PMC

Basic gene content of newly identified chapparvoviruses (ChPVs) and ChPV-derived endogenous parvoviral element (EPV) sequences, shown in relation to a representative ChPV genome (mouse kidney parvovirus). Asterisks indicate contigs that were truncated within the virus-derived portion of the sequence. Abbreviations: non-structural protein (NS); capsid protein (VP); nucleoprotein (NP).

Evolutionary relationships within the family Parvoviridae reconstructed via phylogenetic analysis of the tripartite helicase domain. The four major splits within the Parvoviridae are indicated in the tree as follows: (i) Parvovirinae (ii) Densovirinae (excluding genera He­pan-, Brevi-, and Penstyldensovirus, abbreviated as HBP); (iii) HBP; (iv) Chapparvovirus (ChPV-related viruses and EPVs). Brackets to the right indicate taxonomic groups. The names of established genera are shown in bold italics in the abbreviated form (i.e., with the suffix “parvovirus” omitted). The scale bar shows evolutionary distance in substitutions per site. Numbers adjacent to tree nodes show bootstrap support (based on 100 bootstrap replicates) where >70%.

Representative complete coding sequence and partial genome organizations of the two distinct types of exogenous amniote chapparvoviruses (ChPVs). Open reading frames (ORFs) are represented by rectangular arrows, colored according to homology. Splice donor sites are marked by white-colored bars, acceptor sites by orange-colored bars. Blue-colored bars show predicted polyadenylation signals. Small arrows show predicted promoters and are colored according to prediction score (>0.95 = green; 0.9–0.95 = pink: <0.9 = yellow). Grey boxes indicate regions inferred to be transcribed but not translated. Note: ORF4 is unique to turkey parvovirus and is not found in other avian type 2 ChPVs, such as chicken ChPV2.

Maximum likelihood phylogenetic reconstructions of the ChPV clade based on the complete aligned amino acid sequences of the NS1. Colored boxes indicate the presence of auxiliary open reading frames (ORFs), as shown in the inset key. The “?” character indicates that the presence of an ORF is suspected but not confirmed. Taxa labels in bold italics indicate endogenous sequences, whereas italics indicate sequences known or believed to derive from viruses. Brackets to the right indicate taxonomic groups. The scale bar (top right) shows evolutionary distance in substitutions per site. Numbers adjacent to tree nodes show bootstrap support (based on 100 bootstrap replicates) where >70%.

Genomic structures of newly identified chapparvoviruses (ChPVs) and ChPV-derived endogenous parvoviral element (EPV) sequences. The positions of putative open reading frames (ORFs) and predicted cis transcription elements of ChPVs are shown. ChPV.2-LatHes contains a previously unidentified repetitive element, present as multiple copies scattered in the Latrodectus genome, marked by the white box within the VP gene. The element ChPV.10-OntTau shares its integration site with another endogenous element, disclosing similarity to ambidensoviruses. ORFs are represented by rectangular arrows, colored according to homology. In-frame stop codons are shown as vertical lines. Splice donor sites are marked by white-colored bars, acceptor sites by orange-colored bars. Blue-colored bars show predicted polyadenylation signals. Small arrows show predicted promoters and are colored according to prediction score (>0.95 = green; 0.9–0.95 = pink: <0.9 = yellow). Grey boxes indicate regions inferred to be transcribed but not translated.

Comparison of chapparvoviruses (ChPV) capsid models of various host affiliations. (A) Homology models, shown as ribbon diagrams, representing the probable three different ChPV structural protein types. The first panel shows superposition of VP monomer homology models of amniote ChPV capsids, including reptilian, avian, rodent, chiropteran, and ungulate representatives. Black arrows show variable regions (VRs) previously identified by aligning the VP protein sequences. The next two panels show homology models of capsid monomers from a fish ChPV and an endogenous chapparvoviral element from an arthropod genome. (B) Capsid surface morphology of amniote ChPV homology models compared to that of the polymer structure of a prototypic parvovirus, the minute virus of mice (MVM) (PDB ID: 1Z14 at 3.25 Å resolution). Capsids are orientated by their two-fold symmetry axes, as shown in the line diagram, and are radially colored. Below, the comparison of homology models of complete viral capsid surface morphology of the newly identified fish ChPV and arachnid endogenous chapparvoviral element is shown, with that of the actual capsid structure of two densoviruses (subfamily Densovirinae, genus Ambidensovirus) (PDB ID: 4MGU at 3.5 Å resolution for Acheta domestica densovirus and 1DNV at 3.7 Å for Galleria densovirus).

Structural variation and assembly interfaces of chapparvoviruses (ChPVs). (A) Comparison of VP monomer ribbon diagrams of the protoparvovirus minute virus of mice (PDB ID: 1Z14) from subfamily Parvovirinae to homology models of an amniote, a fish, and a ChPV-derived EPV from an arthropod genome (ChPV.3-LatHes). Variable regions (VRs) of the same number are marked by the same color and mapped to the surface and luminal area of the T = 1 icosahedral capsid model constructed of 60 monomers. In the case of the minute virus of mice, the VRs are marked by both the traditional numbering established for dependoparvoviruses (Roman numerals) and by the special numbering applied for protoparvoviruses only (Arabic numerals). Blue signs indicate the names of the loops linking the beta strands of the conserved jelly roll core. Triangles mark the position of an asymmetric unit within the capsid, the five-fold symmetry axis is marked by a pentagon, the three-fold with the black filled triangles, and the two-fold with an ellipsoid. (B) Homology model of ORF6, the hypothetical structural protein of Syngnathus scovelli ChPV (ScChPV). The trimer of the ScChPV monomer model reveals a gap at each subunit interaction (arrows), unlike in the case of the trimer of even the hitherto smallest parvoviral capsid protein, Penaeus stylirostris densovirus. The gap might accommodate ORF6 in the assembled ScChPV capsid. Symmetry axes are marked by the same symbols as for panel A.