Geographic variation in the eukaryotic virome of human diarrhea

Holtz, Lori R.; Cao, Song; Zhao, Guoyan; Bauer, Irma; Denno, Donna M.; Klein, Eileen J.; Antonio, Martín; Stine, O. Colin; Snelling, Tom; Kirkwood, Carl D.; Wang, David

doi:10.1016/j.virol.2014.09.012

Cited by 69 publications

(65 citation statements)

References 53 publications

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“…Enterovirus infections are common and include numerous human and animal pathogens, as well as highly prevalent genotypes with low or rare pathogenic outcomes (67)(68)(69)(70)(71)(72). Disease induction by enteroviruses is likely to be influenced by viral genotypes, host genetics, and immunological factors.…”

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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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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“…One study has compared the eukaryotic virome in stools of 87 children with diarrhea collected from two different locations-Melbourne, Australia and the Northern Territory, Australia-characterized by distinct environments (a westernized urban setting versus remote communities across a large geographic area) [46]. Diarrhea samples from the Northern Territory contained more viral families per sample than did diarrhea samples from Melbourne.…”

Section: Environmentmentioning

confidence: 99%

“…However, they are more sporadically distributed over time, with generally limited persistence during early development [41,55,56]. The epidemiology of eukaryotic viruses could be driven by a combination of factors such as maternal antibodies, geography, and environmental factors [46,57,58]. For example, the seasonality of influenza and parechovirus infections is well documented [59,60].…”

Section: Dynamic Bacterial Microbiome and Virome In Infancymentioning

confidence: 99%

The Bacterial Microbiome and Virome Milestones of Infant Development

Lim

Wang

Holtz

2016

Trends in Microbiology

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112

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“…Sequence reads are classified based on similarity to reference genomes. This approach allows comprehensive study of the viral component of the microbiome (the virome) and has led to the discovery of novel viruses (for review, see Chiu 2013) and the characterization of viruses present in healthy and sick people (Reyes et al 2010;Minot et al 2011;Lysholm et al 2012;Wylie et al 2012Wylie et al , 2014Holtz et al 2014;Oh et al 2014;Young et al 2014). When adequate numbers of sequence reads are generated, viruses can be characterized with regard to taxonomy and the presence of genes associated with virulence and resistance to antiviral drugs.…”

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confidence: 99%

Enhanced virome sequencing using targeted sequence capture

et al. 2015

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Metagenomic shotgun sequencing (MSS) is an important tool for characterizing viral populations. It is culture independent, requires no a priori knowledge of the viruses in the sample, and may provide useful genomic information. However, MSS can lack sensitivity and may yield insufficient data for detailed analysis. We have created a targeted sequence capture panel, ViroCap, designed to enrich nucleic acid from DNA and RNA viruses from 34 families that infect vertebrate hosts. A computational approach condensed ∼1 billion bp of viral reference sequence into <200 million bp of unique, representative sequence suitable for targeted sequence capture. We compared the effectiveness of detecting viruses in standard MSS versus MSS following targeted sequence capture. First, we analyzed two sets of samples, one derived from samples submitted to a diagnostic virology laboratory and one derived from samples collected in a study of fever in children. We detected 14 and 18 viruses in the two sets, comprising 19 genera from 10 families, with dramatic enhancement of genome representation following capture enrichment. The median fold-increases in percentage viral reads post-capture were 674 and 296. Median breadth of coverage increased from 2.1% to 83.2% post-capture in the first set and from 2.0% to 75.6% in the second set. Next, we analyzed samples containing a set of diverse anellovirus sequences and demonstrated that ViroCap could be used to detect viral sequences with up to 58% variation from the references used to select capture probes. ViroCap substantially enhances MSS for a comprehensive set of viruses and has utility for research and clinical applications.

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Geographic variation in the eukaryotic virome of human diarrhea

Cited by 69 publications

References 53 publications

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

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

The Bacterial Microbiome and Virome Milestones of Infant Development

Enhanced virome sequencing using targeted sequence capture

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