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ARS Home » Midwest Area » Ames, Iowa » National Animal Disease Center » Virus and Prion Research » Research » Publications at this Location » Publication #305899

Title: Identification of several clades of novel single-stranded circular DNA viruses with conserved stem-loop structures in pig feces

item Cheung, Andrew
item NG, TERRY FEI FAN - University Of California
item Lager, Kelly
item Alt, David
item DELWART, ERIC - University Of California
item POGRANICHNIY, ROMAN - Purdue University

Submitted to: Archives of Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/12/2014
Publication Date: 1/1/2015
Citation: Cheung, A.K., Ng, TF., Lager, K.M., Alt, D.P., Delwart, E., Pogranichniy, R.M. 2015. Identification of several clades of novel single-stranded circular DNA viruses with conserved stem-loop structures in pig feces. Archives of Virology. 160(1):353-358.

Interpretive Summary: Ten unique viruses were identified in fecal samples that were pooled together from pigs suffering diarrhea. The individual samples were from a veterinary diagnostic laboratory that received them as part of standard diagnostic investigations. The pooled samples were tested for novel viruses using a sensitive technology that can detect very small amounts of the genetic material from different viruses. The novel viruses were similar in genetic organization, but distinct enough to be classified into 6 different groups. These 6 groups fall into a broader class of viruses that are known as circular Rep-encoding single-stranded DNA viruses. Although this class of viruses has been detected in fecal samples from a variety of species, it is not known if these viruses cause disease in swine, or in other species. This report demonstrates how diverse the population of viruses can be that are found in swine.

Technical Abstract: Metagenomic analysis of fecal samples collected from swine with diarrhea detected sequences encoding a replication initiator protein (Rep) typically found in small circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses. Complete nucleotide sequences of ten novel genomes were cloned and determined. The genome organization of these newly identified viruses is similar. The two putative open reading frames (ORFs) encoding Rep and the capsid protein are bidirectionally transcribed and separated by two intergenic regions. Stem-loop structure(s) typical of genomes that undergo a rolling-circle DNA replication mechanism are consistently detected at the 3'-ends of the Rep ORFs. Phylogenetic analysis revealed that these ten genomes are in a monophyletic clade with porcine stool-associated virus (PoSCV) previously described, but are divergent enough to be further classified into to six distinct virus clades. Two types of well conserved stem-loop structures were detected. Type 1 contains a nonanucleotide sequence in the loop and Type 2 contains a TAAA sequence at the apex. These two stem-loops either present individually or serially, with Type 2 stem-loop immediately followed by a Type 1 stem-loop. Our study provides a snapshot of the divergent CRESS-DNA viruses in porcine feces.