Comparative analysis reveals frequent recombination in the parvoviruses

Abstract

Parvoviruses are small single-stranded DNA viruses that are ubiquitous in nature. Infections with both autonomous and helper-virus dependent parvoviruses are common in both human and animal populations, and many animals are host to a number of different parvoviral species. Despite the epidemiological importance of parvoviruses, the presence and role of genome recombination within or among parvoviral species has not been well characterized. Here we show that natural recombination may be widespread in these viruses. Different genome regions of both porcine parvoviruses and Aleutian mink disease viruses have conflicting phylogenetic histories, providing evidence for recombination within each of these two species. Further, the rodent parvoviruses show complex evolutionary histories for separate genomic regions, suggesting recombination at the interspecies level.

Fig. 1

PPV phylogenies. Separate phylogenetic trees were inferred for nucleotides (a) 1–562, (b) 563–1729 and (c) 1730–2620 of the alignments. Viruses isolated from Germany in 2001, which generally form a tight clade, are outlined in black. Viruses isolated from Germany in 2002, along with a vaccine strain from 1964, which consistently form a clade, are labelled in light grey. Isolate 225b is in dark grey. Nodes with ≥70 % bootstrap support are shown and branch lengths are scaled according to nucleotide substitutions per site.

Fig. 2

ADV phylogenies. Separate phylogenetic trees were inferred for nucleotides (a) 1–542, (b) 543–1050, and (c) 1051–1533. The two groups that show significant changes in topology, with respect to each other, are shaded in light and dark grey. Nodes with ≥70 % bootstrap support are shown and branch lengths are scaled according to nucleotide substitutions per site.

Fig. 3

Rodent parvovirus phylogenies. Phylogenetic trees were inferred for nucleotides (a) 1–854, (b) 855–2226 and (c) 2227–4654. Groups of viruses are shaded or outlined for ease of visualization: MVMs are light grey; HaPV and MPV-3 are dark grey; all MPVs except MPV-3 are circled in black; and LuIII virus is unmarked. Nodes with ≥70 % bootstrap support are shown and branch lengths are scaled according to nucleotide substitutions per site.