Genetic diversity and bioinformatics analysis of HPV types in head and neck benign and cancerous lesions

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ABSTRACT

  • 1Mokobodi CD,
  • 2Lebelo RL ,
  • 3Makua KS
  • 1HIV and Hepatitis Research Unit, Department of Virology, Sefako Makgatho Health Sciences University, Pretoria 0208, South Afric
  • 2HIV and Hepatitis Research Unit, Department of Virology, Sefako Makgatho Health Sciences University, Pretoria 0208, South Afri
  • 31HIV and Hepatitis Research Unit, Department of Virology, Sefako Makgatho Health Sciences University, Pretoria 0208, South Afric

Background

Human papillomavirus (HPV) contributes significantly to anogenital and head and neck cancers and benign lesions. Despite its clinical importance, data on the prevalence and diversity of HPV types in head and neck lesions, especially in Southern Africa, remain limited. This study aimed to investigate the prevalence of HPV types in head and neck benign and cancerous lesions, explore the genetic diversity of HPV types in these lesions, and determine the relationship of identified HPV types.

Method

This study analyzed 218 formalin-fixed paraffin-embedded (FFPE) tissue samples diagnosed as benign or cancerous lesions from the Departments of Oral Pathology and Anatomical Pathology. HPV DNA was detected using nested PCR targeting the L1 gene, followed by Sanger sequencing for genotyping. Bioinformatics tools were employed to assess the genetic diversity and phylogenetic relationships of the identified HPV types.

Result

HPV DNA was found in 95.7% of the samples. The most prevalent type was HPV11 (55.4%), followed by HPV32 (22.8%), HPV6 (10.9%), and HPV16 (10.9%). Squamous cell carcinoma (SCC) exhibited the highest rate of HPV detection (31.3%), while benign lesions (laryngeal papillomatosis and focal epithelial hyperplasia) showed substantial HPV presence. Moderate genetic diversity was observed in SCC, verruca vulgaris, and laryngeal papillomatosis, however focal epithelial hyperplasia showed low diversity. Analysis by gender and age indicated a higher prevalence of HPV-related lesions in males, with SCC more common in older individuals and benign lesions predominating in younger age groups.

Conclusion

These findings highlight the significant role of HPV in head and neck lesion development and emphasize the need for comprehensive HPV testing and tailored vaccination programs in South Africa to reduce the burden of HPV-associated head and neck diseases.
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PRESENTING AUTHOR

Mr. Choene Mokobodi, BSC HONS (MS) IN VIROLOGY

MSc student, Sefako Makgatho Health Sciences University

Mokobodi Choene is a medical scientist graduate with a BSc Hons (MS) in Medical Virology. He is currently pursuing his MSc in Medicine (Medical Virology) at Sefako Makgatho Health Sciences University, where he is conducting research on Human Papillomavirus (HPV). His study focuses on extraction methods and genotyping of the virus from wastewater, building upon the foundation laid during his honors degree. He is passionate about advancing research in the medical field, with a strong interest in virology and infectious diseases. He is recognized for his determined work ethic, scientific curiosity and unwavering commitment to becoming a professional scientist.
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