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SARS-COV-2 Variants in the region of Lisbon: Comparation and validation study between RT-PCR and NGS methodologies

2023-04-14Other Open access
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dc.contributor.authorFranco, Magda
dc.contributor.authorCainé, Laura
dc.contributor.authorRodrigues, Joana
dc.contributor.authorMofreita, Vânia
dc.contributor.authorNascimento, Rui
dc.contributor.authorMukan, Olena
dc.contributor.authorFadoni, Jennifer
dc.contributor.authorCorte-Real, Francisco
dc.contributor.authorAmorim, António
dc.date.accessioned2024-02-05T16:30:37Z
dc.date.available2024-02-05T16:30:37Z
dc.date.issued2023-04-14
dc.descriptionPoster apresentado no 15ª Reunião Científica da Sociedade Portuguesa de Medicina Laboratorial, Porto, Abril 2023pt_PT
dc.description.abstractSARS-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.pt_PT
dc.description.versionN/Apt_PT
dc.identifier.urihttp://hdl.handle.net/10400.26/49617
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/pt_PT
dc.subjectCOVID-19pt_PT
dc.subjectCadaverspt_PT
dc.subjectAllplex™ SARS-CoV-2 Variants Ipt_PT
dc.subjectAllplex™ SARS-CoV-2 Variants IIpt_PT
dc.subjectAllplex™ SARS-CoV-2 Variants Vpt_PT
dc.subjectDelta variantpt_PT
dc.subjectReal Time PCRpt_PT
dc.titleSARS-COV-2 Variants in the region of Lisbon: Comparation and validation study between RT-PCR and NGS methodologiespt_PT
dc.typeother
dspace.entity.typePublication
oaire.citation.conferencePlaceCentro de Congressos da Alfândega do Porto ( Portugal)pt_PT
oaire.citation.title15ª Reunião Científica da Sociedade Portuguesa de Medicina Laboratorialpt_PT
person.familyNamefranco
person.familyNameCainé
person.familyNameCosta Marcos do Nascimento
person.familyNameFadoni
person.familyNameCorte Real Gonçalves
person.familyNameAmorim
person.givenNamemagda
person.givenNameLaura
person.givenNameRui Francisco
person.givenNameJennifer
person.givenNameFrancisco
person.givenNameAntónio
person.identifierAAR-9087-2020
person.identifier.ciencia-id021A-33DD-869D
person.identifier.ciencia-idCB1A-8B8D-78F1
person.identifier.ciencia-id7715-6D9A-CB35
person.identifier.ciencia-id0B18-918A-80ED
person.identifier.orcid0000-0003-1604-334X
person.identifier.orcid0000-0002-6542-4256
person.identifier.orcid0000-0002-0478-336X
person.identifier.orcid0000-0002-7593-1059
person.identifier.orcid0000-0003-1495-9362
person.identifier.orcid0000-0002-7506-4426
person.identifier.ridA-4414-2013
person.identifier.scopus-author-id2311978
person.identifier.scopus-author-id6603582554
person.identifier.scopus-author-id35253426400
rcaap.rightsopenAccesspt_PT
rcaap.typeotherpt_PT
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