About: Metagenomic analysis of the RNA fraction of the fecal virome indicates high diversity in pigs infected by porcine endemic diarrhea virus in the United States

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About: Metagenomic analysis of the RNA fraction of the fecal virome indicates high diversity in pigs infected by porcine endemic diarrhea virus in the United States Goto Sponge NotDistinct Permalink

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Metagenomic analysis of the RNA fraction of the fecal virome indicates high diversity in pigs infected by porcine endemic diarrhea virus in the United States
Creator	Chen, Qi Yoon, Kyoung-Jin Gauger, Phillip Harmon, Karen Zhang, Jianqiang Guo, Baoqing Wang, Leyi Main, Rodger Li, Ganwu Zheng, Ying
Source	Medline; PMC
abstract	BACKGROUND: Emergence and re-emergence of porcine epidemic diarrhea virus (PEDV) in North America, Asia and Europe has caused severe economic loss to the global swine industry. However, the virome of PEDV infected pigs and its effect on disease severity remains unknown. The advancements of sequencing technology have made it possible to characterize the entire microbiome of different body sites for any host. METHODS: The objective of this study was to characterize the RNA virome in PEDV-positive pigs using the hypothesis-free metagenomics approach based on next-generation sequencing. Specifically, 217 PEDV-positive swine fecal swab samples collected from diarrheic piglets over 17 US states during 2015–2016 were analyzed. RESULTS: A Kraken algorithm-based bioinformatics analysis revealed the presence of up to 9 different RNA genera besides PEDV (Alphacoronavirus genus), including Mamastrovirus (52%, 113/217), Enterovirus (39%, 85/217), Sapelovirus (31%, 67/217), Posavirus (30%, 66/217), Kobuvirus (23%, 49/217), Sapovirus (13%, 28/217), Teschovirus (10%, 22/217), Pasivirus (9%, 20/217), and Deltacoronavirus (3%, 6/217). There were 58 out of 217 piglets (27%) have PEDV infection alone whereas the remaining 159 (73%) shed 2 up to 9 different viruses. CONCLUSION: These findings demonstrated that PEDV infected diarrheic pigs had an extensive RNA viral flora consisting of four different families: Astroviridae, Picornaviridae, Caliciviridae, and Coronaviridae.
has issue date	2018-05-25(xsd:dateTime)
bibo:doi	10.1186/s12985-018-1001-z
bibo:pmid	29801460
has license	cc-by
sha1sum (hex)	58432d2ad49266df441de364700684534498b777
schema:url	https://doi.org/10.1186/s12985-018-1001-z
resource representing a document's title	Metagenomic analysis of the RNA fraction of the fecal virome indicates high diversity in pigs infected by porcine endemic diarrhea virus in the United States
has PubMed Central identifier	PMC5970503
has PubMed identifier	29801460
schema:publication	Virol J
resource representing a document's body	covid:58432d2ad49266df441de364700684534498b777#body_text
is schema:about of	named entity 'Europe' named entity 'swine' named entity '2016' named entity 'infection' named entity 'North America' named entity 'RNA' named entity 'endemic' named entity 'VIRUS' named entity 'ANALYSIS' named entity 'BACKGROUND' named entity 'EMERGENCE' named entity 'DISEASE SEVERITY' named entity 'THESE' named entity 'CALICIVIRIDAE' named entity 'SAPELOVIRUS' named entity 'OBJECTIVE' named entity 'INFECTED' named entity 'HIGH' named entity 'UNITED STATES' named entity 'TO CHARACTERIZE' named entity 'GLOBAL' named entity 'COLLECTED' named entity 'MICROBIOME' named entity 'FECAL' named entity 'PIGS' named entity 'SWAB' named entity 'POSAVIRUS' named entity 'KRAKEN' named entity 'PASIVIRUS' named entity 'POSITIVE' named entity 'BIOINFORMATICS ANALYSIS' named entity 'SAMPLES' named entity '283' named entity 'INFECTED' named entity 'INFECTION' named entity 'FINDINGS' named entity 'FAMILIES' named entity 'CORONAVIRIDAE' named entity 'BASED' named entity 'ENTIRE' named entity 'NORTH AMERICA' named entity 'ENDEMIC' named entity 'UP TO' named entity 'METAGENOMICS' named entity 'STUDY' named entity 'REMAINING' named entity 'DIFFERENT' named entity 'PIGS' named entity 'RNA' named entity 'DIVERSITY' named entity 'RNA' named entity 'FRACTION OF' named entity 'PORCINE' named entity 'UNKNOWN' named entity 'PORCINE EPIDEMIC DIARRHEA VIRUS' named entity 'FLORA' named entity 'VIRUSES' named entity 'HOST' named entity 'ALGORITHM' named entity 'ECONOMIC LOSS' named entity 'EXTENSIVE' named entity 'SEVERE' named entity 'EUROPE' named entity 'SAPOVIRUS' named entity 'HYPOTHESIS' named entity 'HAVE' named entity 'STATES' named entity 'ANALYZED' named entity 'EFFECT' named entity 'SITES' named entity 'VIRAL' named entity 'NEXT-GENERATION SEQUENCING'

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