The fecal virome of South and Central American children with diarrhea includes small circular DNA viral genomes of unknown origin

Phan, Tung Gia; Costa, Antônio Charlys da; Valle-Mendoza, Juana del; Bucardo-Rivera, Filemon; Nordgren, Johan; O’Ryan, Miguel; Deng, Xutao; Delwart, Eric

doi:10.1007/s00705-016-2756-4

Cited by 35 publications

(29 citation statements)

References 34 publications

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“…Smacoviruses [15,17], previously also referred to as chipoviruses [22,24], have been identified in faecal matter of various vertebrates, including humans, as well as in the abdomina of dragonflies of two species (Table 1). Thus far, none of these viruses have been cultured or found in animal tissue sample.…”

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confidence: 99%

Smacoviridae: a new family of animal-associated single-stranded DNA viruses

Varsani

Krupovìč

2018

Arch Virol

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Smacoviruses have small (∼2.3-2.9 kb), circular single-stranded DNA genomes encoding rolling circle replication-associated proteins (Rep) and unique capsid proteins. Although smacoviruses are prevalent in faecal matter of various vertebrates, including humans, none of these viruses have been cultured thus far. Smacoviruses display ∼45% genome-wide sequence diversity, which is very similar to that found within other families of circular Rep-encoding single-stranded (CRESS) DNA viruses, including members of the families Geminiviridae (46% diversity) and Genomoviridae (47% diversity). Here, we announce the creation of a new family Smacoviridae and describe a sequence-based taxonomic framework which was used to classify 83 smacovirus genomes into 43 species within six new genera, Bovismacovirus (n=3), Cosmacovirus (n=1), Dragsmacovirus (n=1), Drosmacovirus (n=3), Huchismacovirus (n=7), and Porprismacovirus (n=28). As in the case of genomoviruses, the species demarcation is based on the genome-wide pairwise identity, whereas genera are established based on the Rep amino acid sequence identity coupled with strong phylogenetic support. A similar sequence-based taxonomic framework should guide the classification of an astonishing diversity of other uncultured and currently unclassified CRESS DNA viruses discovered by metagenomic approaches.

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confidence: 99%

Smacoviridae: a new family of animal-associated single-stranded DNA viruses

Varsani

Krupovìč

2018

Arch Virol

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“…Human disease-related viruses, which can cause diarrhea, respiratory diseases, conjunctivitis, meningoencephalitis, and infantile gastroenteritis (Fong et al, 2010;Nguyen et al, 2007) were also identified. Some of these that might cause gastroenteritis, such as human picobirnavirus and human feces pecovirus (Giordano et al, 1999;Phan et al, 2016;Phan et al, 2012), were widely detected in the sewage samples but are usually not tested for at hospital laboratories. To understand their importance for public health, more enteric viruses identified in environmental samples should be incorporated into the routine monitoring of patients with gastroenteritis.…”

Section: Discussionmentioning

confidence: 99%

Differential removal of human pathogenic viruses from sewage by conventional and ozone treatments

Wang

Sikora

Rutgersson

et al. 2018

International Journal of Hygiene and Environmental Health

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Sewage contains a mixed ecosystem of diverse sets of microorganisms, including human pathogenic viruses. Little is known about how conventional as well as advanced treatments of sewage, such as ozonation, reduce the environmental spread of viruses. Analyses for viruses were therefore conducted for three weeks in influent, after conventional treatment, after additional ozonation, and after passing an open dam system at a full-scale treatment plant in Knivsta, Sweden. Viruses were concentrated by adsorption to a positively charged filter, from which they were eluted and pelleted by ultracentrifugation, with a recovery of about 10%. Ion Torrent sequencing was used to analyze influent, leading to the identification of at least 327 viral species, most of which belonged to 25 families with some having unclear classification. Real-time PCR was used to test for 21 human-related viruses in inlet, conventionally treated, and ozone-treated sewage and outlet waters. The viruses identified in influent and further analyzed were adenovirus, norovirus, sapovirus, parechovirus, hepatitis E virus, astrovirus, pecovirus, picobirnavirus, parvovirus, and gokushovirus. Conventional treatment reduced viral concentrations by one to four log10, with the exception of adenovirus and parvovirus, for which the removal was less efficient. Ozone treatment led to a further reduction by one to two log10, but less for adenovirus. This study showed that the amount of all viruses was reduced by conventional sewage treatment. Further ozonation reduced the amounts of several viruses to undetectable levels, indicating that this is a promising technique for reducing the transmission of many pathogenic human viruses.

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“…1). While the tropism of some CRESS DNA viruses, such as circoviruses (infecting vertebrates) and geminivirus (infecting plants), has been clearly defined, the large majority of such genomes have been characterized using metagenomics from environmental or nonsterile samples, such as feces (13,24,26,35,(62)(63)(64)(65). The tropism of the large majority of CRESS DNA viruses is therefore still unknown (66).…”

Section: Discussionmentioning

confidence: 99%

Case-Control Comparison of Enteric Viromes in Captive Rhesus Macaques with Acute or Idiopathic Chronic Diarrhea

Kapusinszky

Ardeshir

Mulvaney

et al. 2017

J Virol

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Diarrhea is the major cause of non-research-associated morbidity and mortality affecting the supply of rhesus macaques and, potentially, their responses to experimental treatments. Idiopathic chronic diarrhea (ICD) in rhesus macaques also resembles ulcerative colitis, one form of human inflammatory bowel disease. To test for viral etiologies, we characterized and compared the fecal viromes from 32 healthy animals, 31 animals with acute diarrhea, and 29 animals with ICD. The overall fractions of eukaryotic viral reads were 0.063% for the healthy group, 0.131% for the acute-diarrhea group, and 0.297% for the chronic-diarrhea group. Eukaryotic viruses belonging to 6 viral families, as well as numerous circular Rep-encoding singlestranded DNA (CRESS DNA) viral genomes, were identified. The most commonly detected sequences were from picornaviruses, making up 59 to 88% of all viral reads, followed by 9 to 17% for CRESS DNA virus sequences. The remaining 5 virus families, Adenoviridae, Astroviridae, Anelloviridae, Picobirnaviridae, and Parvoviridae, collectively made up 1 to 3% of the viral reads, except for parvoviruses, which made up 23% of the viral reads in the healthy group. Detected members of the families Picornaviridae and Parvoviridae were highly diverse, consisting of multiple genera, species, and genotypes. Coinfections with members of up to six viral families were detected. Complete and partial viral genomes were assembled and used to measure the number of matching short sequence reads in feces from the 92 animals in the two clinical and the healthy control groups. Several enterovirus genotypes and CRESS DNA genomes were associated with ICD relative to healthy animals. Conversely, higher read numbers from different parvoviruses were associated with healthy animals. Our study reveals a high level of enteric coinfections with diverse viruses in a captive rhesus macaque colony and identifies several viruses positively or negatively associated with ICD.KEYWORDS enterovirus, sapelovirus, parvovirus, CRESS-DNA, idiopathic diarrhea, rhesus macaques, enteric disease etiology W e compared the enteric viromes of captive rhesus macaques (Macaca mulatta) with acute and idiopathic chronic diarrhea (ICD) to those of healthy animals using a case-control study. The genomes of several known and new viruses were characterized using metagenomics. We showed that some specific enterovirus genotypes and some small circular DNA genomes are associated with chronic idiopathic diarrhea, providing candidates for further testing of their pathogenicity. Other viruses, including some parvoviruses, were found at significantly higher levels in healthy animals.

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The fecal virome of South and Central American children with diarrhea includes small circular DNA viral genomes of unknown origin

Cited by 35 publications

References 34 publications

Smacoviridae: a new family of animal-associated single-stranded DNA viruses

Smacoviridae: a new family of animal-associated single-stranded DNA viruses

Differential removal of human pathogenic viruses from sewage by conventional and ozone treatments

Case-Control Comparison of Enteric Viromes in Captive Rhesus Macaques with Acute or Idiopathic Chronic Diarrhea

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