An investigation into the clinical and genomic diversity of Human Papillomavirus in invasive disease in Scotland and the implications of new technologies

Abstract

This study investigated the prevalence of human papillomavirus (HPV) in different HPV-driven cancers in Scotland, including cervical, oropharyngeal, and anal. The study found that 91.5% of cervical, 55% of oropharyngeal and 88.6% of anal cancers are driven by HPV. Data has shown that most of these infections could potentially be prevented by the HPV vaccines. This research also investigated novel molecular methods for detecting HPV, such as droplet digital PCR (ddPCR) and next-generation sequencing (NGS), which can provide more comprehensive data about the virus and its various (sub)-lineages. ddPCR was used to determine the number of HPV 16 copies per cell in anal cancers. It was found that the qualitative presence of HPV and high viral load was associated with more prolonged survival in anal cancers, consistent with other HPV-driven cancers. Prior to the sequencing, three different extraction methods were examined to identify which one could be best for NGS downstream. Additionally, a bioinformatics pipeline was set up and validated by comparing results with the International HPV Reference Centre. NGS was used to analyse the genome of the HPV 16 detected in anal cancer samples and anal swabs from an asymptomatic male population. By analysing the whole genome of the virus, HPV 16 sub-lineages were identified. Lineages A1 and A2 were the most prevalent in both groups, and only minimal differences were detected for sub-linages B1, C1, and D1. Analysing sub-lineages and clinical data showed no overall survival differences between A1 and non-A1 sub-lineages. In addition, the potential of NGS for HPV diagnosis, compared with conventional HPV testing and how NGS may be applied for the detection and risk stratification for HPV infection and associated diseases was also described. Finally, a case scenario was presented for guidance in implementing direct sequencing in an HPV reference laboratory