Given the uniquely large and diverse collection of HPV-genotyped cervical samples worldwide, we were able to evaluate the genetic diversity within HPV genotypes and report on the geographic distribution of HPV variants, as well as measure their association with cervical cancer in Botswana and Kenya. Several studies have investigated HPV prevalence and type-specific distribution in cervical cancer patients from Botswana and Kenya, and found that HPV-16 or -18 (HPV-16/18) were identified in 93.8% from Kenya, and 61.8% from Botswana. Non-HPV-6/18 genotypes were detected in 17.2% from Kenya, and 47.8% from Botswana [
18,
19]. Again some studies have shown HPV prevalence in Botswana and Kenya [
3,
14,
16‐
26]. However, the numbers of studies investigating the variants within HPV genotypes are limited. In the present study, the molecular characterization of HPV variants was performed in sequences from Botswana and Kenya. By sequencing the
L1 region of HPV positive cervical samples, we were able to confirm the majority of the previously reported HPV genotypes [
14,
16‐
21,
24‐
26]. However, other HPV genotypes” were identified through sequencing in samples that were previously positive for HPV-16 or -18 only in both countries. This is likely due to the fact that the MY09/11 primers are universal primers and sequencing is not limited by the presence of HPV type-specific probes as in the LA-HPV and Abbott realtime PCR methods. Again, detection from FFPE samples could have been suboptimal due to nonuniform coverage of the tissue. In some cases, low-level of HPV replication may be missed because of thresholds standards. Overall, the frequency of the genotypes identified in both countries are the same as previously reported, having HPV-16 as the most frequently detected genotype followed by HPV-18 and the rest. The sequencing analysis illustrated that multiple variants were identified in both countries. Variants of HPV that changed the protein sequence of the capsid protein encoded by
L1 were found. These observations, in light of the slow evolution of HPV at the population level, suggest that strong selection pressures are at play in each infection cycle. We analyzed the mutation frequency in the panel for HPV genotypes in WLWHIV and WNLWHIV and found mutations within HPV genotypes. We could not assess the clinical relevance (i.e., association with HIV infection or cancer stage at presentation) of the detected variants due to small sample size. However, it is interesting that the new variations in high-risk genotypes were only identified in samples from HIV patients. The most striking finding in this report is the high proportion of mutations in the HPV‐genotypes (including both those arising among WLWHIV and those arising among WNLWHIV). Amino acid variations were found in the
L1 region of the HPV genotypes (Additional file
1: Table S1). In this study, 6 novel amino acids variations, which were previously unreported in the literature, were found in HPV-16, HPV-18, HPV-45 and HPV-84 (Table
2). However, two of them were found in only one sample (Y365F and F458L) and may have occurred by PCR amplification. These variations could be related to the early promoter activation of HPV and may play a crucial role in the transcriptional modulation of the HPV
L1 oncogenes via the promoter. Variants identified based on the sequencing of the
L1 region are; HPV-16 (L441P, S343P), HPV-18 (S424P), HPV-45 (Q366H, Y365F), belonged to the HPV HR-HPV group and HPV-84 (F458L) for the LR-HPV group. These alterations are described for the first time, and functional implications resulting from this variation need further analyses. Changes in the
L1 region of the HPV genome may be important for discriminating the infectious potential of different variants, as well as in defining epitopes relevant to vaccine design. Some previous studies investigating HPV-16 full-length sequences in cervical specimens have shown that the contiguous deletions identified to be highly associated with cancer are suggestive of a pattern of HPV integration [
30‐
37]. The findings of this study indicate that there could be variants of HPV circulating within sub-Saharan Africa. Further studies are needed to confirm the presence of new HPV variants and genotypes and to understand the evolution of HPV isolates in Botswana and Kenya by analyzing the complete HPV genome or different regions of HPV genes such as
L2, LCR,
E6 and
E7.
Table 2
Novel genetic mutations found in the 5′ and 3′-ends of HPV-16, -18, -45, -84 -L1 regions
16 | L441P | Positive | 2 | – | √ |
S343P | Positive | n/a | – | √ |
18 | S424P | Positive | n/a | – | √ |
45 | Q366H | Positive | 3 | 51 | √ |
84 | Y365F | Negative | 2 | – | √ |
F458L | Negative | n/a | – | √ |