About: SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies

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About: SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies Goto Sponge NotDistinct Permalink

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
has title	SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies
Creator	Tsiodras, Sotirios Bousali, Maria Karamitros, Timokratis Mentis, Andreas Mexias, Anastasios Papadopoulou, Gethsimani
Source	Elsevier; Medline; PMC
abstract	In December 2019, an outbreak of atypical pneumonia (Coronavirus disease 2019 -COVID-19) associated with a novel coronavirus (SARS-CoV-2) was reported in Wuhan city, Hubei province, China. The outbreak was traced to a seafood wholesale market and human to human transmission was confirmed. The rapid spread and the death toll of the new epidemic warrants immediate intervention. The intra-host genomic variability of SARS-CoV-2 plays a pivotal role in the development of effective antiviral agents and vaccines, as well as in the design of accurate diagnostics. We analyzed NGS data derived from clinical samples of three Chinese patients infected with SARS-CoV-2, in order to identify small- and large-scale intra-host variations in the viral genome. We identified tens of low- or higher- frequency single nucleotide variations (SNVs) with variable density across the viral genome, affecting 7 out of 10 protein-coding viral genes. The majority of these SNVs (72/104) corresponded to missense changes. The annotation of the identified SNVs but also of all currently circulating strain variations revealed colocalization of intra-host as well as strain specific SNVs with primers and probes currently used in molecular diagnostics assays. Moreover, we de-novo assembled the viral genome, in order to isolate and validate intra-host structural variations and recombination breakpoints. The bioinformatics analysis disclosed genomic rearrangements over poly-A / poly-U regions located in ORF1ab and spike (S) gene, including a potential recombination hot-spot within S gene. Our results highlight the intra-host genomic diversity and plasticity of SARS-CoV-2, pointing out genomic regions that are prone to alterations. The isolated SNVs and genomic rearrangements reflect the intra-patient capacity of the polymorphic quasispecies, which may arise rapidly during the outbreak, allowing immunological escape of the virus, offering resistance to anti-viral drugs and affecting the sensitivity of the molecular diagnostics assays.
has issue date	2020-08-11(xsd:dateTime)
bibo:doi	10.1016/j.jcv.2020.104585
bibo:pmid	32818852
has license	no-cc
sha1sum (hex)	3c4d0a00950d1c771e5141749d31572c5a5a66b7
schema:url	https://doi.org/10.1016/j.jcv.2020.104585
resource representing a document's title	SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies
has PubMed Central identifier	PMC7418792
has PubMed identifier	32818852
schema:publication	J Clin Virol
resource representing a document's body	covid:3c4d0a00950d1c771e5141749d31572c5a5a66b7#body_text
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