Genomic Diversity of CRESS DNA Viruses in the Eukaryotic Virome of Swine Feces

Abstract

Replication-associated protein (Rep)-encoding single-stranded DNA (CRESS DNA) viruses are a diverse group of viruses, and their persistence in the environment has been studied for over a decade. However, the persistence of CRESS DNA viruses in herds of domestic animals has, in some cases, serious economic consequence. In this study, we describe the diversity of CRESS DNA viruses identified during the metagenomics analysis of fecal samples collected from a single swine herd with apparently healthy animals. A total of nine genome sequences were assembled and classified into two different groups (CRESSV1 and CRESSV2) of the Cirlivirales order (Cressdnaviricota phylum). The novel CRESS DNA viral sequences shared 85.8–96.8% and 38.1–94.3% amino acid sequence identities for the Rep and putative capsid protein sequences compared to their respective counterparts with extant GenBank record. Data presented here show evidence for simultaneous infection of swine herds with multiple novel CRESS DNA viruses, including po-circo-like viruses and fur seal feces-associated circular DNA viruses. Given that viral genomes with similar sequence and structure have been detected in swine fecal viromes from independent studies, investigation of the association between presence of CRESS DNA viruses and swine health conditions seems to be justified.

Novel Circoviruses from Birds Share Common Evolutionary Roots with Fish Origin Circoviruses

“…The Rep of the BitternCV and Bee-eaterCV contained conserved motifs controlling the RCR processes of eukaryotic CRESS DNA viruses, including the probable N-terminal RCR (I–III) and C-terminal superfamily 3 helicase (Walker-A Walker-B, and C) motifs, as well as an arginine finger ( Table 2 ). These motifs showed the highest similarity with that of typical for circo- and cycloviruses and imply similar course of replication for all these viruses [ 2 , 22 , 27 , 28 ].…”

Detection and Complete Genome Analysis of Porcine Circovirus 2 (PCV2) and an Unclassified CRESS DNA Virus from Diarrheic Pigs in the Dominican Republic: First Evidence for Predominance of PCV2d from the Caribbean Region

“…The complete genomes of the PCV2 strains were evaluated for recombination events using the RDP4 program with default parameters, and were considered as recombinants if supported by two, or >two detection methods (3Seq, BOOTSCAN, CHIMAERA, GENECONV, MAXCHI, RDP, and SISCAN) with a highest acceptable p-value of p < 0.01 with Bonferroni's correction, as described previously [38,39,42]. Phylogenetic analyses of PCV2 were carried out by both maximum-likelihood (ML) and neighbor-joining (NJ) methods using the MEGA7 software, with the Kimura 2-parameter model of substitution and 1000 bootstrap replicates, whereas phylogenetic analysis of CRESSV2/ENG22 was performed by the ML method, supported with 1000 bootstrap replicates and the LG + F + G + I model of substitution, as described in previous studies [8,15,38].…”

“…Since the pigeon circovirus-like sequence was detected in a fecal sample, we could not determine whether the virus infected pigs, or was of dietary origin (consumption of avian feces). The partial rep sequence in ENG22 shared maximum homology with unclassified CRESS DNA viral sequences from porcine feces [8] and was eventually characterized for the complete genome.…”

“…The complete genome of the CRESS DNA virus (CRESSV2/ENG22) in sample ENG22 was 2851 nt in length, and shared maximum nt sequence identities of ~93% with those of porcine-associated CRESS DNA viruses 303_7 and 453_7 from porcine feces in Hungary [8]. Based on the genome organization, CRESSV2/ENG22 was assigned to type V CRESS DNA genomes (Figure 3) [54].…”

“…In pigs, PCV2 has been associated with various clinical and subclinical conditions (post-weaning multisystemic wasting syndrome (PMWS)/PCV2 systemic disease, porcine dermatitis, and nephropathy syndrome (PDNS), PCV2-associated pneumonia, reproductive disorders, and enteric diseases) that are collectively referred to as porcine circovirus-associated diseases (PCVAD) [5][6][7]. Besides circoviruses, several diverse circular replication-associated protein (Rep)-encoding single-stranded DNA (CRESS DNA) viral sequences have been reported from healthy and clinically ill pigs, although the true host/s and pathogenesis of these viruses are largely unknown [8][9][10].…”