About: Molecular analysis of several in-house rRT-PCR protocols for SARS-CoV-2 detection in the context of genetic variability of the virus in Colombia

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About: Molecular analysis of several in-house rRT-PCR protocols for SARS-CoV-2 detection in the context of genetic variability of the virus in Colombia Goto Sponge NotDistinct Permalink

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Molecular analysis of several in-house rRT-PCR protocols for SARS-CoV-2 detection in the context of genetic variability of the virus in Colombia
Creator	Franco-Muñoz, Carlos Franco-Sierra, Nicolás Laiton-Donato, Katherine Mercado, Marcela Usme-Ciro, José Walteros, Diana Barbosa-Ramirez, Juliana Flórez-Sánchez, Astrid Gómez-Rangel, Sergio Ospina-Martinez, Martha Ospitia-Baez, Erika Co, Aflorez@ins Co, Cefrancom@unal Co, Daalvarezd@unal Co, Dwalteros@ins Co, Eospitia@ins Co, Jbarbosa@ins Co, José Co, Lrodriguez@ins Co, Mmercado@ins Co, Mospina@ins Co, Nfranco@humboldt Co, Nicolás Co, Sgomezr@ins Franco-Sierra, Mercado-Reyes, Marcela Rodríguez-Calderon, Luz Usme-Ciro, Usmec@ucc, Jose
source	Elsevier; Medline; PMC
abstract	The COVID-19 pandemic caused by SARS-CoV-2 is a public health problem unprecedented in the recent history of humanity. Different in-house real-time RT-PCR (rRT-PCR) methods for SARS-CoV-2 diagnosis and the appearance of genomes with mutations in primer regions have been reported. Hence, whole-genome data from locally-circulating SARS-CoV-2 strains contribute to the knowledge of its global variability and the development and fine tuning of diagnostic protocols. To describe the genetic variability of Colombian SARS-CoV-2 genomes in hybridization regions of oligonucleotides of the main in-house methods for SARS-CoV-2 detection, RNA samples with confirmed SARS-CoV-2 molecular diagnosis were processed through next-generation sequencing. Primers/probes sequences from 13 target regions for SARS-CoV-2 detection suggested by 7 institutions and consolidated by WHO during the early stage of the pandemic were aligned with Muscle tool to assess the genetic variability potentially affecting their performance. Finally, the corresponding codon positions at the 3′ end of each primer, the open reading frame inspection was identified for each gene/protein product. Complete SARS-CoV-2 genomes were obtained from 30 COVID-19 cases, representative of the current epidemiology in the country. Mismatches between at least one Colombian sequence and five oligonucleotides targeting the RdRP and N genes were observed. The 3′ end of 4 primers aligned to the third codon position, showed high risk of nucleotide substitution and potential mismatches at this critical position. Genetic variability was detected in Colombian SARS-CoV-2 sequences in some of the primer/probe regions for in-house rRT-PCR diagnostic tests available at WHO COVID-19 technical guidelines; its impact on the performance and rates of false-negative results should be experimentally evaluated. The genomic surveillance of SARS-CoV-2 is highly recommended for the early identification of mutations in critical regions and to issue recommendations on specific diagnostic tests to ensure the coverage of locally-circulating genetic variants.
has issue date	2020-06-04(xsd:dateTime)
bibo:doi	10.1016/j.meegid.2020.104390
bibo:pmid	32505692
has license	no-cc
sha1sum (hex)	54621417dcb47ddb375f6c07fecf959194c49ade
schema:url	https://doi.org/10.1016/j.meegid.2020.104390
resource representing a document's title	Molecular analysis of several in-house rRT-PCR protocols for SARS-CoV-2 detection in the context of genetic variability of the virus in Colombia
has PubMed Central identifier	PMC7272177
has PubMed identifier	32505692
schema:publication	Infect Genet Evol
resource representing a document's body	covid:54621417dcb47ddb375f6c07fecf959194c49ade#body_text
is schema:about of	named entity 'SARS-CoV-2' named entity 'history' named entity 'SARS-CoV-2' named entity 'hybridization' named entity 'performance' named entity 'molecular diagnosis' named entity 'experimentally' named entity 'problem' named entity 'detection' named entity 'sequences' named entity 'primer' named entity 'oligonucleotides' named entity 'positions' named entity 'product' named entity 'virus' named entity 'SARS-CoV-2' named entity 'IN-HOUSE' named entity 'IMPACT' named entity 'GUIDELINES' named entity 'N A' named entity 'GENOMES' named entity 'PANGOLIN' named entity 'VARIABILITY' named entity 'GENETIC DIVERSITY' named entity 'ASSESS' named entity 'OF EACH' named entity 'RATES' named entity 'MOLECULAR DIAGNOSIS' named entity 'EARLY IDENTIFICATION' named entity 'RECOMMENDED' named entity 'POSITION' named entity 'caused' named entity 'Materials' named entity 'inspection' named entity 'oligonucleotides' named entity 'describe' named entity 'mutations' named entity 'regions' named entity 'COVID-19' named entity 'epidemiology' named entity 'representative' named entity 'SARS-CoV-2' named entity 'evaluated' named entity 'genomes' named entity 'highly' named entity 'COVID-19' named entity 'gene' named entity 'public health' named entity 'potential' named entity 'consolidated' named entity 'SARS-CoV-2' named entity 'codon' named entity 'isolate'

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