Genetic diversity in L1 ORF of human papillomavirus in women with cervical cancer with and without human immunodeficiency virus in Botswana and Kenya

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dc.contributor.authorTawe, Leabaneng
dc.contributor.authorChoga, Wonderful T
dc.contributor.authorPaganotti, Giacomo M
dc.contributor.authorBareng, Ontlametse T
dc.contributor.authorNtereke, Tlhalefo D
dc.contributor.authorRamatlho, Pleasure
dc.contributor.authorDitshwanelo, Doreen
dc.contributor.authorGaseitsiwe, Simani
dc.contributor.authorKasvosve, Ishmael
dc.contributor.authorRamogola-Masire, Doreen
dc.contributor.authorOrang’o, Omenge E
dc.contributor.authorRobertson, Erle
dc.contributor.authorZetola, Nicola
dc.contributor.authorMoyo, Sikhulile
dc.contributor.authorGrover, Surbhi
dc.contributor.authorErmel, Aaron C
dc.date.accessioned2022-04-07T11:05:20Z
dc.date.available2022-04-07T11:05:20Z
dc.date.issued2022-01-27
dc.date.updated2022-01-30T04:13:10Z
dc.description.abstractBackground The variation of human papillomavirus (HPV) genotypes shapes the risks of cervical cancer and these variations are not well defined in Africa. Nucleotide changes within the L1 gene, nucleotide variability, and phylogeny were explored in relation to HIV in samples from Botswana and Kenya. Methods A total of 98 HPV-positive cervical samples were sequenced to identify different HPV variants. Phylogenetic inferences were used to determine HPV genotypes and investigate the clustering of sequences between women living with HIV (WLWHIV) and -women not living with HIV (WNLWHIV). Results Out of 98 generated sequences, 83.7% (82/98) participants had high-risk (HR) HPV genotypes while 16.3% (16/98) had low-risk (LR) HPV genotypes. Among participants with HR-HPV genotypes, 47.6% (39/82) were coinfected with HIV. The prevalence of HR-HPV genotypes was statistically higher in the Botswana population compared to Kenya (p-value < 0.001). Multiple amino acid mutations were identified in both countries. Genetic diversity differed considerably among WLWHIV and WNLWHIV. The mean pairwise distances between HPV-16 between HIV and HIV/HPV as well as for HPV-18 were statistically significant. Six (6) new deleterious mutations were identified in the HPV genotypes based on the sequencing of the L1 region, HPV-16 (L441P, S343P), HPV-18 (S424P), HPV-45 (Q366H, Y365F), and HPV-84 (F458L). The majority of the patients with these mutations were co-infected with HIV. Conclusions Genomic diversity and different genomic variants of HPV sequences were demonstrated. Candidate novel mutations within the L1 gene were identified in both countries which can be further investigated using functional assays.
dc.identifier.apacitationTawe, L., Choga, W. T., Paganotti, G. M., Bareng, O. T., Ntereke, T. D., Ramatlho, P., ... Ermel, A. C. (2022). Genetic diversity in L1 ORF of human papillomavirus in women with cervical cancer with and without human immunodeficiency virus in Botswana and Kenya. <i>BMC Infectious Diseases</i>, http://hdl.handle.net/11427/36294en_ZA
dc.identifier.chicagocitationTawe, Leabaneng, Wonderful T Choga, Giacomo M Paganotti, Ontlametse T Bareng, Tlhalefo D Ntereke, Pleasure Ramatlho, Doreen Ditshwanelo, et al "Genetic diversity in L1 ORF of human papillomavirus in women with cervical cancer with and without human immunodeficiency virus in Botswana and Kenya." <i>BMC Infectious Diseases</i> (2022) http://hdl.handle.net/11427/36294en_ZA
dc.identifier.citationTawe, L., Choga, W.T., Paganotti, G.M., Bareng, O.T., Ntereke, T.D., Ramatlho, P., Ditshwanelo, D. & Gaseitsiwe, S. et al. 2022. Genetic diversity in L1 ORF of human papillomavirus in women with cervical cancer with and without human immunodeficiency virus in Botswana and Kenya. <i>BMC Infectious Diseases.</i> http://hdl.handle.net/11427/36294en_ZA
dc.identifier.risTY - Journal Article AU - Tawe, Leabaneng AU - Choga, Wonderful T AU - Paganotti, Giacomo M AU - Bareng, Ontlametse T AU - Ntereke, Tlhalefo D AU - Ramatlho, Pleasure AU - Ditshwanelo, Doreen AU - Gaseitsiwe, Simani AU - Kasvosve, Ishmael AU - Ramogola-Masire, Doreen AU - Orang’o, Omenge E AU - Robertson, Erle AU - Zetola, Nicola AU - Moyo, Sikhulile AU - Grover, Surbhi AU - Ermel, Aaron C AB - Background The variation of human papillomavirus (HPV) genotypes shapes the risks of cervical cancer and these variations are not well defined in Africa. Nucleotide changes within the L1 gene, nucleotide variability, and phylogeny were explored in relation to HIV in samples from Botswana and Kenya. Methods A total of 98 HPV-positive cervical samples were sequenced to identify different HPV variants. Phylogenetic inferences were used to determine HPV genotypes and investigate the clustering of sequences between women living with HIV (WLWHIV) and -women not living with HIV (WNLWHIV). Results Out of 98 generated sequences, 83.7% (82/98) participants had high-risk (HR) HPV genotypes while 16.3% (16/98) had low-risk (LR) HPV genotypes. Among participants with HR-HPV genotypes, 47.6% (39/82) were coinfected with HIV. The prevalence of HR-HPV genotypes was statistically higher in the Botswana population compared to Kenya (p-value < 0.001). Multiple amino acid mutations were identified in both countries. Genetic diversity differed considerably among WLWHIV and WNLWHIV. The mean pairwise distances between HPV-16 between HIV and HIV/HPV as well as for HPV-18 were statistically significant. Six (6) new deleterious mutations were identified in the HPV genotypes based on the sequencing of the L1 region, HPV-16 (L441P, S343P), HPV-18 (S424P), HPV-45 (Q366H, Y365F), and HPV-84 (F458L). The majority of the patients with these mutations were co-infected with HIV. Conclusions Genomic diversity and different genomic variants of HPV sequences were demonstrated. Candidate novel mutations within the L1 gene were identified in both countries which can be further investigated using functional assays. DA - 2022-01-27 DB - OpenUCT DP - University of Cape Town KW - Botswana KW - Kenya KW - Cervical cancer KW - Human papillomavirus KW - HPV variants phylogenetic analysis KW - HIV KW - L1 gene KW - HIV co-infection LK - https://open.uct.ac.za PY - 2022 T1 - Genetic diversity in L1 ORF of human papillomavirus in women with cervical cancer with and without human immunodeficiency virus in Botswana and Kenya TI - Genetic diversity in L1 ORF of human papillomavirus in women with cervical cancer with and without human immunodeficiency virus in Botswana and Kenya UR - http://hdl.handle.net/11427/36294 ER -en_ZA
dc.identifier.urihttps://doi.org/10.1186/s12879-022-07081-3
dc.identifier.urihttp://hdl.handle.net/11427/36294
dc.identifier.vancouvercitationTawe L, Choga WT, Paganotti GM, Bareng OT, Ntereke TD, Ramatlho P, et al. Genetic diversity in L1 ORF of human papillomavirus in women with cervical cancer with and without human immunodeficiency virus in Botswana and Kenya. BMC Infectious Diseases. 2022; http://hdl.handle.net/11427/36294.en_ZA
dc.language.rfc3066en
dc.publisher.departmentDivision of Human Genetics
dc.publisher.facultyFaculty of Health Sciences
dc.rights.holderThe Author(s)
dc.sourceBMC Infectious Diseases
dc.source.urihttps://bmcinfectdis.biomedcentral.com/
dc.subjectBotswana
dc.subjectKenya
dc.subjectCervical cancer
dc.subjectHuman papillomavirus
dc.subjectHPV variants phylogenetic analysis
dc.subjectHIV
dc.subjectL1 gene
dc.subjectHIV co-infection
dc.titleGenetic diversity in L1 ORF of human papillomavirus in women with cervical cancer with and without human immunodeficiency virus in Botswana and Kenya
dc.typeJournal Article
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