About: Identification and characterization of Coronaviridae genomes from Vietnamese bats and rats based on conserved protein domains

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An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Identification and characterization of Coronaviridae genomes from Vietnamese bats and rats based on conserved protein domains
Creator	Kellam, Paul Cotten, Matthew Baker, Stephen Phan, My Anh, Pham, Hong Consortium, Vizions Tri, Ngo Tue, †
source	Medline; PMC
abstract	The Coronaviridae family of viruses encompasses a group of pathogens with a zoonotic potential as observed from previous outbreaks of the severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus. Accordingly, it seems important to identify and document the coronaviruses in animal reservoirs, many of which are uncharacterized and potentially missed by more standard diagnostic assays. A combination of sensitive deep sequencing technology and computational algorithms is essential for virus surveillance, especially for characterizing novel- or distantly related virus strains. Here, we explore the use of profile Hidden Markov Model-defined Pfam protein domains (Pfam domains) encoded by new sequences as a Coronaviridae sequence classification tool. The encoded domains are used first in a triage to identify potential Coronaviridae sequences and then processed using a Random Forest method to classify the sequences to the Coronaviridae genus level. The application of this algorithm on Coronaviridae genomes assembled from agnostic deep sequencing data from surveillance of bats and rats in Dong Thap province (Vietnam) identified thirty-four Alphacoronavirus and eleven Betacoronavirus genomes. This collection of bat and rat coronaviruses genomes provided essential information on the local diversity of coronaviruses and substantially expanded the number of coronavirus full genomes available from bat and rats and may facilitate further molecular studies on this group of viruses.
has issue date	2018-12-15(xsd:dateTime)
bibo:doi	10.1093/ve/vey035
bibo:pmid	30568804
has license	cc-by
sha1sum (hex)	3c5dd991f2d7b334cc56b2715d73af3fcf1cdca4
schema:url	https://doi.org/10.1093/ve/vey035
resource representing a document's title	Identification and characterization of Coronaviridae genomes from Vietnamese bats and rats based on conserved protein domains
has PubMed Central identifier	PMC6295324
has PubMed identifier	30568804
schema:publication	Virus Evol
resource representing a document's body	covid:3c5dd991f2d7b334cc56b2715d73af3fcf1cdca4#body_text
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