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- SARS-COV-2 Variants in the region of Lisbon: Comparation and validation study between RT-PCR and NGS methodologiesPublication . Franco, Magda; Cainé, Laura; Rodrigues, Joana; Mofreita, Vânia; Nascimento, Rui; Mukan, Olena; Fadoni, Jennifer; Corte-Real, Francisco; Amorim, AntónioSARS-CoV-2 is a recent coronavirus that appeared in the end of 2019. The World Health Organization named the infection, caused by this new coronavirus, Coronavirus Disease 2019 (COVID-19). This disease was considered a pandemic on March 11th 2020 by the same organization. Coronaviruses rapidly acquire new mutations and, consequently, new variants keep emerging. There are some variants with an associated risk in the increase of the transmissibility and that cause more severe disease and reduction in the neutralization by antibodies and, for this reason, are called variants of concern. The aim of this project was to identify the main VOCs and VOIs circulating in the region of Lisbon, applying the methodology of real time RT-PCR in cadavers that tested positive for SARS-CoV-2. To meet this goal, we used three assays: Allplex™ SARS-CoV-2 Variants I, Allplex™ SARS-CoV-2 Variants II and Allplex™ SARS-CoV-2 Variants V. The first one detects defining mutations of the Alpha, Beta and Gamma variants (N501Y, E454K and HV69/70del), the second assay detects mutations present in the Delta, Beta, Gamma and California variants (L452R, K417T, K417N and W152C) and the third one detects defining mutations of the Delta and Lambda variants (L452R, P681R, L452Q and F690S). In addition, we also wanted to understand if these RT-PCR assays were efficient to correctly identify these variants, comparing the results obtained to the reference methods for the determination of variants – Next Genration Sequencing (NGS). Two different NGS methodologies were used to compare the results – NGS-ONT (Oxford Nanopore Technologies) and NGS-Sanger based. We concluded that 30% of the samples belonged to the Alpha variant and 70% belonged to the Delta variant and that, in general, the three RT-PCR assays applied in this study were efficient in correctly identifying these two variants, based on the comparison to the NGS results.