ArticleVirology journal2018
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.
Article in Virology journal, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers, 1 of them a synthesis that pooled it.
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Who cites it
53 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Virus Metagenomics in Farm Animals: A Systematic Review.Viruses · 2020Pooled it
- Genomic epidemiology, evolution, and transmission dynamics of porcine sapelovirus associated with diarrheic piglets.Virulence · 2026Article
- RNA in Plasma Extracellular Vesicles of Adolescent Rhesus Macaques Reveals Immune, Bioenergetic, and Microbial Imprints of Early-Life Adversity: An Exploratory Analysis.Biological psychiatry · 2026Article
- Molecular insights into astrovirus, kobuvirus and rotavirus a coinfection in pigs (Sus domesticus) from Haryana, India.Tropical animal health and production · 2026Article
- Experimental Porcine Astrovirus 4-Associated Tracheitis and Bronchitis in Pigs.Transboundary and emerging diseases · 2026Article
- Metagenomic characterization of the porcine respiratory virome on farms in northern Kazakhstan.Frontiers in veterinary science · 2026Article
- Active surveillance for influenza A virus in swine reveals within-farm reassortment and cocirculation of distinct subtypes and genetic clades.Veterinary microbiology · 2025Article
- Gut Virome and Aging: Phage-Driven Microbial Stability and Immune Modulation.Aging and disease · 2025Review
- Isolation and characterization of avian metapneumovirus subtypes A and B associated with the 2024 disease outbreaks among poultry in the USA.Journal of clinical microbiology · 2025Article
- Metagenomic Investigation of Pathogenic RNA Viruses Causing Diarrhea in Sika Deer Fawns.Viruses · 2025Article
- Epidemiological Study and Genetic Diversity Assessment of Porcine Epidemic Diarrhea Virus (PEDV) in Yunnan Province, China.Viruses · 2025Article
- Exploring viral diversity in diarrheic porcine feces: a metagenomic analysis from an Indian swine farm.Frontiers in cellular and infection microbiology · 2025Article
- Investigation of Transmission and Evolution of PEDV Variants and Co-Infections in Northeast China from 2011 to 2022.Animals : an open access journal from MDPI · 2024Article
- Article
- Evaluation of different genomic regions of rotavirus B and rotavirus C for development of real-time RT‒PCR assays.Virology journal · 2024Article
- Modulation of Equid Herpesvirus-1 Replication DynamicsViruses · 2024Article
- Phylogenetic analysis and molecular characterization of the co-infection of the new variant of the porcine epidemic diarrhea virus and the novel porcine kobuvirus isolated from piglets with diarrhea.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2023Article
- A Customized Novel Blocking ELISA for Detection of Bat-Origin Swine Acute Diarrhea Syndrome Coronavirus Infection.Microbiology spectrum · 2023Article
- Porcine Sapovirus in Northern Vietnam: Genetic Detection and Characterization Reveals Co-Circulation of Multiple Genotypes.Veterinary sciences · 2023Article
- Development of an indirect ELISA method based on the VP1 protein for detection of IgG antibodies against porcine sapelovirus.Canadian journal of veterinary research = Revue canadienne de recherche veterinaire · 2023Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
backgroundEmergence 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.
methodsThe 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.
resultsA 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.
conclusionThese findings demonstrated that PEDV infected diarrheic pigs had an extensive RNA viral flora consisting of four different families: Astroviridae, Picornaviridae, Caliciviridae, and Coronaviridae.
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