Amino acid sequence diversity of the major human papillomavirus capsid protein: implications for current and next generation vaccines

Abstract

Despite the fidelity of host cell polymerases, the human papillomavirus (HPV) displays a degree of genomic polymorphism resulting in distinct genotypes and intra-type variants. The current HPV vaccines target the most prevalent genotypes associated with cervical cancer (HPV16/18) and genital warts (HPV6/11). Although these vaccines confer some measure of cross-protection, a multivalent HPV vaccine is in the pipeline that aims to broaden vaccine protection against other cervical cancer-associated genotypes including HPV31, HPV33, HPV45, HPV52 and HPV58. Both current and next generation vaccines comprise virus-like particles, based upon the major capsid protein, L1, and vaccine-induced, type-specific protection is likely mediated by neutralizing antibodies targeting L1 surface-exposed domains. The aim of this study was to perform an in silico analysis of existing full length L1 sequences representing vaccine-relevant HPV genotypes in order to address the degree of naturally-occurring, intra-type polymorphisms. In total, 1281 sequences from the Americas, Africa, Asia and Europe were assembled. Intra-type entropy was low and/or limited to non-surface-exposed residues for HPV6, HPV11 and HPV52 suggesting a minimal effect on vaccine antibodies for these genotypes. For HPV16, intra-type entropy was high but the present analysis did not reveal any significant polymorphisms not previously identified. For HPV31, HPV33, HPV58, however, intra-type entropy was high, mostly mapped to surface-exposed domains and in some cases within known neutralizing antibody epitopes. For HPV18 and HPV45 there were too few sequences for a definitive analysis, but HPV45 displayed some degree of surface-exposed residue diversity. In most cases, the reference sequence for each genotype represented a minority variant and the consensus L1 sequences for HPV18, HPV31, HPV45 and HPV58 did not reflect the L1 sequence of the currently available HPV pseudoviruses. These data highlight a number of variant amino acid residues that warrant further investigation for vaccine and natural history studies of HPV.

Keywords: Diversity; Entropy; HPV; L1; Papillomavirus.

Fig. 1

Geographical distribution of HPV full length L1 sequences. Total numbers of available full length L1 sequences for each HPV type are indicated beneath each chart. Alpha-papillomavirus species groups are as indicated: A10 (HPV6, HPV11), A9 (HPV16, HPV31, HPV33, HPV52 and HPV58) and A7 (HPV18, HPV45). The regional proportion of L1 sequences are colored according to the inset map: Americas (green), Europe (yellow), Africa (blue) and Asia (red).

Fig. 2

Intra-type, site-specific amino acid residue entropy. Residue variation estimated using Shannon entropy, wherein a value of zero reflects site-specific conservation and higher values indicate increasing degrees of site-specific variation. A level of 5% residue variation equates to an entropy score of ca. 0.18. Site-specific variation(s) above this level are indicated by convention, numbered according to the reference sequence for that HPV type. The positions of major structural elements are indicated.

Fig. 3

Crystal model surface representation of variant amino acid residues. (A) top view (left panel) and side view (right panel) of HPV16 pentamer (PDB code: 2R5H) with variable loops shaded as indicated. (B) Shannon entropy scores for indicated A9 HPV types are mapped onto top view of HPV16 pentamer structure according to the indicated scheme. Only those variant amino acid residues located on the surface of the capsomer are shown. While all five monomers of the capsomer are pictured, and all appropriate sites of variation are highlighted, only one of the five copies of a residue are indicated with the amino acid mutation (black arrows), and all the variations for a given HPV type may not be indicated on the same monomer.