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IDENTIFICATION OF A DIVERGENT SINGLE-STRANDED CIRCULAR DNA VIRUS IN PORK MEAT

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Pigs play a major role in the agricultural industry and represent an important source of food worldwide. On the other hand, pork meat products are a potential source of several known and previously unrecognized viruses capable of causing human diseases. Recently, using a metagenomic approach, studies have unveiled previously unknown single–stranded (ss) circular DNA viruses in beef samples that may have a role in disease. This study describes a new circular DNA genome identified in pork meat, which is highly divergent from the genomes of members of the Circoviridae, Geminiviridae, or any other known viral families with small circular replication initiator protein (Rep)-encoding ssDNA (CRESS-DNA) genomes. A pork meat sample was purchased in a supermarket. Pieces of meat (25 mg) were thawed, homogenized, filtered and ultracentrifuged to concentrate viral population. Viral nucleic acids were extracted, enriched and submitted to next generation sequencing. A total of 464,602 reads were obtained and assembled into contigs with SPAdes 3.6. One circular contig, which corresponded to a complete viral genome was assembled from 155 reads and was named pork-associated circular DNA virus (PaCV-1). Such genome displayed 51 % amino acid (aa) identity to Sewage-associated circular DNA virus-17 (SaCV-17). The PaCV-1 genome is 2,465 nucleotides (nt) in length and contains two putative major ORFs arranged in the same orientation. ORF1 is 924 nt (307 aa) in length and putatively encodes a Rep protein involved in rolling-circle DNA replication. Another ORF is 1,113 nt long (370 aa) and potentially encodes the capsid protein (Cap). Nucleotide sequence analysis revealed that (PaCV-1) contain a canonical nonanucleotide motif (NANTATTAC) at the apex of a stem-loop structure which is found in members of Circovirus, Geminivirus and Nanovirus genuses. Phylogenetic analysis of the PaCV-1 Rep aa sequence indicated that does not cluster significantly with Rep from other CRESS-DNA viruses.