Fur Seal Feces-Associated Circular DNA Virus Identified in Pigs in Anhui, China

Abstract

Fur seal feces-associated circular DNA virus (FSfaCV) is an unclassified circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA virus that has been detected in mammals (fur seals and pigs). The biology and epidemiology of the virus remain largely unknown. To investigate the virus diversity among pigs in Anhui Province, China, we pooled 600 nasal samples in 2017 and detected viruses using viral metagenomic methods. From the assembled contigs, 12 showed notably high nucleotide acid sequence similarities to the genome sequences of FSfaCVs. Based on these sequences, a full-length genome sequence of the virus was then obtained using overlapping PCR and sequencing, and the virus was designated as FSfaCV-CHN (GenBank No. MK462122). This virus shared 91.3% and 90.9% genome-wide nucleotide sequence similarities with the New Zealand fur seal strain FSfaCV-as50 and the Japanese pig strain FSfaCV-JPN1, respectively. It also clustered with the two previously identified FSfaCVs in a unique branch in the phylogenetic tree based on the open reading frame 2 (ORF2), Rep-coding gene, and the genome of the reference CRESS DNA viruses. Further epidemiological investigation using samples collected in 2018 showed that the overall positive rate for the virus was 56.4% (111/197) in Anhui Province. This is the first report of FSfaCVs identified in pigs in China, and further epidemiological studies are warranted to evaluate the influence of the virus on pigs.

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

“…Metagenomic analysis mapped numerous sequence reads to the genomes of CRESS DNA viruses in nearly all (20/23) samples ( Figure 1 ). Based on BLAST search, the vast majority of reads (1–312 reads per virus per sample) in these 20 samples filtered for CRESS DNA viruses mapped to the sequences of porcine circovirus-like viruses (po-circo-like virus 21 and 22, 41 and 51, GenBank accession numbers: JF713716–719) and fur seal feces-associated circular DNA viruses (FSfaCVs, GenBank accession numbers: KF246569, LC133373, MK462122) [ 14 , 16 , 17 , 19 , 28 ].…”

“…The virome composition of healthy and diseased pigs has been investigated in studies processing fecal, nasal, lymph node, and blood samples collected in numerous geographic areas, including Germany, Sweden, the USA, Brazil, Japan, China, Vietnam, Korea, and New Zealand [ 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 33 ]. However, the number of studies reporting the simultaneous presence of variable CRESS DNA viruses in the same sample is limited [ 12 , 14 ].…”

“…One of the known porcine circoviruses, Porcine circovirus 2 , is associated with multisystemic diseases in swine, posing threat to swine herds and losses for the breeders [ 9 ]. Besides that, both classified and unclassified CRESS DNA viruses have been identified in fecal samples of both healthy and diseased pigs [ 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 ]. The microbial community of the swine intestine is highly complex, and, as of now, very little is known about how the viruses, including these non-classified porcine-associated CRESS DNA viruses, interact with host cells and other microbes.…”

“…In this study, we examined the occurrence of CRESS DNA viruses in porcine fecal specimens originally collected for metagenomic analysis of eukaryotic viruses. Representative genomes of novel viruses that showed similarities with porcine circovirus-like (po-circo-like) viruses and fur seal feces-associated circular DNA viruses were sequenced and characterized [ 16 , 17 ]. The study confirms high occurrence of diverse CRESS DNA viruses in the swine feces.…”

A New Circular Single-Stranded DNA Virus Related with Howler Monkey Associated Porprismacovirus 1 Detected in Children with Acute Gastroenteritis

“…The extensive use of next-generation sequencing on a variety of biological samples revealed an enormous variety of new viruses [ 1 , 2 , 3 ]. Particularly, viruses recently identified and coined as circular, Rep-encoding ssDNA (CRESS DNA) has a huge diversity and were detected in samples of eukaryotic hosts [ 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 ]. Many of the species belong to the phylum Cressdnaviricota and were classified into two genera, eight orders, eleven families, and sixty-six genera; many of the species are uncultured and remain unclassified [ 15 ].…”