Abstract:
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 liv‑
ing 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 func‑
tional assays.