Bessong, Pascal ObongMitchell, Emma McKimRikhotso, Rixongile Rhenny2025-10-092025-10-092025-09-05Rikhotso, R.R. 2025. Indentification and molecular characterization of human papillomavirus infection among women living with and without HIV in selected health facilities in Limpopo Province, South Africa. . .https://univendspace.univen.ac.za/handle/11602/2991PhD (Microbiology)Department of Biochemistry and MicrobiologyBackground: Co-infection of human papillomavirus (HPV) and human immunodeficiency virus (HIV) has been well established. Both viruses are sexually transmitted with paramount public health implications due to their interaction with cervical cancer (CC). Globally, the estimated prevalence of HPV is 11.7%, with high-risk (hr-) HPV 16 and HPV 18 attributing for most cases of CC. Due to the high genetic diversity of HPV, it is important to study the virus in different geographic locations, people, and in persons living with HIV, to inform the selection of genes for vaccine improvements and potential vaccine trial sites. Consequently, it is important to describe the prevalence, genotype distribution and genomes of HPV in Limpopo Province, where there is limited data. The general objective of this study was to therefore to identify and characterize HPV DNA among women living with and without HIV in selected health facilities in Limpopo Province, South Africa. The specific objectives were: (1) To provide a narrative literature review on the prevalence and distribution of selected cervical HPV genotypes among women living with and without HIV in South Africa; (2) To determine the prevalence of cervical HPV infection among women living with and without HIV in selected health facilities in Limpopo Province, South Africa; (3) To describe HPV genotypes among women living with and without HIV in selected health facilities in Limpopo Province, South Africa; and (4) To generate and characterize HPV full genomes among women living with and without HIV in selected health facilities in Limpopo Province, South Africa. Methods: A systematic review of the available literature was conducted in the quest to understand and determine the prevalence and distribution of cervical HPV among women living with HIV (WLWH) and those without HIV in South Africa, following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) workflow. Records were retrieved from PubMed and Web of Science databases. An analytic cross-sectional study on HPV prevalence and genotype distribution among 450 women who were living with and without HIV from selected health facilities in Limpopo Province was done. In this regard, total DNA was purified from cervical specimens and amplified using a double-nested polymerase chain reaction (PCR) strategy, targeting the L1 gene. A sample that shows an amplification product of 450 bp in the first nested PCR or a product of 150 bp in the second nested reaction was taken as positive for the presence of HPV DNA. Statistical analysis, using models in R-statistical package, was done to determine comparative inferences of the presence of HPV DNA and associated risk factors. HPV genotypes were determined through deep sequencing of the 450 bp PCR products on an Illumina MiniSeq platform. The generated sequences were quality assured and analyzed for viral genotypes. Rolling circle amplification (RCA) was used for enriching DNA in samples that tested positive for HPV DNA to generate and characterize near-full length HPV genomes. The enriched DNA was purified with AMPure XP beads and quantified with Qubit, followed by DNA library preparation, and then sequenced on an Illumina MiniSeq platform following the manufacturer’s protocols. Results Prevalence and distribution of selected cervical HPV genotypes in South Africa A total of sixty-nine (69) articles met the inclusion criteria for determining the prevalence and distribution of cervical HPV genotypes among South African women who were either living with HIV or not. These articles were on studies done in 5 of the 9 South African Provinces. The studies were conducted between 1989-2021. Sequencing was the least genotyping tool used in these studies, while most studies utilized PCR-based hybridization commercial kits. Compared to other investigated genotypes, HPV 16, HPV 18, and HPV 35 were predominant in the study population regardless of the HIV status. Prevalence of HPV DNA and genotype distribution in selected health facilities in Limpopo Province, South Africa The HPV DNA was detected in cervical specimens from 147 of 450 women (32.7%), significantly higher at 52.21% (p = 0.00) among WLWH compared to women living without HIV. Forty-eight samples were of acceptable quality and analyzed for viral diversity. The study detected 41 HPV genotypes, all of which belong to the Alphapapillomavirus genus of the Papillomaviridae family. In general, HPV 45 (16.7%) was the predominant genotype. However, HPV 81 (18.8%) and HPV 56 (25.0%) were the most common genotypes among women living with and without HIV, respectively. Multiple infections and high-risk HPV genotypes were more common among WLWH. Characterization of whole genomes of cervical human papillomavirus Six full genomes of HPV genotypes 34 (n=1), 35 (n=1), 42 (n=1), 45 (n=2), and 90 (n=1) are reported herein. The study further identified variant sub-lineages, including the A1 sub-lineages of hr-HPV 35 and hr-HPV 45. The genome sequences are available at the National Center for Biotechnology Information (NCBI) in the Sequence Read Archive (SRA) database. Interpretations and conclusions Prevalence and distribution of selected cervical HPV genotypes in South Africa The narrative review of the literature indicated that there are limited studies on cervical HPV prevalence and genotype distribution in South Africa. Therefore, further research is required to identify HPV genotypes, including the use of sensitive approaches such as next generation sequencing. This will enhance our understanding of HPV geo-diversity patterns in various provinces across South Africa, and subsequently inform decisions on screening strategies, and selection of geographically relevant genes for vaccine improvement and development. The high prevalence of hr-HPV 16, HPV 18 and HPV 35 regardless of HIV status in the country is a public health concern, considering their significant contribution to the burden of CC. Consequently, routine HPV screening and prevention measures such as HPV vaccination for all individuals remain critical. Because current vaccines exclude HPV 35 as a target, there is a need to consider this genotype in future vaccine development efforts. Prevalence of HPV DNA and genotype distribution in selected health facilities in Limpopo Province, South Africa The study reported a relatively high prevalence of HPV infection among the study participants, which signified the burden of HPV in the province. The prevalence was significantly higher among WLWH, including more HPV genotypes and hr-HPV genotypes as compared to women living without HIV, potentially due to immunosuppression. Considering the high rate of HPV-HIV co-infection observed in this study and other studies in South Africa, prioritizing women living with HIV for cervical HPV screening and HPV vaccination is recommended. Strengthening integrated HPV and HIV screening programs and ensuring regular monitoring of cervical health among WLWH remains a public health imperative. Moreover, the study also showed that women living with and without HIV may have different profiling in terms of HPV infections which is important in intervention strategies, example development of targeted HPV screening strategies. The current study also fills a significant gap of limited data by providing baseline information on the prevalence and genotype distribution of cervical HPV infection among women living with and without HIV in the study area. The study findings further encourage national-level surveillance with the inclusion of expanded regional representation. Characterization of whole genomes of cervical HPV Near full-length genomes of six HPV genotypes were successfully characterized in the study population. These sequences could serve as a valuable resource for further research and vaccine development studies. The identified variant sub-lineages may underscore the need to strengthen HPV vaccine coverage, routine cervical screening, and genomic monitoring in underrepresented areas such as Limpopo Province. Moreover, this data supports the development of risk stratification models aimed at identifying women at high-risk for persistent infection and progression to CC, thereby enabling early, tailored interventions to reduce the HPV related disease burden.1 online resource ( )enUniversity of VendaHuman papillomavirusUCTDGenotypesGenomesHuman immunodeficiency virusLimpopo Province616.9110968257Papillomaviruses -- South Africa -- LimpopoPapovaviruses -- South Africa -- LimpopoVirus diseases -- South Africa -- LimpopoPapilloma -- South Africa -- LimpopoPapillomavirus diseases - South Africa -- LimpopoWomen -- Diseases -- South Africa -- LimpopoWomen -- South Africa -- LimpopoWomen -- Health and hygiene -- South Africa -- LimpopoAIDS (Disease) in womenThesisRikhotso RR. Indentification and molecular characterization of human papillomavirus infection among women living with and without HIV in selected health facilities in Limpopo Province, South Africa. []. , 2025 [cited yyyy month dd]. Available from:Rikhotso, R. R. (2025). <i>Indentification and molecular characterization of human papillomavirus infection among women living with and without HIV in selected health facilities in Limpopo Province, South Africa</i>. (). . Retrieved fromRikhotso, Rixongile Rhenny. <i>"Indentification and molecular characterization of human papillomavirus infection among women living with and without HIV in selected health facilities in Limpopo Province, South Africa."</i> ., , 2025.TY - Thesis AU - Rikhotso, Rixongile Rhenny AB - Background: Co-infection of human papillomavirus (HPV) and human immunodeficiency virus (HIV) has been well established. Both viruses are sexually transmitted with paramount public health implications due to their interaction with cervical cancer (CC). Globally, the estimated prevalence of HPV is 11.7%, with high-risk (hr-) HPV 16 and HPV 18 attributing for most cases of CC. Due to the high genetic diversity of HPV, it is important to study the virus in different geographic locations, people, and in persons living with HIV, to inform the selection of genes for vaccine improvements and potential vaccine trial sites. Consequently, it is important to describe the prevalence, genotype distribution and genomes of HPV in Limpopo Province, where there is limited data. The general objective of this study was to therefore to identify and characterize HPV DNA among women living with and without HIV in selected health facilities in Limpopo Province, South Africa. The specific objectives were: (1) To provide a narrative literature review on the prevalence and distribution of selected cervical HPV genotypes among women living with and without HIV in South Africa; (2) To determine the prevalence of cervical HPV infection among women living with and without HIV in selected health facilities in Limpopo Province, South Africa; (3) To describe HPV genotypes among women living with and without HIV in selected health facilities in Limpopo Province, South Africa; and (4) To generate and characterize HPV full genomes among women living with and without HIV in selected health facilities in Limpopo Province, South Africa. Methods: A systematic review of the available literature was conducted in the quest to understand and determine the prevalence and distribution of cervical HPV among women living with HIV (WLWH) and those without HIV in South Africa, following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) workflow. Records were retrieved from PubMed and Web of Science databases. An analytic cross-sectional study on HPV prevalence and genotype distribution among 450 women who were living with and without HIV from selected health facilities in Limpopo Province was done. In this regard, total DNA was purified from cervical specimens and amplified using a double-nested polymerase chain reaction (PCR) strategy, targeting the L1 gene. A sample that shows an amplification product of 450 bp in the first nested PCR or a product of 150 bp in the second nested reaction was taken as positive for the presence of HPV DNA. Statistical analysis, using models in R-statistical package, was done to determine comparative inferences of the presence of HPV DNA and associated risk factors. HPV genotypes were determined through deep sequencing of the 450 bp PCR products on an Illumina MiniSeq platform. The generated sequences were quality assured and analyzed for viral genotypes. Rolling circle amplification (RCA) was used for enriching DNA in samples that tested positive for HPV DNA to generate and characterize near-full length HPV genomes. The enriched DNA was purified with AMPure XP beads and quantified with Qubit, followed by DNA library preparation, and then sequenced on an Illumina MiniSeq platform following the manufacturer’s protocols. Results Prevalence and distribution of selected cervical HPV genotypes in South Africa A total of sixty-nine (69) articles met the inclusion criteria for determining the prevalence and distribution of cervical HPV genotypes among South African women who were either living with HIV or not. These articles were on studies done in 5 of the 9 South African Provinces. The studies were conducted between 1989-2021. Sequencing was the least genotyping tool used in these studies, while most studies utilized PCR-based hybridization commercial kits. Compared to other investigated genotypes, HPV 16, HPV 18, and HPV 35 were predominant in the study population regardless of the HIV status. Prevalence of HPV DNA and genotype distribution in selected health facilities in Limpopo Province, South Africa The HPV DNA was detected in cervical specimens from 147 of 450 women (32.7%), significantly higher at 52.21% (p = 0.00) among WLWH compared to women living without HIV. Forty-eight samples were of acceptable quality and analyzed for viral diversity. The study detected 41 HPV genotypes, all of which belong to the Alphapapillomavirus genus of the Papillomaviridae family. In general, HPV 45 (16.7%) was the predominant genotype. However, HPV 81 (18.8%) and HPV 56 (25.0%) were the most common genotypes among women living with and without HIV, respectively. Multiple infections and high-risk HPV genotypes were more common among WLWH. Characterization of whole genomes of cervical human papillomavirus Six full genomes of HPV genotypes 34 (n=1), 35 (n=1), 42 (n=1), 45 (n=2), and 90 (n=1) are reported herein. The study further identified variant sub-lineages, including the A1 sub-lineages of hr-HPV 35 and hr-HPV 45. The genome sequences are available at the National Center for Biotechnology Information (NCBI) in the Sequence Read Archive (SRA) database. Interpretations and conclusions Prevalence and distribution of selected cervical HPV genotypes in South Africa The narrative review of the literature indicated that there are limited studies on cervical HPV prevalence and genotype distribution in South Africa. Therefore, further research is required to identify HPV genotypes, including the use of sensitive approaches such as next generation sequencing. This will enhance our understanding of HPV geo-diversity patterns in various provinces across South Africa, and subsequently inform decisions on screening strategies, and selection of geographically relevant genes for vaccine improvement and development. The high prevalence of hr-HPV 16, HPV 18 and HPV 35 regardless of HIV status in the country is a public health concern, considering their significant contribution to the burden of CC. Consequently, routine HPV screening and prevention measures such as HPV vaccination for all individuals remain critical. Because current vaccines exclude HPV 35 as a target, there is a need to consider this genotype in future vaccine development efforts. Prevalence of HPV DNA and genotype distribution in selected health facilities in Limpopo Province, South Africa The study reported a relatively high prevalence of HPV infection among the study participants, which signified the burden of HPV in the province. The prevalence was significantly higher among WLWH, including more HPV genotypes and hr-HPV genotypes as compared to women living without HIV, potentially due to immunosuppression. Considering the high rate of HPV-HIV co-infection observed in this study and other studies in South Africa, prioritizing women living with HIV for cervical HPV screening and HPV vaccination is recommended. Strengthening integrated HPV and HIV screening programs and ensuring regular monitoring of cervical health among WLWH remains a public health imperative. Moreover, the study also showed that women living with and without HIV may have different profiling in terms of HPV infections which is important in intervention strategies, example development of targeted HPV screening strategies. The current study also fills a significant gap of limited data by providing baseline information on the prevalence and genotype distribution of cervical HPV infection among women living with and without HIV in the study area. The study findings further encourage national-level surveillance with the inclusion of expanded regional representation. Characterization of whole genomes of cervical HPV Near full-length genomes of six HPV genotypes were successfully characterized in the study population. These sequences could serve as a valuable resource for further research and vaccine development studies. The identified variant sub-lineages may underscore the need to strengthen HPV vaccine coverage, routine cervical screening, and genomic monitoring in underrepresented areas such as Limpopo Province. Moreover, this data supports the development of risk stratification models aimed at identifying women at high-risk for persistent infection and progression to CC, thereby enabling early, tailored interventions to reduce the HPV related disease burden. DA - 2025-09-05 DB - ResearchSpace DP - Univen KW - Human papillomavirus KW - Genotypes KW - Genomes KW - Human immunodeficiency virus KW - Limpopo Province LK - https://univendspace.univen.ac.za PY - 2025 T1 - Indentification and molecular characterization of human papillomavirus infection among women living with and without HIV in selected health facilities in Limpopo Province, South Africa TI - Indentification and molecular characterization of human papillomavirus infection among women living with and without HIV in selected health facilities in Limpopo Province, South Africa UR - ER -