About: Comprehensive codon usage analysis of porcine deltacoronavirus

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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	Comprehensive codon usage analysis of porcine deltacoronavirus
Creator	Su, Shuo Li, Gairu Wang, Ruyi Zhou, Jiyong Wang, Ningning He, Wei Guan, Haifei Shi, Xinze Tan, Jimin Yang, Yichen Ye, Rui Zheng, Yuna
source	Elsevier; Medline; PMC
abstract	Porcine deltacoronavirus (PDCoV) is a newly identified coronavirus of pigs that was first reported in Hong Kong in 2012. Since then, many PDCoV isolates have been identified worldwide. In this study, we analyzed the codon usage pattern of the S gene using complete coding sequences and complete PDCoV genomes to gain a deeper understanding of their genetic relationships and evolutionary history. We found that during evolution three groups evolved with a relatively low codon usage bias (effective number of codons (ENC) of 52). The factors driving bias were complex. However, the primary element influencing the codon bias of PDCoVs was natural selection. Our results revealed that different natural environments may have a significant impact on the genetic characteristics of the strains. In the future, more epidemiological surveys are required to examine the factors that resulted in the emergence and outbreak of this virus.
has issue date	2019-09-16(xsd:dateTime)
bibo:doi	10.1016/j.ympev.2019.106618
bibo:pmid	31536759
has license	no-cc
sha1sum (hex)	d39f04584293e05c47a5c4039a8c76b69c1f473a
schema:url	https://doi.org/10.1016/j.ympev.2019.106618
resource representing a document's title	Comprehensive codon usage analysis of porcine deltacoronavirus
has PubMed Central identifier	PMC7111727
has PubMed identifier	31536759
schema:publication	Mol Phylogenet Evol
resource representing a document's body	covid:d39f04584293e05c47a5c4039a8c76b69c1f473a#body_text
is schema:about of	named entity 'genomes' named entity 'genetic' named entity 'future' named entity 'natural' named entity 'Porcine' covid:arg/d39f04584293e05c47a5c4039a8c76b69c1f473a named entity 'epidemiological' named entity 'surveys' named entity 'evolution' named entity 'codon' named entity 'impact' named entity 'However' named entity 'complete' named entity 'deltacoronavirus' named entity 'deeper understanding' named entity 'genomes' named entity 'evolution' named entity 'coding sequences' named entity 'gene' named entity 'porcine' named entity 'outbreak' named entity 'gene' named entity 'expressed genes' named entity 'mutation pressure' named entity 'nucleotide' named entity 'GC3' named entity 'Vietnam' named entity 'codon usage bias' named entity 'DNA viruses' named entity 'genomes' named entity 'codon usage' named entity 'mutation pressure' named entity 'gene map' named entity 'abscissa' named entity 'GC2' named entity 'gene' named entity 'swine farm' named entity 'stop codons' named entity 'mutation pressure' named entity 'Vietnam' named entity 'mutation pressure' named entity 'amino acid' named entity 'Dinucleotide' named entity 'mutation pressure' named entity 'virus' named entity 'codon usage bias' named entity 'recombination' named entity 'Dinucleotide' named entity 'genomes' named entity 'genomes' named entity 'natural selection' named entity 'Japan' named entity 'Phylogenetic analysis' named entity 'Codon usage bias' named entity 'Viet Nam' named entity 'codon usage bias' named entity 'China' named entity 'gene' named entity 'GC3' named entity 'antigen' named entity 'China' named entity 'standard curve' named entity 'NCBI' named entity 'PEDV' named entity 'codon usage bias' named entity 'PHEV' named entity 'virus' named entity 'amino acid' named entity 'tRNA' named entity 'genome'

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