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

This study investigated the prevalence of human papillomavirus (HPV) in different HPV-driven cancers inScotland, including cervical, oropharyngeal, and anal. The study found that 91.5% of cervical, 55% oforopharyngeal and 88.6% of anal cancers are driven by HPV. Data has shown that most of these infectionscould 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 thevirus and its various (sub)-lineages. ddPCR was used to determine the number of HPV 16 copies per cellin anal cancers. It was found that the qualitative presence of HPV and high viral load was associated withmore 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 couldbe best for NGS downstream. Additionally, a bioinformatics pipeline was set up and validated bycomparing 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 froman asymptomatic male population. By analysing the whole genome of the virus, HPV 16 sub-lineages wereidentified. Lineages A1 and A2 were the most prevalent in both groups, and only minimal differences weredetected for sub-linages B1, C1, and D1. Analysing sub-lineages and clinical data showed no overallsurvival differences between A1 and non-A1 sub-lineages.In addition, the potential of NGS for HPV diagnosis, compared with conventional HPV testing and howNGS may be applied for the detection and risk stratification for HPV infection and associated diseases wasalso described. Finally, a case scenario was presented for guidance in implementing direct sequencing inan HPV reference laboratory