Worldwide genomic diversity of the high-risk human papillomavirus types 31, 35, 52, and 58, four close relatives of human papillomavirus type 16

Abstract

Among the more than one hundred formally described human papillomavirus (HPV) types, 18 are referred to as high-risk HPV types due to their association with anogenital cancer. Despite pathogenic similarities, these types form three remotely related taxonomic groups. One of these groups is called HPV species 9 and is formed by HPV-16, the most common and best-studied type, together with HPV-31, -33, -35, -52, -58, and -67. Previous worldwide comparisons of HPV-16 samples showed about 2% nucleotide diversity between isolates, which were subsequently termed variants. The distribution of divergent variants has been found to correlate frequently with the geographic origin and the ethnicity of the infected patients and led to the concept of unique African, European, Asian, and Native American HPV-16 variants. In the current study, we address the question of whether geography and ethnicity also correlate with sequence variations found for HPV-31, -35, -52, and -58. This was done by sequencing the long control region in samples derived from Europe, Asia, and Africa, and from immigrant populations in North and South America. We observed maximal divergence between any two variants within each of these four HPV types ranging from 1.8 to 3.6% based on nucleotide exchanges and, occasionally, on insertions and deletions. Similar to the case with HPV-16, these mutations are not random but indicate a relationship between the variants in form of phylogenetic trees. An interesting example is presented by a 16-bp insert in select variants of HPV-35, which appears to have given rise to additional variants by nucleotide exchanges within the insert. All trees showed distinct phylogenetic topologies, ranging from dichotomic branching in the case of HPV-31 to star phylogenies of the other three types. No clear similarities between these types or between these types and HPV-16 exist. While variant branches in some types were specific for Europe, Africa, or East Asia, none of the four trees reflected human evolution and spread to the extent illustrated by HPV-16. One possible explanation is that the rare HPV types that we studied spread and thereby diversified more slowly than the more abundant HPV-16 and may have established much of today's variant diversity already before the worldwide spread of humans 100,000 years ago. Most variants had prototypic amino acid sequences within the E6 oncoprotein and a segment of the L1 capsid protein. Some had one, two, or three amino acid substitutions in these regions, which might indicate biological and pathogenic diversity between the variants of each HPV type.

FIG. 1.

The intratype diversity of HPV-31. The phylogenetic trees represent the relationship between HPV-31 variants based on a 503-bp segment of the LCR. The large tree is based on the UPGMA, and the small tree is based on the neighbor-joining algorithm. The UPGMA tree represents all isolates, while those that were chosen to represent a particular variant in the neighbor-joining tree are indicated by black triangles. BR, Sao Paulo (Brazil); ED, Edinburgh (Scotland); HE, Heidelberg (Germany); HK, Hong Kong; ML, Mali; MR, Morocco; MX, Monterrey (Mexico); OK, Oklahoma City (Oklahoma); SA, Cape Town (South Africa); PH, The Philippines; TL, Thailand; TW, Taipei (Taiwan); USA, Los Angeles (California).

FIG. 2.

Mutational patterns in HPV-35 variants. The two top rows indicate the genomic position in the HPV-35 reference clone and the corresponding nucleotides. In the following rows, nucleotide exchanges are shown by letters, deletions relative to the reference clone by a hyphen, and an insert in some variants by an open square in variants that lack this insert. The positions 7412 and 7413 are listed to indicate the position of the insert.

FIG. 3.

The intratype diversity of HPV-35. The phylogenetic trees represent the relationship between HPV-35 variants based on an 814-bp segment of the LCR. The large tree is based on the UPGMA, and the small tree is based on the neighbor-joining algorithm. For further details, see the legend to Fig. 1.

FIG. 4.

Mutational patterns in HPV-52 variants. The two top rows indicate the genomic position in the published HPV-52 reference sequence and the corresponding nucleotides. Positions 7387 to 8391 could not be detected by resequencing the original reference clone or in any variants, leading to the corrected sequence of the HPV-52 reference clone in the third row (refer. cor.). In the following rows, nucleotide exchanges are shown by letters, deletions relative to the reference clone by a hyphen, and an insert in one variant (between positions 7701 and 7702) by an open square in variants that lack this insert.

FIG. 5.

The intratype diversity of HPV-52. The phylogenetic trees represent the relationship between HPV-52 variants based on a 637-bp segment of the LCR. The large tree is based on the UPGMA, and the small tree is based on the neighbor-joining algorithm. For further details, see the legend to Fig. 1.

FIG. 6.

The intratype diversity of HPV-58. The phylogenetic trees represent the relationship between HPV-52 variants based on a 461-bp segment of the LCR. The large tree is based on the UPGMA, and the small tree is based on the neighbor-joining algorithm. For further details, see the legend to Fig. 1.

FIG. 7.

Diversity of the E6 genes (four panels on the right side of the figure) and part of the L1 genes (left side of the figure) in distantly related variants of HPV-31, -35, -52, and -58. Within each panel, the first column lists the variants, whose relative phylogenetic position can be found in Fig. 1, 3, 5, and 6. The central part of the figure identifies nucleotide exchanges (letters) or maintenance of the sequence of the reference genome (gray squares). The box on the right side of each panel indicates whether the amino acid sequence of the reference clone has been maintained (“prototype”) and if not, what kind of amino acid exchanges have occurred.