Genetic variants of human parvovirus B19 in South Africa: cocirculation of three genotypes and identification of a novel subtype of genotype 1

Abstract

Parvovirus B19 comprises three distinct genotypes (1, 2, and 3). The distribution of B19 genotypes has not before been examined in South Africa. Two hundred thirty-nine laboratory samples submitted to a diagnostic virology laboratory for parvovirus DNA detection were analyzed retrospectively. Of the 53 PCR-positive samples investigated, 40 (75.4%) were identified as genotype 1 by genotype-specific PCR or consensus NS1 PCR and sequencing and 3 (5.7%) as genotype 2 and 10 (18.9%) as genotype 3 by analysis of NS1 sequences. Furthermore, phylogenetic analysis identified two genotype 1 sequences which were distinct from the previously described genotypes 1A and 1B. Interestingly, a genotype 2 virus was detected in the serum of an 11-year-old child, providing evidence for its recent circulation. This is the first study to demonstrate the concurrent circulation of all three genotypes of B19 in South Africa and the provisional identification of a novel subtype of genotype 1. The implications of parvovirus B19 variation are discussed.

FIG. 1.

Phylogenetic tree constructed from partial parvovirus B19 NS1 sequences rooted with simian parvovirus (GenBank accession number U26342). Thirty-eight B19-positive samples (boldface type) were aligned with comparative reference sequences identified by their GenBank accession numbers. B19 DNA-positive samples from this study clustered with genotypes 1A, 2, and 3B. Two samples clustered with genotype 1 but were separate from 1A and 1B and are indicted as a “novel variant.” Only significant bootstrap values (≥70%) are shown. Bar, 0.05 nucleotide substitutions per site. Asterisks refer to samples that were B19 DNA positive with the consensus NS1 PCR but negative with the genotype 1 VP2 PCR.

FIG. 2.

Phylogenetic tree constructed from NS1-VP1-u junction sequences rooted with simian parvovirus (GenBank accession number U26342). Sixteen B19-positive samples (boldface type) were aligned with comparative reference sequences identified by their GenBank accession numbers. The presence of all three genotypes and a novel variant of genotype 1 was confirmed with this phylogenetic analysis. Only significant bootstrap values (≥70%) are shown. Bar, 0.05 nucleotide substitutions per site.