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
Authors: Herranz Marta , Buenestado-Serrano Sergio , Martín-Escolano Javier , Molero-Salinas Andrea , Alonso Roberto , Catalán Pilar , Muñoz Patricia , García de Viedma Darío , Pérez-Lago Laura ,   Gregorio Marañón Microbiology-ID COVID 19 Study Group, Alcalá Luis , Aldámiz Teresa , Alonso Roberto , Álvarez Beatriz , Álvarez-Uría Ana , Arias Alexi , Bermúdez Elena , Bouza Emilio , Burillo Almudena , Carrillo Raquel , Catalán Pilar , Cercenado Emilia , Cobos Alejandro , Díez Cristina , Escribano Pilar , Estévez Agustín , Fanciulli Chiara , Galar Alicia , García M Dolores , García de Viedma Darío , Gijón Paloma , González Adolfo , Guillén Helmuth , Guinea Jesús , Irigoyen Álvaro , Haces Laura Vanessa , Kestler Martha , López Juan Carlos , Losada Carmen Narcisa , Machado Marina , Marín Mercedes , Martín-Rabadán Pablo , Montilla Pedro , Muñoz Patricia , Olmedo María , Padilla Belén , Palomo María , Pérez-Granda María Jesús , Pérez-Lago Laura , Pérez Leire , Reigadas Elena , Rincón Cristina , Rodríguez Belén , Rodríguez Sara , Rojas Adriana , Ruiz-Serrano María Jesús , Sánchez Carlos , Sánchez Mar , Serrano Julia , Tejerina Francisco , Valerio Maricela , Veintimilla M Cristina , Vesperinas Lara , Vicente Teresa , de la Villa Sofía 
Published: September 2023

ABSTRACT
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.