The intestinal virome of malabsorption syndrome-affected and unaffected broilers through shotgun metagenomics

Lima, Diane Alves de; Cibulski, Samuel Paulo; Tochetto, Caroline; Varela, Ana Paula Muterle; Finkler, Fabrine; Teixeira, Thaís Fumaco; Loiko, Márcia Regina; Cerva, Cristine; Junqueira, Dennis Maletich; Mayer, Fabiana Quoos; Roehe, Paulo Michel

doi:10.1016/j.virusres.2018.12.005

Cited by 62 publications

(57 citation statements)

References 64 publications

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“…Chicken astrovirus, parvovirus, calicivirus and rotavirus have been identified as causes of gastrointestinal tract infections in poultry, such as RSS, which is also called malabsorption syndrome [27]. A few studies using viral metagenomics could not specify any particular pathogen from the viral community in the chicken flocks with RSS because the distributions of enteric viruses in diseased and healthy flocks were not significantly different [17,28,29]. Chicken astrovirus has been distributed worldwide for decades and is nearly ubiquitous constituent of the chicken gut [30].…”

Section: Discussionmentioning

confidence: 99%

“…In this study, chicken picobirnaviruses from the Republic of Korea were firstly identified using metagenomics, and viral sequences were grouped into genogroups I and II. Avian picobirnaviruses in genogroup I have primarily been noted to date, and those in genogroup II are rarely detected in chickens [17,29,38]. We could not design a primer set to detect picobirnaviruses due to the high genetic diversity between chicken picobirnaviruses.…”

Section: Discussionmentioning

confidence: 99%

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Viral metagenomic analysis of chickens with runting-stunting syndrome in the Republic of Korea

Kim

Kwon

Jang

et al. 2020

Virol J

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Background and aims: Runting-stunting syndrome (RSS) in chickens, also known as malabsorption syndrome, which is characterized by mild to severe enteritis and diagnosed through typical histopathologic examination as well as clinical signs, results in considerable economic losses. Despite the many studies carried out over decades to determine the etiologic agents of RSS involved in the disease, several outbreaks remained without the elucidation of, potentially multiple, etiologies involved. Methods: We performed comparative analysis of viral metagenomes from four chicken flocks affected with RSS using next-generation sequencing. Primers for the detection of chicken enteric viruses were designed from the sequencing data obtained with metagenomics. Multiplex reverse transcription-polymerase chain reaction (PCR) and PCR were performed to detect a variety of etiological agents previously described in natural cases of RSS.Results: The most abundant viral families identified in this study were Astroviridae, Picornaviridae, Parvoviridae, Caliciviridae, Reoviridae and Picobirnaviridae. Chicken astrovirus sequences were present in all four samples, suggesting an association between chicken astrovirus and RSS and chicken astrovirus as a candidate pathogen responsible for RSS. Picobirnavirus and the newly identified chapparvovirus were found in chickens in the Republic of Korea for the first time, and the genetic diversity of enteric viruses and viral communities was showed. Conclusions: Chicken astrovirus was consistently detected in broilers affected with RSS and the result of this study may contribute to knowledge of enteric diseases and viruses in chickens.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Viral metagenomic analysis of chickens with runting-stunting syndrome in the Republic of Korea

Kim

Kwon

Jang

et al. 2020

Virol J

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“…However, our study shows that GyV11 can be dispersed by the faeces of, at least, two different avian species (Myrmeciza ferruginea and Pithys albifrons) and is likely circulating among different bird species within the same community. In fact, in a closer area such as Brazil, the circulation of a phylogenetically close genotype (GyV4) has been detected in chickens and three other gyroviruses (CAV, GyV2, and GyV3) have been found in the fecal virome of wild birds [3,36].…”

Section: Discussionmentioning

confidence: 99%

A Novel and Divergent Gyrovirus with Unusual Genomic Features Detected in Wild Passerine Birds from a Remote Rainforest in French Guiana

Truchado

Diaz-Piqueras

Gómez-Lucı́a

et al. 2019

Viruses

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Sequence-independent amplification techniques have become important tools for virus discovery, metagenomics, and exploration of viral diversity at the global scale, especially in remote areas. Here, we describe the detection and genetic characterization of a novel gyrovirus, named GyV11, present in cloacal, oral, and blood samples from neotropical wild birds in French Guiana. The molecular epidemiology revealed the presence of GyV11 only in passerine birds from three different species at a low prevalence (0.73%). This is the first characterization and prevalence study of a gyrovirus carried out in resident wild bird populations in a remote region, and provides evidence of the fecal-oral route transmission and local circulation of the virus. The molecular phylogeny of gyroviruses reveals the existence of two distinct gyrovirus lineages in which GyV11 is phylogenetically distinct from previously reported gyroviruses. Furthermore, GyV11 is placed basal in the gyrovirus phylogeny, likely owing to its ancestral origin and marked divergence. This study also provides important insights into the ecology, epidemiology, and genomic features of gyroviruses in a remote neotropical rainforest. The pathogenesis of this virus in avian species or whether GyV11 can infect humans and/or chickens needs to be further investigated.

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“…The assembly of a closely-related chapparvovirus sequence from primate kidney DNA In addition to MKPV/MuCPV, metagenomics or mining of draft genome assemblies has assembled several near-complete chapparvoviral genomes from five mammals (vampire bat (14), fruit bat (20), rat (21), pig (11) and the marsupial Sarcophilus harrisii (Tasmanian devil) (15), three birds (chicken (22), brown mesite (14) and red-crowned crane (23)), and a reptile (the pit viper (14)). Partial genomes lacking substantial 5'-or 3'-coding sequences have also been assembled from numerous species, including from the draft genome of the capuchin monkey (Cebus capucinus imitator) (14).…”

Section: Mkpv Prevalencementioning

confidence: 99%

“…(C) Maps (same scale, colours and symbols as panel A) indicating conserved p10, p15, NS2, NS1 and VP1 ORFs and putative introns in ten other tetrapod chapparvoviral genomes. The sources for the genomes are: (11,14,15,(20)(21)(22)(23). Ragged ends indicate incomplete ORFs that continue beyond the currently available sequence.…”

Section: Competing Interestsmentioning

confidence: 99%

MKPV (aka MuCPV) and related chapparvoviruses are nephro-tropic and encode novel accessory proteins p15 and NS2

Jolly

Lee

Padula

et al. 2019

Preprint

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Mouse kidney parvovirus (MKPV) is a member of the provisional Chapparvovirus genus that causes renal disease in immune-compromised mice, with a disease course reminiscent of polyomavirus-associated nephropathy in immune-suppressed kidney transplant patients. Here we map four MKPV transcripts, created by alternative splicing, to a common transcription initiation region, and use mass spectrometry to identify "p10" and "p15" as novel chapparvovirus accessory proteins produced in MKPV-infected kidneys. p15 and a splicing-dependent putative accessory protein NS2 are conserved in all near-complete tetrapod chapparvovirus genomes currently available (from mammals, birds and a reptile). In contrast, p10 may be encoded only by viruses with >60% amino acid identity to MKPV. We show that MKPV is kidney-tropic and that the bat Nephro-tropic chapparvoviruses 2 chapparvovirus DrPV-1 and a non-human primate chapparvovirus, CKPV, are also found in the kidneys of their hosts. We propose, therefore, that chapparvoviruses with >60% VP1 amino acid identity to MKPV be classified into a genus dubbed Nephroparvovirus, which is consistent with nomenclature for the genus Erythroparvovirus.

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The intestinal virome of malabsorption syndrome-affected and unaffected broilers through shotgun metagenomics

Cited by 62 publications

References 64 publications

Viral metagenomic analysis of chickens with runting-stunting syndrome in the Republic of Korea

Viral metagenomic analysis of chickens with runting-stunting syndrome in the Republic of Korea

A Novel and Divergent Gyrovirus with Unusual Genomic Features Detected in Wild Passerine Birds from a Remote Rainforest in French Guiana

MKPV (aka MuCPV) and related chapparvoviruses are nephro-tropic and encode novel accessory proteins p15 and NS2

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