Exploring HPV-linked head and neck cancer in Southern Punjab, Pakistan: Insights from HPV-16 phylogenetic analysis

Head and neck region squamous cell carcinoma (HNSCC) is a heterogeneous disease that can be categorized into human papillomavirus (HPV)-positive (20 %) and HPV-negative (80 %) subtypes. However, the prevalence of HPV genotypes is not clear in Pakistan. This study investigated how common the HPV-16 genotype is in patients with HNSCC in the Southern Punjab region of Pakistan, and the specific molecular features of this genotype.

For this cross-sectional study, 85 tissue samples were collected from diagnosed cases of HNSCC. Formalin-fixed paraffin-embedded tissue sections were used for genomic DNA extraction. The L1 region was amplified using GP5+ and GP6+ primers to detect HPV DNA. Real-time PCR was conducted to genotype high-risk HPV (HR-HPV). Whole genome sequencing was used for phylogenetic analysis of HPV-16 and to detect mutations/single nucleotide polymorphisms (SNPs).

Among the 85 samples, 7.1 % were positive for HPV, where 4.7 % were positive for HPV-16 and 2.4 % were positive for HPV-18. A significant association was found between HR-HPV positivity and histological grade (p < 0.05). The HPV-16 genome sequence obtained in this study was closely related to those from Thailand, the United States, India, China, and Europe, and 11 mutations/SNPs were detected in the sequenced genome, where four were novel.

The findings obtained in the present study demonstrate the low prevalence of HR-HPV associated HNSCC in Pakistan. Phylogenetic analysis showed that HPV-16 genome isolated and sequenced in this study had a distinct genetic structure and it also shared similarities with genomes reported from Thailand, the United States, India, China, and Europe.