Virome capture sequencing for comprehensive HPV genotyping in cervical samples

ObjectiveThis study aims to explore HPV genotyping in the cervical specimen using VirCapSeq by comparing the results with the reverse blot hybridization assay (REBA).MethodsA secondary cross-sectional data of HPV genotypes in 35 cervical specimens was obtained from VirCapSeq and REBA methods. The .FASTQ files were downloaded from the NCBI Sequence Read Archive (SRA) (accession number PRJNA766412) and HPV genotyping was bioinformatically analyzed by mapping the sequences to the PaVE database. HPV genotypes detected by REBA and NGS were compared. All specimens were stratified by histology into cervical intraepithelial neoplasia grades 1 (CIN1) and 2/3 (CIN2/3).ResultsNGS via VirCapSeq detected HPV DNA in 100% of the samples, whereas the REBA (hybridization-based) assay diagnosed HPV DNA in 85.71%. While the limitation of the conventional methods for HPV genotyping is the use of primers or probes, NGS detected a broader range. The results showed that mixed infections were detected in all samples by NGS, with HPV16 and HPV52 being the most abundant genotypes.ConclusionsHPV genome abundance, coverage, and diversity were associated with detection discrepancies between the methods, highlighting the enhanced sensitivity and diagnostic capabilities of NGS. These findings underscore the potential of NGS technologies for comprehensive HPV genotyping, advancing cervical cancer screening, and epidemiological studies. Future research should address cost barriers and expand cohort sizes to validate these findings.