Whole-genome characterization and genotyping of global WU polyomavirus strains

Abstract

Exploration of the genetic diversity of WU polyomavirus (WUV) has been limited in terms of the specimen numbers and particularly the sizes of the genomic fragments analyzed. Using whole-genome sequencing of 48 WUV strains collected in four continents over a 5-year period and 16 publicly available whole-genome sequences, we identified three main WUV clades and five subtypes, provisionally termed Ia, Ib, Ic, II, IIIa, and IIIb. Overall nucleotide variation was low (0 to 1.2%). The discriminatory power of the previous VP2 fragment typing method was found to be limited, and a new, larger genotyping region within the VP2/1 interface was proposed.

FIG. 1.

Entropy plot showing the levels of nucleotide variation in the 64 aligned WUV genomes along each genomic position as well as the locations of each gene, the NCCR, and the two evaluated typing regions. Numbering is based on prototype strain B0. Open stars along entropy bars indicate type-specific SNPs, which correlate with the SNP table positioned below each graph. A type-specific SNP was defined as a position which consistently holds a different nucleotide in one or more subtypes in comparison to the consensus sequence. G/a or G/c indicates a conserved change where a minority of type-specific SNPs contain an alternate base, such as adenine or cystine. Shaded positions in the SNP table indicate one or more non-type-specific variations at that position from other publicly available sequences. Dashes indicate a point deletion. The consensus sequence (^a) was defined as the majority nucleotide at that position between all genotypes.

FIG. 2.

Unrooted consensus neighbor-joining tree using 1,000 bootstraps of the 64 NCCR-excised WUV genomes.

FIG. 3.

Unrooted consensus neighbor-joining trees using 1,000 bootstraps of the widely used typing region comprising VP2 nt 1354 to 1560 and the proposed typing region comprising VP2/1 nt 1620 to 2299.