A comparative analysis exposes an amplification delay distinctive to SARS-CoV-2 Omicron variants of clinical and public health relevance

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dc.contributor.authorBrown, Katherine L.en
dc.contributor.authorCeci, Alessandroen
dc.contributor.authorRoby, Clintonen
dc.contributor.authorBriggs, Russell B.en
dc.contributor.authorZiolo, D.en
dc.contributor.authorKorba, R.en
dc.contributor.authorMejia, R.en
dc.contributor.authorKelly, S. T.en
dc.contributor.authorToney, D.en
dc.contributor.authorFriedlander, Michael J.en
dc.contributor.authorFinkielstein, Carla V.en
dc.date.accessioned2023-03-21T16:39:36Zen
dc.date.available2023-03-21T16:39:36Zen
dc.date.issued2023en
dc.description.abstractMutations in the SARS-CoV-2 genome may negatively impact a diagnostic test, have no effect, or turn into an opportunity for rapid molecular screening of variants. Using an in-house Emergency Use Authorized RT-qPCR-based COVID-19 diagnostic assay, we combined sequence surveillance of viral variants and computed PCR efficiencies for mismatched templates. We found no significant mismatches for the N, E, and S set of assay primers until the Omicron variant emerged in late November 2021. We found a single mismatch between the Omicron sequence and one of our assay's primers caused a > 4 cycle delay during amplification without impacting overall assay performance. Starting in December 2021, clinical specimens received for COVID-19 diagnostic testing that generated a Cq delay greater than 4 cycles were sequenced and confirmed as Omicron. Clinical samples without a Cq delay were largely confirmed as the Delta variant. The primer-template mismatch was then used as a rapid surrogate marker for Omicron. Primers that correctly identified Omicron were designed and tested, which prepared us for the emergence of future variants with novel mismatches to our diagnostic assay's primers. Our experience demonstrates the importance of monitoring sequences, the need for predicting the impact of mismatches, their value as a surrogate marker, and the relevance of adapting one's molecular diagnostic test for evolving pathogens.en
dc.description.notesThis work was supported by Fralin Biomedical Research Institute [Grant Number N/A]; Department of General Services of the Commonwealth of Virginia [Grant Number DGS-201020-UVT].en
dc.description.sponsorshipFralin Biomedical Research Institute; Department of General Services of the Commonwealth of Virginia [DGS-201020-UVT]en
dc.description.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1080/22221751.2022.2154617en
dc.identifier.eissn2222-1751en
dc.identifier.issue1en
dc.identifier.other2154617en
dc.identifier.pmid36458572en
dc.identifier.urihttp://hdl.handle.net/10919/114137en
dc.identifier.volume12en
dc.language.isoenen
dc.publisherTaylor & Francisen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectOmicron varianten
dc.subjectSARS-CoV-2en
dc.subjectDelta varianten
dc.subjectRT-qPCRen
dc.subjectdiagnosisen
dc.subjectmismatchen
dc.subjectamplification efficiencyen
dc.subjectCOVID-19en
dc.titleA comparative analysis exposes an amplification delay distinctive to SARS-CoV-2 Omicron variants of clinical and public health relevanceen
dc.title.serialEmerging Microbes & Infectionsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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Scholarly Works, Fralin Biomedical Research Institute at VTC
Scholarly Works, Center for Emerging, Zoonotic, and Arthropod-borne Pathogens (CeZAP)
Scholarly Works, Virginia Tech Carilion School of Medicine (VTCSOM)