Data from: Human papillomavirus genotypes and factors associated with major cervical smears abnormalities in a sickle cell endemic area of Kisangani, Democratic Republic of the Congo
Data files
May 26, 2026 version files 163.71 KB
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README.md
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YN_datafile.xlsx
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Abstract
Background
Cervical cancer due to high-risk human papillomavirus (HR-HPV) is the leading gynecological cancer in the Democratic Republic of the Congo (DRC), where approximately one-quarter of people carry the sickle cell allele. We aim to identify the HPV genotypes and factors associated with major cervical abnormalities among women living in Kisangani, DRC.
Methods
This analytical cross-sectional, hospital-based study was conducted from February 2023 to February 2024 in Kisangani, DRC. 712 women underwent cervical and sickle cell screenings, and their HIV serostatus has been documented. The sickle cell status was confirmed using liquid chromatography coupled with mass spectrometry. We reached 130 women with hemoglobin AS (HbAS) instead of the required 175. Cervical smears were collected using the ThinPrep® Pap-test solution. The HPV test was performed using the Cobas® 6800 system (Roche Molecular Systems, Somerville, USA), supplemented by viral genome sequencing on the Oxford Nanopore platform (Oxford Nanopore Technologies, Oxford, England).
Results
The prevalence of HR-HPV was 28.4% (95% CI: 25–32). HPV35, HPV52, and HPV3 were the most common genotypes, while the sequencing identified two new variants of HPV103 and HPV223. The following factors were associated with HR-HPV infection: between 25 and 34 years old (aOR: 2.10, 95% CI:1.22–3.69), being unmarried (aOR: 1.54, 95% CI: 1.05–2.27), and HIV positive status (aOR: 14.85,95% CI: 2.36-288.25; p-value = 0.015). There was no correlation between HbAS and HR-HPV infection or cytological abnormalities. Women aged 45 to 54 (aOR: 3.8, 95% CI: 1.34 –11.65), those using intravaginal herbal remedies (aOR: 3.59, 95% CI: 1.26 –111.28), or those infected with HPV33 (aOR: 8.45, 95%CI: 1.68–34.05) were more likely to have major cervical abnormalities.
Conclusion
HPV types 35, 52, and 31 are most prevalent in Kisangani, DRC. Within the limits of our sample size, current screening remains appropriate for HbAS women.
Dataset DOI: 10.5061/dryad.5qfttdzkt
Dataset Overview
We submitted a database of 712 women who had undergone simultaneous cervical smear screening and sickle-cell screening. Women from the general population were recruited in a hospital setting, and their status regarding the human immunodeficiency virus (HIV serostatus) was documented. This database includes four categories of variables: sociodemographic characteristics, gynecological and obstetric history and risk factors, blood tests results (sickle cell screening , HIV serostatus) and liquid-based cervical smear analysis results. The smears were examined using the Hologic 5000 Processor for cytology. Human papillomavirus (HPV) detection was performed using the Cobas 6800 and supplemented by sequencing on the Nanopores Oxford platform. A total of 692 and 705 cervical samples were satisfactory for cytological analysis and HPV testing, respectively.
File details
- File Name: YN_datafile.xlsx
- File Format: XLSX,TXT
- Date: May 19, 2026
Data description and file structure
Numbering
Socio-demographic characteristics: in the following columns
₋ Sampling site
₋ Age group (years)
₋ Marital status
₋ Level of education
₋ Profession
Risk factors and gynecological-obstetric history: Data included in the following columns:
₋ Parity
₋ Age at first intercourse (years)
₋ Sexual partners
₋ Previous screening
₋ Intravaginal plants
₋ Oral contraception
Blood tests
₋ Sickle cell status: HbAA (women without sickle cell disease or controls) and HbAS (women with sickle cell trait)
₋ HIV serostatus: HIV-positive and VIH-negative
Cytology results
₋ Abnormal Pap smear : ASC-US ,LSIL, ASC-H, HSIL, AGC-Nos, AGC -in favor of neoplasia).
₋ NILM : negative for intraepithelial lesion or malignancy
₋ Inflammatory smear
₋ LSIL : low-grade squamous intraepithelial lesion
₋ invalid smears : unsatisfactory smears for evaluation
₋ ASC-US : atypical squamous cells of undetermined significance
₋ AGC-NOS, AGC-eccNeo : atypical glandular endocervical cells not otherwise specified (AGC-NOS) and atypical glandular endocervical cells, favor neoplastic (AGC-ecc Neo)
₋ ASC-H, HSIL : atypical squamous cells that cannot exclude HSIL(ASC-H) and high-grade squamous intraepithelial lesion (HSIL)
₋ ≥ASC-US = Abnormal Pap smear
₋ No lesions : including NILM and inflammatory smear
₋ Minor abnomality : ASC-US and LSIL
₋ Major abnormality : ASC-H, HSIL, AGC-Nos, AGC -in favor of neoplasia)
HPV test results (Cobas 6800):
Results presented in the following 6 columns:
₋ Cobas HPV test : results of HPVHR screening with Cobas
₋ HPV test invalid : unsatisfactory smears for test HPV
₋ hpv16_cobas : Detection of HPV 16 using Cobas 6800
₋ hpv18_cobas : Detection of HPV 18 using Cobas 6800
₋ hpv16_18_cobas: Detection of HPVs 16 and 18 using Cobas 6800
₋ hpv_other_cobas : Detection of HPVs 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68 in samples using Cobas 6800
Results of viral DNA sequencing on the Oxford Nanopores platform
Viral DNA sequencing was performed on 128 cervical samples out of the 200 that tested positive on Cobas 6800.
₋ hpv31_seq : Detection of HPV 31 during sequencing
₋ hpv33_seq : Detection of HPV 33 during sequencing
₋ hpv35_seq : Detection of HPV 35 during sequencing
₋ hpv39_seq : Detection of HPV 39 during sequencing
₋ hpv51_seq : Detection of HPV 51 during sequencing
₋ hpv52_seq : Detection of HPV 52 during sequencing
₋ hpv56_seq : Detection of HPV 56 during sequencing
₋ hpv58_seq : Detection of HPV 58 during sequencing
₋ hpv59_seq : Detection of HPV 59 during sequencing
₋ hpv66_seq : Detection of HPV 66 during sequencing
₋ hpv68_seq : Detection of HPV 68 during sequencing
₋ hpv16_seq : Detection of HPV 16 during sequencing
₋ hpv18_seq : Detection of HPV 18 during sequencing
₋ hpv45_seq : Detection of HPV 45 during sequencing
₋ hr-hpv_ gardasil 9 : At least HPV type 16/18/31/33/45/52/58 detected during sequencing
₋ Hr-hpv_non_gardasil9 : At least HPV type 35 /39/51/56/59/66/68 detected during sequencing
₋ Sequencing_done_contributive
₋ Detailed hr-hpv testing (cobas supplemented with nanopore sequencing)
other HPV genotypes (Co-infections)
₋ HPV103_nov(new) : Detection of HPV 103’s new variant during sequencing
₋ hpv223_nov(new) : Detection of HPV 223’s new variant during sequencing
₋ Other HPV types detected in co-infections
₋ Co-infection hr-hpv/ other hpv
: Co-infection of High-risk (HR)-HPV with one or more of the following HPV types:
HPV types 30, 34, 53, 67, 69, 70 , 82 , 40, 42, 44, 54, 61, 62, 72, 74, 81, 83, 86, 87, 89 , 90, 5, 103, 103 Like-novel , 223, 223 Like-novel and, 226
- phr-hpv: HPV types 30, 34, 53, 67, 69, 70 and 82
- lr-hpv: HPV types 40, 42, 44, 54, 61, 62, 72, 74, 81, 83, 86, 87, 89 and 90;
- Uncategorized: HPV types 5, 103, 103 Like-novel , 223, 223 Like-novel and 226. These are HPV types Beta and Gamma.
Code/software
Data were entered using Microsoft Excel 2019 and analyzed with R software (version 4.4.3)
Human subjects data
All participants provided written informed consent to be screened for sickle cell disease, for HIV and for cervical cancer. They also gave their written consent to have their samples transported abroad, and to have their de-identified data published. To depersonalize the data, the participants' identifiers were removed from the publicly available database. The respondents' ages and ages at first sexual intercourse were presented in age ranges. We assigned a number from 0 to 5 to categorize the other variables depending on their respective numbers.
Data collection
We carried out an analytical cross-sectional study from February 2023 to February 2024, in the city of Kisangani, Democratic Republic of the Congo (DRC). After obtaining written consent, we interviewed the participants. We recorded their sociodemographic data, gynecological and obstetric history, and potential risk factors on a data collection form. We took two samples from each respondent: (i) a capillary blood sample from the fingertip to screen for sickle cell disease (SCD) and HIV; (ii) a liquid-based blood smear in PreservCyte (Thinprep). It should be noted that HIV serological screening, using the current testing algorithm in force in the DRC, was performed immediately in the field on whole blood collected via finger prick RDC ( The National Institute of Statistics, the Kinshasa School of Public Health, and ICF, 2025) The cervical smears and dried blood samples used to confirm SCD were analyzed in the laboratory at the University Hospital Center of Liège in Belgium. We performed the rapid SCD diagnosis using HemoTypeSC™ (Silver Lake Research Corporation, 1300 West Optical Drive, Azusa, CA 91702, USA) (Steele C et al., 2019).
In Belgium, the clinical hematology laboratory used the triple quadrupole mass spectrometer system TQ5500 ( Sciex, Nieuwerkerkerlaan, Netherlands) for liquid chromatography coupled with mass spectrometry (LC-MS) analysis following the manufacturer's technical specifications, as described for analyzing blood samples taken on blotting paper (Boemer F et al., 2008). The ThinPrep vial containing the sample was placed in the ThinPrep 5000 processor with Autoloader System (Hologic Inc, Marlborough, USA) for cytological analysis (Hologic,2018. The cytology results were reported according to the 2014 Bethesda nomenclature ( Nayar R and Wilbur DC, 2015). The HPV test was performed using the Cobas® 6800 systems, Roche Diagnostics ( Saville M et al., 2019), supplemented by whole genome viral sequencing on the Nanopore platform (Oxford Nanopore Technologies, Oxford, England). BLAST was used to identify new HPV types in relation to known reference HPV genomes.
Statistical analyses
Data were entered using Microsoft Excel 2019 and analyzed with R software (version 4.4.3).
Categorical variables were summarized using absolute and relative frequencies, while continuous variables were described using the mean ± standard deviation. Comparisons of participant characteristics by sickle cell status (HbAS vs HbAA) were conducted using Fisher’s exact test for categorical variables and the Wilcoxon rank-sum test for continuous variables. Determinants of HR-HPV infection and cervical lesions were first assessed using univariate analyses. Variables with p-value ≤ 0.20 were considered eligible for inclusion in the multivariable logistic regression model. A forward stepwise selection procedure based on the Akaike Information Criterion (AIC) was then applied to identify the final model. In cases of multicollinearity, one of the correlated variables was excluded from the model. Associations between explanatory variables and outcomes were reported as adjusted odds ratios (aORs) with corresponding 95% confidence intervals (CIs). A two-sided p-value < 0.05 was considered statistically significant.
References
Institut National de la Statistique, École de Santé Publique de Kinshasa et ICF. Enquête Démographique et de Santé de la République Démocratique du Congo 2023–2024 : Rapport final. Kinshasa, RDC et Rockville, Maryland, USA : ICF.; 2025. Available from:
https://drc.unfpa.org/sites/default/files/pub-pdf/2025-02/RDC%2C%20EDS%202023-2024.pdf
Steele C, Sinski A, Asibey J, Hardy‐Dessources M, Elana G, Brennan C, et al. Point‐of‐care screening for sickle cell disease in low‐resource settings: A multi‐center evaluation of HemoTypeSC, a novel rapid test. American J Hematol. 2019 Jan;94(1):39–45. doi:10.1002/ajh.25305
Boemer F, Ketelslegers O, Minon JM, Bours V, Schoos R. Newborn Screening for Sickle Cell Disease Using Tandem Mass Spectrometry. Clinical Chemistry. 2008 Dec 1;54(12):2036–41. doi:10.1373/clinchem.2008.106369
Hologic. Processeur ThinPrep® 5000 avec Auto Loader Manuel d’utilisation . AW-04688-901 Rev. 005 Available from: https://www.hologic.com/sites/default/files/2018-05/MAN-01783-901_007_02_0.pdf
Nayar R, Wilbur DC. The bethesda system for reporting cervical cytology: Definitions, criteria, and explanatory notes. Springer International Publishing; 2015. Available from: https://www.scholars.northwestern.edu/en/publications/the-bethesda-system-for-reporting-cervical-cytology
Saville M, Sultana F, Malloy MJ, Velentzis LS, Caruana M, Ip ELO, et al. Clinical Validation of the cobas HPV Test on the cobas 6800 System for Cervical Screening. Miller MB, editor. J Clin Microbiol. 2019 Feb;57(2):e01239-18. doi:10.1128/JCM.01239-18