Mutation Profiles, Glycosylation Site Distribution and Codon Usage Bias of Human Papillomavirus Type 16

Abstract

Human papillomavirus type 16 (HPV16) is the most prevalent HPV type causing cervical cancers. Herein, using 1597 full genomes, we systemically investigated the mutation profiles, surface protein glycosylation sites and the codon usage bias (CUB) of HPV16 from different lineages and sublineages. Multiple lineage- or sublineage-conserved mutation sites were identified. Glycosylation analysis showed that HPV16 lineage D contained the highest number of different glycosylation sites from lineage A in both L1 and L2 capsid proteins, which might lead to their antigenic distances between the two lineages. CUB analysis showed that the HPV16 open reading frames (ORFs) preferred codons ending with A/T. The CUB of HPV16 ORFs was mainly affected by natural selection except for E1, E5 and L2. HPV16 only shared some of the preferred codons with humans, which might help reduce competition in translational resources. These findings increase our understanding of the heterogeneity between HPV16 lineages and sublineages, and the adaptation mechanism of HPV in human cells. In summary, this study might facilitate HPV classification and improve vaccine development and application.

Keywords: HPV16; codon usage bias; glycosylation; lineage and sublineage; mutation.

Figure 1

Mutation distribution across the HPV16 genome. The x axis shows HPV16 gene positions, and the y axis shows the 12 nucleotide mutation patterns. The bubble size indicates the occurrence of nucleotide mutations.

Figure 2

The lineage distribution of potential glycosylation sites in L1 and L2 proteins.

Figure 3

ENC plot of the eight ORFs of HPV16. The continuous curve plots the relationship between GC3 and ENC in the absence of selection. The horizontal dotted line represents the ENC value of 35. Almost all points lie below the curve.

Figure 4

Neutrality plot analysis of GC12 and GC3 for HPV16 ORFs.

Figure 5

Relative synonymous codon usage (RSCU) analysis revealed over-representation of codons ending in A/T in HPV16 ORFs. Columns correspond to the 59 codons (three stop codons and those for Trp, Met were excluded). Rows correspond to the eight ORFs. Blue cells indicate under-represented codons (RSCU < 0.6) and red cells indicate over-represented codons (RSCU > 1.6). “X3s” indicates the nucleotide at the 3rd codon position.

Figure 6

Pairwise correlation analysis of RSCU for 59 codons in eight HPV16 ORFs versus those of humans. The R-squared values of linear regression analysis are shown. The embedded table denotes the number of commonly preferred (RSCU ≥ 0.6) codons and unpreferred (RSCU < 0.6) codons for HPV16 and human genes, and the number of preferred codons in humans but unpreferred in HPV16 and preferred codons in HPV16 but unpreferred in humans.