Genetic Variability of Human Papillomavirus Types 52, 58, and 16 Based on L1 Genes in Central China

Persistent exposure to high-risk human papillomavirus (HR-HPV) is a major contributing factor to cervical cancer. HPV-52, -58, and -16 are the top three prevalent HR-HPV types in Jingzhou. In this study, samples monoinfected with HPV-52 (n = 96), -58 (n = 98), and -16 (n = 100) were collected between August 2022 and October 2023. The L1 genes were sequenced and analyzed to characterize genetic diversity. After constructing phylogenetic trees, secondary structure analysis and B-cell epitope prediction were conducted. The HPV-52 L1 sequences contained 35 single-nucleotide variations in total. Six of them were recently figured out, while 29 were synonymous and 6 were nonsynonymous. Of the 44 single-nucleotide polymorphisms (SNPs) found for HPV-58 L1, 10 were newly discovered. For HPV‑16 L1, 29 SNPs, one deletion and one insertion were identified, with four newly detected variants. Phylogenetic analysis revealed that all HPV-52 L1 sequences were clustered within sublineage B2, whereas 58.33% of the variations in HPV-58 L1 sequences were distributed in sublineage A1, and the majority of the variations in HPV-16 L1 sequences were located in sublineage A4 (55/70). No positively selected site was detected in the HPV-52, -58, and -16 L1 sequences. The predicted B-cell epitopes may be impacted by the nonconservative substitutions K200R and E468D in HPV-52 L1; L150F, I325M, K523T, K523N, K524R, and K524Q in HPV-58 L1; and N16D in HPV-16 L1. This study establishes a foundational data set on L1 genetic diversity of HPV-52, -58, and -16 prevalent in Central China and offers valuable insights for the development of region-specific prophylactic vaccines.