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Article

OmniSARS2: A Highly Sensitive and Specific RT-qPCR-Based COVID-19 Diagnostic Method Designed to Withstand SARS-CoV-2 Lineage Evolution

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Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
2
ICVS/3B’s—PT Government Associate Laboratory, 4806-909 Guimarães, Portugal
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Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
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Hospital de Braga, 4710-243 Braga, Portugal
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CINBIO, Universidade de Vigo, 36310 Vigo, Spain
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Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36213 Vigo, Spain
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Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310 Vigo, Spain
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Virology Service and Molecular Oncology and Viral Pathology Group (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal
*
Authors to whom correspondence should be addressed.
Shared senior authorship.
Academic Editor: Thomas Mohr
Biomedicines 2021, 9(10), 1314; https://doi.org/10.3390/biomedicines9101314
Received: 15 July 2021 / Revised: 15 September 2021 / Accepted: 21 September 2021 / Published: 26 September 2021
(This article belongs to the Special Issue Bioinformatics and Its Application in Biomedicine)
Extensive 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. View Full-Text
Keywords: SARS-CoV-2; COVID-19; RT-qPCR; B.1.1.7 SARS-CoV-2; COVID-19; RT-qPCR; B.1.1.7
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MDPI and ACS Style

Carvalho-Correia, E.; Calçada, C.; Branca, F.; Estévez-Gómez, N.; De Chiara, L.; Varela, N.; Gallego-García, P.; Posada, D.; Sousa, H.; Sousa, J.; Veiga, M.I.; Osório, N.S. OmniSARS2: A Highly Sensitive and Specific RT-qPCR-Based COVID-19 Diagnostic Method Designed to Withstand SARS-CoV-2 Lineage Evolution. Biomedicines 2021, 9, 1314. https://doi.org/10.3390/biomedicines9101314

AMA Style

Carvalho-Correia E, Calçada C, Branca F, Estévez-Gómez N, De Chiara L, Varela N, Gallego-García P, Posada D, Sousa H, Sousa J, Veiga MI, Osório NS. OmniSARS2: A Highly Sensitive and Specific RT-qPCR-Based COVID-19 Diagnostic Method Designed to Withstand SARS-CoV-2 Lineage Evolution. Biomedicines. 2021; 9(10):1314. https://doi.org/10.3390/biomedicines9101314

Chicago/Turabian Style

Carvalho-Correia, Eduarda, Carla Calçada, Fernando Branca, Nuria Estévez-Gómez, Loretta De Chiara, Nair Varela, Pilar Gallego-García, David Posada, Hugo Sousa, João Sousa, Maria Isabel Veiga, and Nuno S. Osório. 2021. "OmniSARS2: A Highly Sensitive and Specific RT-qPCR-Based COVID-19 Diagnostic Method Designed to Withstand SARS-CoV-2 Lineage Evolution" Biomedicines 9, no. 10: 1314. https://doi.org/10.3390/biomedicines9101314

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