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Wednesday 21 December 2016
The fecal virome of South and Central American children

This week WAidid suggests an article published on Archives of VirologyThe fecal virome of South and Central American children with diarrhea includes small circular DNA viral genomes of unknown origin.

The known diversity of small circular Rep-encoding ssDNA (CRESS-DNA) genomes has rapidly increased, largely due to the analysis of environmental and animal samples using deep sequencing following rolling-circle amplification. Members of the family Circoviridae include circoviruses known to infect birds and mammals, sometimes with pathogenic consequences. Genomes closely related to those of circoviruses, named ‘‘cycloviruses’’, have been detected in mammalian tissues and feces.
58 fecal samples from Peruvian children with diarrhea of unknown etiology, that pre-tested negative for rotavirus, adenovirus, norovirus, campylobacter, shigella, salmonella and Escherichia coli, were analyzed.
Complete circular DNA viral genomes were amplified using inverse PCR (iPCR) with specific primers designed from short sequence fragments. Three sets of primers for nested PCR based on the Rep coding regions were designed to screen nucleic acids from fecal supernatants.
To facilitate description and discussion of that clade, the authors provisionally refer to that group of viral genomes as ‘‘pecoviruses’’ (the circular human-fecesderived pecovirus genome, PeCV-PE).
During the initial viral metagenomics analysis, the authors found eight sequence reads, showing similarities to a chimpanzee-feces-associated CRESS-DNA genome.  They provisionally called these and related viruses ‘‘smacoviruses’’.
To investigate whether other viral pathogens were present in the pecovirus- and smacovirus-containing fecal samples from diarrheic patients, five PCR-positive samples, from which whole CRESS-DNA genomes were derived, were individually analyzed by deep sequencing. As expected, the PeCV sequences were found in the individual feces from Peru, Nicaragua and Chile. The following enteric pathogens were also found in the PeCV-positive samples: group A rotavirus in the Peruvian sample, enterovirus A in the Nicaraguan sample and enterovirus B in the Chilean sample. The presence of known enteric pathogens indicates that the diarrhea experienced by the sample donors could be explained by these mammalian viruses rather than by the CRESS-DNA viruses.
The authors concluded that cell tropism of CRESS-DNA genomes and their possible roles remain unknown. Detection of these genomes in feces could reflect replication in human gut cells, passive transit of viruses in the food consumed by these individuals, or conceivably, even replication in gut-residing protozoa, fungi, or bacteria.

AUTHORS: Tung Gia Phan, Antonio Charlys da Costa, Juana Del Valle Mendoza, Filemon Bucardo-Rivera, Johan Nordgren, Miguel O'Ryan, Xutao Deng, Eric Delwart