Please use this identifier to cite or link to this item: http://hdl.handle.net/10316/95897
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dc.contributor.authorCarvalho-Correia, Eduarda-
dc.contributor.authorCalçada, Carla-
dc.contributor.authorBranca, Fernando-
dc.contributor.authorEstévez-Gómez, Nuria-
dc.contributor.authorDe Chiara, Loretta-
dc.contributor.authorVarela, Nair-
dc.contributor.authorGallego-García, Pilar-
dc.contributor.authorPosada, David-
dc.contributor.authorSousa, Hugo-
dc.contributor.authorSousa, João-
dc.contributor.authorVeiga, Maria Isabel-
dc.contributor.authorOsório, Nuno S.-
dc.date.accessioned2021-10-12T11:44:23Z-
dc.date.available2021-10-12T11:44:23Z-
dc.date.issued2021-
dc.identifier.issn2227-9059pt
dc.identifier.urihttp://hdl.handle.net/10316/95897-
dc.description.abstractExtensive transmission of SARS-CoV-2 during the COVID-19 pandemic allowed the generation of thousands of mutations within its genome. While several of these become rare, others largely increase in prevalence, potentially jeopardizing the sensitivity of PCR-based diagnostics. Taking advantage of SARS-CoV-2 genomic knowledge, we designed a one-step probe-based multiplex RT-qPCR (OmniSARS2) to simultaneously detect short fragments of the SARS-CoV-2 genome in ORF1ab, E gene and S gene. Comparative genomics of the most common SARS-CoV-2 lineages, other human betacoronavirus and alphacoronavirus, was the basis for this design, targeting both highly conserved regions across SARS-CoV-2 lineages and variable or absent in other Coronaviridae viruses. The highest analytical sensitivity of this method for SARS-CoV-2 detection was 94.2 copies/mL at 95% detection probability (~1 copy per total reaction volume) for the S gene assay, matching the most sensitive available methods. In vitro specificity tests, performed using reference strains, showed no cross-reactivity with other human coronavirus or common pathogens. The method was compared with commercially available methods and detected the virus in clinical samples encompassing different SARS-CoV-2 lineages, including B.1, B.1.1, B.1.177 or B.1.1.7 and rarer lineages. OmniSARS2 revealed a sensitive and specific viral detection method that is less likely to be affected by lineage evolution oligonucleotide–sample mismatch, of relevance to ensure the accuracy of COVID-19 molecular diagnostic methods. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.pt
dc.description.sponsorshipFunding: This work has been funded by Portuguese National funds, through the Foundation for Science and Technology (FCT) (project UIDB/50026/2020, UIDP/50026/2020 and RESEARCH 4 COVID-19 1st edtion_208; fellowships: PD/BD/127826/2016 to C. C. and contract funding 2020.03113.CEECIND to M.I.V.); by the projects NORTE-01-0145-FEDER-072555 and NORTE-01-0145-FEDER-000039, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). Lineage assignments were provided by the EPICOVIGAL consortium, funded by FONDO SUPERA COVID-19 CRUE/CSIC/Banco Santander and Programa TRASLACIONA COVID-19 (Ref CT850A-2) from Xunta de Galicia.pt
dc.language.isoengpt
dc.relation2020.03113pt
dc.relationNORTE-01-0145-FEDER-000039pt
dc.relationNORTE-01-0145-FEDER-072555pt
dc.relationPD/BD/127826/2016pt
dc.relationRESEARCH 4 COVID-19 1st edtion_208pt
dc.relationUIDB/50026/2020pt
dc.relationUIDP/50026/2020pt
dc.rightsopenAccesspt
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt
dc.subjectB.1.1.7pt
dc.subjectCOVID-19pt
dc.subjectRT-qPCRpt
dc.subjectSARS-CoV-2pt
dc.titleOmniSARS2: A Highly Sensitive and Specific RT-qPCR-Based COVID-19 Diagnostic Method Designed to Withstand SARS-CoV-2 Lineage Evolutionpt
dc.typearticle-
degois.publication.firstPage1314pt
degois.publication.issue10pt
degois.publication.titleBiomedicinespt
dc.peerreviewedyespt
dc.identifier.doi10.3390/biomedicines9101314pt
degois.publication.volume9pt
dc.date.embargo2021-01-01*
uc.date.periodoEmbargo0pt
item.fulltextCom Texto completo-
item.languageiso639-1en-
item.grantfulltextopen-
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