Human papillomavirus genotype distribution, persistence, clearance, and characterizing cervicovaginal microbiota: A population- based follow up study
| dc.contributor.advisor | Abebe,Tamrat (MSc., PhD) | |
| dc.contributor.advisor | Kaufmann,Andreas M(PhD) | |
| dc.contributor.advisor | Kantelhardt,Eva J(Prof.,PhD) | |
| dc.contributor.advisor | Mihret,Adane(PhD) | |
| dc.contributor.author | Endallew,Brhanu Teka(Phd) | |
| dc.date.accessioned | 2025-08-13T07:53:00Z | |
| dc.date.available | 2025-08-13T07:53:00Z | |
| dc.date.issued | 2023-04 | |
| dc.description.abstract | Background: Human papillomaviruses (HPVs) are a group of small, non-enveloped, naked icosahedral (55nm) viruses that can cause cervical cancer (CC) and other cancers. Cervical cancer is by far the most common HPV-related disease, and it is the second leading cause of morbidity and mortality from all cancers in Ethiopian women. Persistent infection with hr-HPVs and progression to precancerous lesions are the most important steps in the carcinogenesis process. However, most infections are transient and rarely persist implying development of CC is a multifactorial and step by step process and may require other co-factors like cervicovaginal microbiome within the local microenvironment for its development. Objective: To determine the prevalence of HPV infection, genotype distribution, the persistence and clearance rates within two years and compare the performance of different HPV tests. Furthermore, it aimed to characterize the cervicovaginal microbiota in women with premalignant dysplasia or invasive cervical cancer compared with that of healthy women. Methods: The study was conducted in two cohorts; a population-based cohort from rural women in Butajira, south-central Ethiopia and women attending gynaecological clinic at Tikur Anbessa Specialized Hospital from October 2017 to February 2020. From Butajira, a total of 893 samples were tested at baseline. A self-sampling brush (Evalyn Brush®, Rovers, Oss, The Netherlands) was used for cervical specimen collection and HPV testing was performed using multiplexed genotyping (MPG) by BSGP5+/6+ PCR with Luminex read out. Follow-up testing was done at 6 and 24 months for baseline hr-HPV positive women. Moreover, three HPV DNA testing assays (MPG-Luminex Assay, Anyplex II HPV HR Detection, and EUROArray HPV) were compared and the analytical sensitivity and specificity of the assays in detecting hr-HPV infections was computed. At Tikur Anbessa Specialized Hospital, cervicovaginal microbiota of 120 women was characterised using the 16S rRNA cervical microbiome sequencing. Shannon and Simpson diversity indexes were used to evaluate alpha diversity. Beta diversity was examined using principal coordinate analysis (PCoA) of unweighted Unifrac distances. Results: At baseline screening, the population-based HPV positivity rate was 23.2% (95% CI: 23.54‐22.86%), of these 20.5% (95% CI=20.79‐20.21), and 10.3% (95% CI=10.52‐10.08) women were hr‐ and lr‐ HPV positives, respectively. Age‐specific hr‐HPV infection peaked in the age‐ group 30‐34 years old (58.6%) and decreased in 35‐39, 40‐44, and 45‐49 years to 20.4%, 4.5% and 3.8% respectively. The top five prevalent hr‐HPV genotypes were HPV16 (57.1%), 35 (20.3%), 52 (15.8%), 31 (14.1%), and 45 (9.6%) in the Butajira district. hr-HPV infection clearance was observed in 70 women (73.7%) within 6 months and among 77 women (84.6%) within 2 years. In the control women (negatives at baseline), the hr-HPV incidence was 4.1%. v HPV68, 82, 53, 52, 56 were the most persisted genotypes with 100%, 75%, 42.9%, 31%, and 25% persistence rates respectively while after 24 months, HPV59, 68, 66, 52 and 16 were found to have persistence with 50%, 50%, 20%, 15.8% and 3.5% respectively. Twenty-nine (29.9%) of the 6 month follow up attended women were with abnormal cytology including ASCUS and HSIL constituted 10.3% of the tested women. Of the three HPV testing assays compared in this study, MPG-Luminex Assay found 18.2% positive for the 14 hr-HPV and 7.3% for the probable hr-HPV genotypes. Anyplex™ II HPV HR Detection assay and EUROArray HPV Assay identified 21.82% and 12.7% samples, respectively, for the 14 hr-HPVs and both 7.3% for the probable hr-HPV genotypes (κ=0.734). Among the 14 hr-HPV genotypes, the genotype-specific agreement of the three HPV genotyping assays was moderate or better for HPV16, 31, 35, 39, 52, 56, 66 and 68. The aggregated sensitivity in detecting the 14 hr-HPV infections of Anyplex™ II HPV HR Detection and EUROArray HPV assays was high, 100% and 70%, respectively. The specificities of Anyplex™ II HPV HR Detection and EUROArray HPV were 95.6% and 100%, respectively. In this study, alpha diversity was significantly higher in patients with cervical cancer than in patients with dysplasia and in healthy women (p < 0.01). Beta diversity was also significantly different in cervical cancer patients compared with the other groups (weighted UniFrac Bray- Curtis, p < 0.01). Microbiota composition differed between the dysplasia and cervical cancer groups. Lactobacillus iners was particularly enriched in patients with cancer, and a high relative abundance of Lactobacillus species was identified in the dysplasia and healthy groups, whereas Porphyromonas, Prevotella, Bacteroides, and Anaerococcus species predominated in the cervical cancer group. Conclusion: This study provided new data on the overall prevalence of HPV infection and distribution of specific HPV types in rural Ethiopia. As a first population‐based study in the country, our results can serve as valuable reference to guide nationwide cervical cancer screening and HPV vaccination programs in Ethiopia. HPV16, HPV35, HPV52, HPV31 and HPV45 were the most prevalent genotypes. Most of the hr-HPV infections among rural Ethiopian women were cleared within 2 years. This study has found differences in cervicovaginal microbiota diversity, composition, and relative abundance between women with cervical cancer, women with dysplasia, and healthy women. Additional studies need to be carried out in Ethiopia or in any other regions to further validate the role of cervical microbiome in development of cervical cancer. From this study, the three evaluated assays showed similar analytical performance in the detection of hr- HPV infections and moderate or better concordance in HPV genotyping. | |
| dc.identifier.uri | https://etd.aau.edu.et/handle/123456789/6677 | |
| dc.language.iso | en_US | |
| dc.publisher | Addis Ababa University | |
| dc.subject | Ethiopia | |
| dc.subject | Butajira | |
| dc.subject | high-risk HPV | |
| dc.subject | HPV testing | |
| dc.subject | HPV persistence | |
| dc.subject | analytical performance | |
| dc.subject | cervical dysplasia | |
| dc.subject | cervical microbiota | |
| dc.title | Human papillomavirus genotype distribution, persistence, clearance, and characterizing cervicovaginal microbiota: A population- based follow up study | |
| dc.type | Thesis |