
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Christiansen IK, Sandve GK, Schmitz M, Dürst M, Hovig E. Transcriptionally active regions are the preferred targets for chromosomal HPV integration in cervical carcinogenesis. PLoS One 2015; 10:e0119566. [PMID: 25793388 PMCID: PMC4368827 DOI: 10.1371/journal.pone.0119566] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 01/15/2015] [Indexed: 01/23/2023] Open
Abstract
Integration of human papillomavirus (HPV) into the host genome is regarded as a determining event in cervical carcinogenesis. However, the exact mechanism for integration, and the role of integration in stimulating cancer progression, is not fully characterized. Although integration sites are reported to appear randomly distributed over all chromosomes, fragile sites, translocation break points and transcriptionally active regions have all been suggested as being preferred sites for integration. In addition, more recent studies have reported integration events occurring within or surrounding essential cancer-related genes, raising the question whether these may reflect key events in the molecular genesis of HPV induced carcinomas. In a search for possible common denominators of the integration sites, we utilized the chromosomal coordinates of 121 viral-cellular fusion transcripts, and examined for statistical overrepresentation of integration sites with various features of ENCODE chromatin information data, using the Genomic HyperBrowser. We find that integration sites coincide with DNA that is transcriptionally active in mucosal epithelium, as judged by the relationship of integration sites to DNase hypersensitivity and H3K4me3 methylation data. Finding an association between integration and transcription is highly informative with regard to the spatio-temporal characteristics of the integration process. These results suggest that integration is an early event in carcinogenesis, more than a late product of chromosomal instability. If the viral integrations were more likely to occur in destabilized regions of the DNA, a completely random distribution of the integration sites would be expected. As a by-product of integration in actively transcribing DNA, a tendency of integration in or close to genes is likely to be observed. This increases the possibility of viral signals to modulate the expression of these genes, potentially contributing to the progression towards cancer.
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Affiliation(s)
- Irene Kraus Christiansen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | | | - Martina Schmitz
- Department of Gynaecology, Jena University Hospital, Jena, Germany
| | - Matthias Dürst
- Department of Gynaecology, Jena University Hospital, Jena, Germany
| | - Eivind Hovig
- Department of Informatics, University of Oslo, Oslo, Norway
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway
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