Genetic variations of the L2 gene in human papillomavirus (HPV) type 16 from cervical cancer patients in Sumatra region, Indonesia

Maya Savira; Arnaldi Farniga; Zidny Ilmiah; Rachmadina Rachmadina; Ika A. Rini; Rahmat A. Kemal; Azza E. Mahargyarani; Muhammad Z. Admiral; Amru Sofian; Renardy R. Razali; Donel Suhaimi; Andani E. Putra

doi:10.52225/narra.v5i2.1653

Authors

Maya Savira Department of Microbiology, Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia https://orcid.org/0000-0003-4663-030X
Arnaldi Farniga School of Food Industry, King Mongkut’s Institute of Technology Ladkrabang, Bangkok, Thailand https://orcid.org/0000-0001-5889-7947
Zidny Ilmiah Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Riau, Pekanbaru, Indonesia https://orcid.org/0000-0003-3096-396X
Rachmadina Rachmadina Master Program in Biomedical Sciences, Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia; Universitas Awal Bros, Pekanbaru, Indonesia https://orcid.org/0009-0000-7468-8061
Ika A. Rini Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea https://orcid.org/0009-0002-7984-1402
Rahmat A. Kemal Department of Medical Biology, Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia https://orcid.org/0000-0002-1630-9526
Azza E. Mahargyarani Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia https://orcid.org/0009-0000-3985-6170
Muhammad Z. Admiral Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia https://orcid.org/0009-0003-9355-0836
Amru Sofian Department of Physiology, Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia
Renardy R. Razali Department of Obstetrics-Gynecology, Faculty of Medicine, Universitas Riau-Arifin Achmad General Hospital, Pekanbaru, Indonesia
Donel Suhaimi Department of Obstetrics-Gynecology, Faculty of Medicine, Universitas Riau-Arifin Achmad General Hospital, Pekanbaru, Indonesia
Andani E. Putra Department of Microbiology, Faculty of Medicine, Universitas Andalas, Padang, Indonesia

DOI:

https://doi.org/10.52225/narra.v5i2.1653

Keywords:

Cervical cancer, human papillomavirus, HPV16, L2 gene, L2 protein

Abstract

The L2 protein, a minor capsid component of human papillomavirus (HPV), plays a critical role in the HPV life cycle by packaging the viral genome with the L1 protein and facilitating DNA transport to the nucleus. Identifying genetic variations in the L2 gene is essential for improving vaccine development, diagnostic accuracy, and understanding viral evolution, potentially contributing to more effective HPV vaccines. The aim of this study was to investigate the genetic variation of the L2 gene in cervical cancer specimens collected from patients in Riau Province, Indonesia. A single-center, cross-sectional study was conducted at Arifin Achmad General Hospital, Riau Province, involving cervical cancer patients with confirmed HPV16 infection between January 2018 and August 2020. Demographic, clinical, and risk factor data were collected through structured interviews and direct assessments. Cervical biopsy specimens were collected, and viral DNA was extracted for L2 gene amplification using polymerase chain reaction (PCR). Sequencing was conducted on PCR products, followed by single-nucleotide polymorphism (SNP) identification through alignment with the HPV16 reference genome. The amplification and sequencing of the HPV16 L2 gene from 22 cervical cancer specimens revealed 36 SNPs, including 31 nonsynonymous and five synonymous mutations. High-frequency mutations were observed at nucleotide positions 4,074 and 4,177, each detected in 95.45% of the samples. Notable insertions were found at positions 3,668–3,669 and 4,275–4,276, indicating substantial sequence variation. Phylogenetic analysis grouped the sequences into three clusters, with most belonging to sub-lineage A2 (European), while others aligned with A4 (Asian) and East Asian lineages. The observed genetic diversity in the HPV16 L2 gene may reflect regional viral evolution and has potential implications for future vaccine development.