Endogenous amdoparvovirus-related elements reveal insights into the biology and evolution of vertebrate parvoviruses

Abstract

Amdoparvoviruses (family Parvoviridae: genus Amdoparvovirus) infect carnivores, and are a major cause of morbidity and mortality in farmed animals. In this study, we systematically screened animal genomes to identify endogenous parvoviral elements (EPVs) disclosing a high degree of similarity to amdoparvoviruses, and investigated their genomic, phylogenetic and protein structural features. We report the first examples of full-length, amdoparvovirus-derived EPVs in the genome of the Transcaucasian mole vole (Ellobius lutescens). We also identify four EPVs in mammal and reptile genomes that are intermediate between amdoparvoviruses and their sister genus (Protoparvovirus) in terms of their phylogenetic placement and genomic features. In particular, we identify a genome-length EPV in the genome of a pit viper (Protobothrops mucrosquamatus) that is more similar to a protoparvovirus than an amdoparvovirus in terms of its phylogenetic placement and the structural features of its capsid protein (as revealed by homology modeling), yet exhibits characteristically amdoparvovirus-like genome features including: (1) a putative middle ORF gene; (2) a capsid gene that lacks a phospholipase A2 domain; (3) a genome structure consistent with an amdoparvovirus-like mechanism of capsid gene expression. Our findings indicate that amdoparvovirus host range extends to rodents, and that parvovirus lineages possessing a mixture of proto- and amdoparvovirus-like characteristics have circulated in the past. In addition, we show that EPV sequences in the mole vole and pit viper encode intact, expressible replicase genes that have potentially been co-opted or exapted in these host species.

Keywords: amdoparvovirus; endogenous virus; paleovirology; parvovirus; protoparvovirus.

Figure 1.

Genomic organization of six amdoparvovirus-like EPVs. (a) Genomic structure of EPV loci, showing features identified in all six frames. Regions of homology to parvovirus proteins are indicated as arrows (NS in green and VP in cyan). Stop codons are indicated by vertical black lines, putative promoters with small black arrows. The characteristic M-ORF homologs of amdoparvoviruses are shown in pink. In the EilLut.2 element, dark green represents the potentially expressed, NS-fused region of the MafG transcription factor. The remaining portion of the MafG pseudogene is shown in grey. (b) Genomic organization of EPVs, shown in relation to a representative amdoparvovirus genome. NS, nonstructural protein; VP, capsid protein; VP1u, VP1 unique region; LINE, long interspersed nuclear element; SINE, short interspersed nuclear element; LTR, long terminal repeat; PLA2, phospholipase A2 domain.

Figure 2.

ML phylogenies of amdoparvoviruses, protoparvovirus and EPVs. Phylogenies based on NS (a) and VP (b) peptide sequences. Viral taxa are shown in bold text. The taxa names of EPVs are shown in italics. Brackets to the right indicate viral genera (Amdoparvovirus, Protoparvovirus) and EPV clades. Asterisks indicate nodes with bootstrap support >90%. The scale bar shows genetic distance in substitutions per site. AMDV, Aleutian mink disease virus; CPV, Canine parvovirus; PPV, Porcine parvovirus; MVM, Minute virus of mice; H1, H-1 parvovirus; AP, Proto-Amdo clade of EPVs. Details of EPVs examined here are contained in Table 1. Supplementary Table S1 contains the accession numbers and other details of amdoparvovirus and protoparvovirus reference sequences.

Figure 3.

(a) Alignment of the EPV VP protein sequences with those of exogenous amdoparvoviruses. VRs are indicated by horizontal lines. (b) Results of homology modeling; the capsid structure of CPV served as a reference structure for all the three further models. The bar shows the distance from the capsid center in Ångströms and the structures are colored accordingly. The pentagon marks the fivefold, the triangles the threefold, and the twofold is indicated by an ellipse. The arrows mark the VRIII region of ProMuc.1 and the VRVII of the EllLut-1 capsids, which contain the only insertions compared to amdoparvovirus VR regions. (c) Ribbon diagrams of the VRVIII (left) and VRVIII (right) loops of CPV (blue), AMDV (black), EllLut-1 (pink), and ProMuc.1 (yellow). racoond, racoondog amdoparvovirus; gfox, grey fox amdoparvovirus; skunk, skunk amdoparvovirus; mink, AMDV; vole, Transcaucasian mole vole EPV EilLut.1; Pit_viper, pit viper EPV ProMuc.1.