Multiplex RT-qPCR strategy for SARS-CoV-2 variants detection in developing countries without ngs: The Bolivian experience

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dc.catalogadorjlo
dc.contributor.authorParrado, Rudy
dc.contributor.authorCuba-Grandy, Carolina X.
dc.contributor.authorFuentes-Luppichini, Eugenia
dc.contributor.authorVillarroel, Nattaly Grecia Torrico
dc.contributor.authorMamani-Ortiz, Yercin
dc.contributor.authorMéndez, Jacqueline
dc.contributor.authorMelgarejo, Betty
dc.contributor.authorCoronado-Arrázola, Irenice
dc.contributor.authorMontaño, Nair A.
dc.contributor.authorAlmonacid Cárdenas, Leonardo Iván
dc.contributor.authorMedina, Rafael A.
dc.contributor.authorGarcia, Lineth
dc.contributor.authorPardo Roa, Catalina
dc.date.accessioned2025-12-15T12:28:59Z
dc.date.available2025-12-15T12:28:59Z
dc.date.issued2025
dc.description.abstractThe rapid evolution of SARS-CoV-2 has led to the emergence of variants of concern (VOCs) characterized by increased transmissibility, pathogenicity, and resistance to neutralizing antibodies. Identifying these variants is essential for guiding public health efforts to control COVID-19. Although whole genome sequencing (WGS) is the gold standard for variant identification, its implementation is often limited in developing countries due to resource constraints. In Bolivia, genomic surveillance is a challenge due to its limited technological infrastructure and resources. An RT-qPCR-based strategy was designed to address these limitations and detect the mutations associated with VOCs and variants of interest (VOIs). The multiplex RT-qPCR commercial kits AllplexTM Master and Variants I (Seegene®) and the ValuPanelTM (Biosearch®) were used to target mutations such as HV69/70del, E484K, N501Y, P681H, and K417N/T. They are characteristic of the Alpha (B.1.1.7), Beta (B.1.531), Gamma (P.1), Omicron (B.1.1.529), Mu (B.1.621), and Zeta (P.2) variants. A total of 157 samples collected in Cochabamba from January to November 2021 were evaluated, identifying 44 Gamma, 2 Zeta, 20 Mu, and 10 Omicron were identified. The strategy’s effectiveness was validated against WGS data generated with Oxford NanoporeTM technology, showing a concordance rate of 0.96. This highlights the value of the RT-qPCR strategy in guiding the selection of samples for WGS, enabling broader detection of new variants that cannot be identified by RT-qPCR alone.
dc.fechaingreso.objetodigital2025-12-15
dc.format.extent4 páginas
dc.fuente.origenORCID
dc.identifier.doi10.1017/S095026882510037X
dc.identifier.urihttps://doi.org/10.1017/S095026882510037X
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/107403
dc.information.autorucFacultad de Ciencias Biológicas; Almonacid Cárdenas, Leonardo Iván; S/I; 250112
dc.information.autorucFacultad de Ciencias Biológicas; Pardo Roa, Catalina; 0000-0002-5409-225X; 225251
dc.language.isoen
dc.nota.accesocontenido completo
dc.revistaEpidemiology and Infection
dc.rightsacceso abierto
dc.subject.ddc610
dc.subject.ods03 Good health and well-being
dc.subject.odspa03 Salud y bienestar
dc.titleMultiplex RT-qPCR strategy for SARS-CoV-2 variants detection in developing countries without ngs: The Bolivian experience
dc.typeartículo
dc.volumen153
sipa.codpersvinculados250112
sipa.codpersvinculados225251
sipa.trazabilidadORCID;2025-12-09
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