Whole-genome Sanger sequencing was used to identify HPV18 variant diversity in the population. In addition conservation of HPV18 infections over time and the occurrence of HPV18 type-specific (TS) reinfection events were assessed. SNPs occurring in clearing infections and persistent infections were compared to identify possible differences between groups.
Vaginal self-samples were collected annually in up to four rounds from women (16-29y) participating in the Chlamydia trachomatis Screening Implementation program in the Netherlands. HPV-DNA detection and genotyping was performed using the SPF10-DEIA-LiPA25 system. Persisting and clearing HPV16 infections were selected and subjected to Sanger WGS. Persisting infections were defined as HPV18 positive by genotyping at two subsequent sampling moments. Clearing infections were defined as HPV18 positive initially, with at least one HPV18 negative follow-up sample.
Complete genome sequences were obtained from 51 study participants having 24 persistent and 27 clearing infections, resulting in a total of 52 unique HPV18 variants (including one HPV18 reinfection event). Persistent infections were completely conserved through time, with up to three years between the initial sample and the last follow-up sample. One reinfection event was identified, initially considered a persisting HPV18 infection, with unique HPV18 variants at both sampling moments. The identified variants predominantly clustered with sublineages A3 (31 variants) and A1 (11 variants). Other sublineages identified in this cohort are A4 (2 variants), A5 (1 variant), B1 (5 variants) and B2 (1 variant). Although the dataset size is limited, SNP comparison did not identify strongly acting nucleotide differences resulting in infections clearing or persisting.
A remarkably high HPV18 variant diversity was found in a Dutch cohort from sequencing 51 HPV18 infections . Lineages A1 and A3 are predominantly present in the Netherlands. Persistent infections are completely conserved through time with up to three years follow-up. One HPV18 variant reinfection event was identified, initially considered a persistent HPV18 infection by conventional genotyping.