RT Journal Article
T1 Alternative molecular and genomic strategies to provide a rapid response to alerts concerning the introduction of new emerging SARS-CoV-2 variants: the Omicron alert
A1 Herranz, Marta
A1 Buenestado Serrano, Sergio
A1 Martín Escolano, Javier
A1 Molero Salinas, Andrea
A1 Alonso Fernández, Roberto Alfonso
A1 Catalán Alonso, Pilar
A1 Muñoz García, Patricia Carmen
A1 García de Viedma, Darío
A1 Pérez Lago, Laura
A1 Alcalá Hernández, Luis
A1 Bouza Santiago, Emilio
A1 Burillo Albizua, Almudena
A1 Kestler Hernández, Martha Jeannette
A1 Martín-Rabadán Caballero, Pablo
AB Este estudio describe y compara cuatro estrategias moleculares y genómicas alternativas para la detección rápida de variantes emergentes de SARS-CoV-2, evaluadas durante la alerta generada por el primer caso sospechoso de la variante Ómicron en España en noviembre de 2021. Las estrategias incluyen: (1) cribado rápido mediante RT-PCR con análisis de curvas de fusión dirigidas a mutaciones clave del gen S; (2) secuenciación ultrarrápida del genoma completo mediante tecnología Oxford Nanopore; (3) secuenciación Sanger de regiones seleccionadas del gen S; y (4) secuenciación del genoma completo mediante tecnología Illumina. Los métodos permitieron una pre-asignación de Ómicron en 2 horas y una confirmación genómica en 3 horas, facilitando una notificación temprana a las autoridades de salud pública. El trabajo demuestra que la combinación de enfoques adaptados a diferentes niveles de recursos técnicos permite responder eficazmente a alertas por variantes de preocupación, optimizando el equilibrio entre rapidez, coste y resolución analítica.
AB During the COVID-19 pandemic, several SARS-CoV-2 variants of concern (VOCs) of particular relevance emerged. Early detection of VOCs entering a country is essential to control spread. The alert triggered by the first suspected case of the Omicron variant in Spain in a traveler arriving from South Africa in November 2021 provided a unique opportunity to evaluate four different methodological strategies tailored to rapid identification of Omicron. The different approaches were designed to respond to the different technical resources available in different settings. First, we used melting probes in RT-PCR to determine the presence of four Omicron signatures (K417N, E484A, P681H, and absence of L452R): three probes showed deviations in temperature (Tm) values relative to the reference codons (E484K-15.8°C, P681H-5.2°C, and L452R-7.2°C) and one maintained the reference value (K417N). The deviation in Tm of P681H suggested the presence of the characteristic Omicron N679K mutation in the probe hybridization region; these data pointed to the presence of Omicron alleles. Second, the presence of 29 of the 33 characteristic single nucleotide polymorphisms (SNPs) in the Omicron variant S-gene was identified by Sanger sequencing of nine amplicons. The final two strategies involved identification of 47 of the 50 non-synonymous and indel mutations attributed to Omicron by rapid nanopore whole genome sequencing (WGS) and by Illumina WGS technology. These strategies enabled us to pre-assign the first Omicron case in Spain with high certainty 2 h after receipt of RNA and to confirm it genomically 3 h later, so that the Public Health authorities could be rapidly notified. IMPORTANCE The study presents different experimental alternatives to identify new variants of concern (VOCs) of SARS-CoV-2 entering a certain population. Early detection of a new VOC is crucial for surveillance and control of spread. The objective is to provide laboratories with tools adapted to their resource capabilities that offer a sufficient level of resolution to rule out, confirm, or pre-assign the presence of a suspected VOC. The study describes four different techniques that were applied simultaneously to the first suspected Omicron case in Spain, highlighting the level of resolution and response time achieved in each case. These techniques are based on the detection of mutations in the S-gene of the virus that can easily adapt to potential emerging variants. The results of the study allow any laboratory to prepare for new alerts of SARS-CoV-2 VOCs.
PB American Society for Microbiology
SN 2165-0497
YR 2023
FD 2023-10-17
LK https://hdl.handle.net/20.500.14352/130200
UL https://hdl.handle.net/20.500.14352/130200
LA eng
NO Herranz M, Buenestado-Serrano S, Martín-Escolano J, Molero-Salinas A, Alonso R, Catalán P, Muñoz P, García de Viedma D, Pérez-Lago L; Gregorio Marañón Microbiology-ID COVID 19 Study Group. Alternative molecular and genomic strategies to provide a rapid response to alerts concerning the introduction of new emerging SARS-CoV-2 variants: the Omicron alert. Microbiol Spectr. 2023 Sep 22;11(5):e0107523. doi: 10.1128/spectrum.01075-23
NO Varios autores pertenecen al grupo de investigación: Gregorio Marañón Microbiology-ID COVID 19 Study Group.Financiado con Fondos FEDER
NO Instituto de Salud Carlos III (España)
NO European Commission
NO Consorcio Centro de Investigación Biomédica en Red (España)
NO Instituto de Investigación sanitaria Gregorio Marañón (España)
DS Docta Complutense
RD 20 ene 2026