Assessment of Mutations Associated With Genomic Variants of SARS-CoV-2: RT-qPCR as a Rapid and Affordable Tool to Monitoring Known Circulating Variants in Chile, 2021

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dc.article.number100754
dc.contributor.authorAngulo, Jenniffer
dc.contributor.authorMartinez-Valdebenito, Constanza
dc.contributor.authorPardo-Roa, Catalina
dc.contributor.authorAlmonacid, Leonardo I. I.
dc.contributor.authorFuentes-Luppichini, Eugenia
dc.contributor.authorContreras, Ana Maria
dc.contributor.authorMaldonado, Constanza
dc.contributor.authorLe Corre, Nicole
dc.contributor.authorMelo, Francisco
dc.contributor.authorMedina, Rafael A. A.
dc.contributor.authorFerres, Marcela
dc.date.accessioned2024-01-31T14:30:20Z
dc.date.available2024-01-31T14:30:20Z
dc.date.issued2022
dc.description.abstractSince the first report of SARS-CoV-2 infection in humans, the virus has mutated to develop new viral variants with higher infection rates and more resistance to neutralization by antibodies elicited after natural SARS-CoV-2 infection or by vaccines. Therefore, rapid identification of viral variants circulating in the population is crucial for epidemiological assessment and efforts to contain the resurgence of the pandemic. Between January and November 2021, we performed a large variant RT-qPCR-based screening of mutations in the spike protein of 1851 SARS-CoV-2-positive samples derived from outpatients from the UC-Christus Health Network in Chile. In a portion of samples (n = 636), we validated our RT-qPCR-pipeline by WGS, obtaining a 99.2% concordance. Our results indicate that from January to March 2021 there was a dominance of non-identifiable variants by the RT-qPCR-based screening; however, throughout WGS we were able to identify the Lambda (C.37) variant of interest (VOI). From March to July, we observed the rapid emergence of mutations associated with the Gamma variant (P.1), which was quickly replaced by the appearance of a combination of samples harboring mutations associated with the Delta variant (B.1.617.2), which predominated until the end of the study. Our results highlight the applicability of cost-effective RT-qPCR-based screening of mutations associated with known variants of concern (VOC), VOI and variants under monitoring (VUM) of SARS-CoV-2, being a rapid and reliable tool that complements WGS-based surveillance.
dc.description.funderAgencia Nacional de Investigacion y Desarrollo (ANID)
dc.description.funderANID/Millennium Science Initiative
dc.fechaingreso.objetodigital2024-10-22
dc.format.extent14 páginas
dc.fuente.origenWOS
dc.identifier.doi10.3389/fmed.2022.841073
dc.identifier.eisbn978-3-030-28856-3
dc.identifier.eissn2296-858X
dc.identifier.isbn978-3-030-28855-6
dc.identifier.issn2352-8273
dc.identifier.pubmedidMEDLINE:34181007
dc.identifier.scopusidSCOPUS_ID:85113148921
dc.identifier.urihttps://doi.org/10.3389/fmed.2022.841073
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/81145
dc.identifier.wosidWOS:000770804000001
dc.information.autorucFacultad de Medicina; Pardo Roa, Catalina; S/I; 225251
dc.issue.numero7
dc.language.isoen
dc.nota.accesocontenido completo
dc.pagina.final31
dc.pagina.inicio22
dc.publisherSPRINGER INTERNATIONAL PUBLISHING AG
dc.relation.ispartofPediatric Obesity
dc.revistaJOURNALS OF GERONTOLOGY SERIES B-PSYCHOLOGICAL SCIENCES AND SOCIAL SCIENCES
dc.rightsacceso abierto
dc.subjectSARS-CoV-2
dc.subjectvariants of concern (VOCs)
dc.subjectvariants of interest
dc.subjectvariants under monitoring
dc.subjectRT-qPCR-based surveillance
dc.subject.ddc610
dc.subject.deweyMedicina y saludes_ES
dc.subject.ods03 Good Health and Well-being
dc.subject.odspa03 Salud y bienestar
dc.titleAssessment of Mutations Associated With Genomic Variants of SARS-CoV-2: RT-qPCR as a Rapid and Affordable Tool to Monitoring Known Circulating Variants in Chile, 2021
dc.typeartículo
dc.volumen9
sipa.codpersvinculados225251
sipa.indexWOS
sipa.trazabilidadCarga SIPA;31-01-2024
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