Unique Circovirus-Like Genome Detected in Pig Feces

Cheung, Andrew; Ng, Terry Fei-fan; Lager, Kelly M.; Alt, David P.; Delwart, Eric; Pogranichniy, Roman M.

doi:10.1128/genomea.00251-14

Cited by 12 publications

(7 citation statements)

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“…The first human-feces-associated PeCV was reported in a patient during an outbreak of acute gastroenteritis in the Netherlands (VS6600022) [27]. Other related genomes were found in feces from asymptomatic mammals [4, 24, 30]. Here, we also report PeCV genomes in human feces from Peru, Nicaragua and Chile, while diarrhea samples from Brazil and Venezuela were PCR negative.…”

Section: Discussionmentioning

confidence: 50%

“…Another distinct clade of viruses with CRESS-DNA genomes was also described in the feces of chimpanzees and other mammals, including pigs, rats [1, 3–5, 10, 18, 21, 22, 25, 26, 30], and recently humans [14], whose cellular hosts are also unknown. Yet another clade of CRESS-DNA genomes whose cellular hosts are not known was reported in the feces of pigs, seals, dromedaries and humans [4, 24, 27, 30]. Here we describe five CRESS-DNA genomes in human fecal samples that cluster within two of these phylogenetic clades of unknown cellular origin.…”

Section: Introductionmentioning

confidence: 93%

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

et al. 2016

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Viral metagenomics of feces collected from 58 Peruvian children with unexplained diarrhea revealed several small circular ssDNA genomes. Two genomes related to sequences previously reported in feces from chimpanzees and other mammals and recently named smacoviruses were characterized and then detected by PCR in 1.7 % (1/58) and 19 % (11/58) of diarrheal samples, respectively. Another three genomes from a distinct small circular ssDNA viral group provisionally called pecoviruses encoded Cap and Rep proteins with <35 % identity to those in related genomes reported in human, seal, porcine and dromedary feces. Pecovirus DNA was detected in 15.5 % (9/58), 5.9 % (3/51) and 3 % (3/100) of fecal samples from unexplained diarrhea in Peru, Nicaragua and Chile, respectively. Feces containing these ssDNA genomes also contained known human enteric viral pathogens. The cellular origins of these circular ssDNA viruses, whether human cells, ingested plants, animals or fungal foods, or residents of the gut microbiome, are currently unknown.

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Section: Discussionmentioning

confidence: 50%

Section: Introductionmentioning

confidence: 93%

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

et al. 2016

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“…Only one study sequenced with the Nanopore platform (0.8%). Four studies (3.3%) did not specify which sequencing platforms were used [40][41][42][43]. The earliest included study was published in 2009.…”

Section: Overall Descriptions Of All Studiesmentioning

confidence: 99%

Virus Metagenomics in Farm Animals: A Systematic Review

Kwok

Nieuwenhuijse

Phan

et al. 2020

Viruses

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A majority of emerging infectious diseases are of zoonotic origin. Metagenomic Next-Generation Sequencing (mNGS) has been employed to identify uncommon and novel infectious etiologies and characterize virus diversity in human, animal, and environmental samples. Here, we systematically reviewed studies that performed viral mNGS in common livestock (cattle, small ruminants, poultry, and pigs). We identified 2481 records and 120 records were ultimately included after a first and second screening. Pigs were the most frequently studied livestock and the virus diversity found in samples from poultry was the highest. Known animal viruses, zoonotic viruses, and novel viruses were reported in available literature, demonstrating the capacity of mNGS to identify both known and novel viruses. However, the coverage of metagenomic studies was patchy, with few data on the virome of small ruminants and respiratory virome of studied livestock. Essential metadata such as age of livestock and farm types were rarely mentioned in available literature, and only 10.8% of the datasets were publicly available. Developing a deeper understanding of livestock virome is crucial for detection of potential zoonotic and animal pathogens and One Health preparedness. Metagenomic studies can provide this background but only when combined with essential metadata and following the "FAIR" (Findable, Accessible, Interoperable, and Reusable) data principles.Viruses 2020, 12, 107 2 of 22 flocks and wild birds, suggesting that pre-existing biosecurity measurements could not keep up with the rate of livestock intensification [16]. In 2007-2010, a large-scale Q fever outbreak was reported in the Netherlands, affecting more than 3500 human cases and resulting in a huge economic loss [17,18]. A steep increase in the number of goat farms most likely was the driver for the increased prevalence of Coxiella burnetii infections, with animal abortion waves that had gone unnoticed. The policy of voluntary reporting abortion outbreaks to the Animal Health Service hindered the timely detection of the circulation of Q fever, and therefore early interventions. These examples indicate that zoonotic risks in the livestock industry should be carefully managed and adapted to livestock intensification. The One Health approach has been coined for advocating collaboration between multiple stakeholders including veterinarians, clinicians, epidemiologists, virologists, microbiologists, ecologists, and policy makers to prevent and control EIDs through the human-animal-environment interface [19]. Surveillance of livestock and the surrounding environment is a hallmark of early detection but is currently targeted to known risks.Advances in Next-Generation Sequencing (NGS) technologies and rapid development of bioinformatics and computational tools offer new opportunities for EID surveillance in quality and in scale. Particularly, metagenomic NGS (mNGS) allows unbiased detection of all microbes and viruses in a sample, showing potential for timely detection of rare or novel infectio...

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“…However, over the past decade metagenomic approaches have revealed the ubiquitous nature of eukaryotic CRESS-DNA viruses, with reports from various environments, including deep-sea vents ( Yoshida et al, 2013 ), Antarctic lakes and ponds ( López-Bueno et al, 2009 ; Zawar-Reza et al, 2014 ), wastewater ( Rosario et al, 2009b ; Roux et al, 2013 ; Kraberger et al, 2015 ; Phan et al, 2015 ), freshwater lakes ( Roux et al, 2012 , 2013 ), oceans ( Rosario et al, 2009a ; Labonte and Suttle, 2013 ; Roux et al, 2013 ), hot springs ( Diemer and Stedman, 2012 ), the near-surface atmosphere ( Whon et al, 2012 ; Roux et al, 2013 ), and soils ( Kim et al, 2008 ; Reavy et al, 2015 ). Novel CRESS-DNA viruses have also been discovered from fecal samples of a variety of vertebrates ( Blinkova et al, 2010 ; Li et al, 2010a , b ; Phan et al, 2011 ; Ge et al, 2012 ; Ng et al, 2012 ; Sachsenroder et al, 2012 ; van den Brand et al, 2012 ; Cheung et al, 2013 , 2014 ; Sikorski et al, 2013a ; Garigliany et al, 2014 ; Lian et al, 2014 ; Smits et al, 2014 ; Zhang et al, 2014 ; Sasaki et al, 2015 ). Notably, CRESS-DNA viruses similar to circoviruses, which were previously thought to only infect vertebrates, have now been identified in a myriad of invertebrates, including insects ( Ng et al, 2011 ; Rosario et al, 2011 , 2012b ; Dayaram et al, 2013 ; Padilla-Rodriguez et al, 2013 ; Pham et al, 2013a , b ; Garigliany et al, 2015 ), crustaceans ( Dunlap et al, 2013 ; Hewson et al, 2013a , b ; Ng et al, 2013 ; Pham et al, 2014 ), cnidarians ( Soffer et al, 2014 ), and gastropods ( Dayaram et al, 2015a ), suggesting that CRESS-DNA viruses may be prevalent amongst unexplored taxa.…”

Section: Introductionmentioning

confidence: 99%

Novel circular single-stranded DNA viruses identified in marine invertebrates reveal high sequence diversity and consistent predicted intrinsic disorder patterns within putative structural proteins

et al. 2015

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Viral metagenomics has recently revealed the ubiquitous and diverse nature of single-stranded DNA (ssDNA) viruses that encode a conserved replication initiator protein (Rep) in the marine environment. Although eukaryotic circular Rep-encoding ssDNA (CRESS-DNA) viruses were originally thought to only infect plants and vertebrates, recent studies have identified these viruses in a number of invertebrates. To further explore CRESS-DNA viruses in the marine environment, this study surveyed CRESS-DNA viruses in various marine invertebrate species. A total of 27 novel CRESS-DNA genomes, with Reps that share less than 60.1% identity with previously reported viruses, were recovered from 21 invertebrate species, mainly crustaceans. Phylogenetic analysis based on the Rep revealed a novel clade of CRESS-DNA viruses that included approximately one third of the marine invertebrate associated viruses identified here and whose members may represent a novel family. Investigation of putative capsid proteins (Cap) encoded within the eukaryotic CRESS-DNA viral genomes from this study and those in GenBank demonstrated conserved patterns of predicted intrinsically disordered regions (IDRs), which can be used to complement similarity-based searches to identify divergent structural proteins within novel genomes. Overall, this study expands our knowledge of CRESS-DNA viruses associated with invertebrates and explores a new tool to evaluate divergent structural proteins encoded by these viruses.

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Unique Circovirus-Like Genome Detected in Pig Feces

Cited by 12 publications

References 4 publications

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

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

Virus Metagenomics in Farm Animals: A Systematic Review

Novel circular single-stranded DNA viruses identified in marine invertebrates reveal high sequence diversity and consistent predicted intrinsic disorder patterns within putative structural proteins

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