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dc.contributor.authorCarvalho Correia, Eduarda
dc.contributor.authorCalçada, Carla
dc.contributor.authorBranca, Fernando
dc.contributor.authorEstevez Gomez, Nuria 
dc.contributor.authorDe Chiara Prada, Loretta 
dc.contributor.authorVarela Rouco, Nair 
dc.contributor.authorGallego Garcia, Maria Del Pilar 
dc.contributor.authorPosada González, David 
dc.contributor.authorSousa, Hugo
dc.contributor.authorSousa, João
dc.contributor.authorVeiga, Maria Isabel
dc.contributor.authorOsório, Nuno S.
dc.date.accessioned2022-01-10T12:32:04Z
dc.date.available2022-01-10T12:32:04Z
dc.date.issued2021-09-26
dc.identifier.citationBiomedicines, 9(10): 1314 (2021)en
dc.identifier.issn22279059
dc.identifier.urihttp://hdl.handle.net/11093/2951
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.en
dc.description.sponsorshipFundação para a Ciência e a Tecnologia | Ref. UIDB / 50026/2020spa
dc.description.sponsorshipFundação para a Ciência e a Tecnologia | Ref. UIDP / 50026/2020spa
dc.description.sponsorshipFundação para a Ciência e a Tecnologia | Ref. 2020.03113.CEECINDspa
dc.description.sponsorshipXunta de Galicia | Ref. CT850A-2spa
dc.description.sponsorshipEuropean Commission | Ref. NORTE-01-0145-FEDER-072555spa
dc.description.sponsorshipEuropean Commission | Ref. NORTE-01-0145- FEDER-000039spa
dc.language.isoengspa
dc.publisherBiomedicinesspa
dc.rightsAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.titleOmniSARS2: a highly sensitive and specific RT-qPCR-based COVID-19 diagnostic method designed to withstand SARS-CoV-2 lineage evolutionen
dc.typearticlespa
dc.rights.accessRightsopenAccessen
dc.identifier.doi10.3390/biomedicines9101314
dc.identifier.editorhttps://www.mdpi.com/2227-9059/9/10/1314spa
dc.publisher.departamentoBioquímica, xenética e inmunoloxíaspa
dc.publisher.grupoinvestigacionXenómica e Biomedicinaspa
dc.subject.unesco2420.08 Virus Respiratoriosspa
dc.subject.unesco3202 Epidemiologíaspa
dc.subject.unesco2412 Inmunologíaspa
dc.date.updated2022-01-10T12:23:37Z
dc.computerCitationpub_title=Biomedicines|volume=9|journal_number=10|start_pag=1314|end_pag=spa
dc.referencesThe following reagent was obtained through BEI Resources, NIAID, NIH: Human Coronavirus, 229E, NR-52726; Human Coronavirus, OC43, NR-52725; Genomic RNA from Human Coronavirus (HCoV), NL63, NR-44105.en


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    Attribution 4.0 International
    Except where otherwise noted, this item's license is described as Attribution 4.0 International