The COVID-19 pandemic was a major challenge for global public health. The responsible etiological agent, namely SARS-CoV-2, has accumulated mutations over time which, in many cases, have given an evolutionary advantage to the virus. From 2020 to date have appeared several viral variants as a result of the acquisition of mutations which have provided the virus with greater transmissibility, resistance to therapies and the ability to evade the immune response developed with previous infections or vaccination. For the monthly monitoring of SARS-CoV-2 by the Istituto Superiore di Sanità, SARS-CoV-2 positive samples were sequenced and analysed using Next Generation Sequencing technology. The aim of the study was to estimate and analyse the variants circulating in the Marche region in the year 2023, to better understand the epidemiological trend, comparing it with the data referring to the entire pandemic period. Omicron recombinant variants, i.e. the XBB lineage and its sub-lineages, emerged in February and substituted the previous Omicron variants. By contrast, different recombinants co-circulated, without replacing each other, until the last months of 2023, when the new variant BA.2.86 was identified for the first time. This variant, phylogenetically linked to the previous Omicron 2 variants, is hypermutated in the S gene compared to the other circulating variants, and it became rapidly the predominant variant in our region. Furthermore, the mutations found in the various clades were analysed in order to characterize the SARS-CoV-2 variants and to study their potential impact viral evolution. The widespread diffusion of the virus and the rise of new viral variants over time, identify SARS-CoV-2 as an important pathogen to study, both in terms of pathogenicity and clinical impact, but also from a genetic-epidemiological point of view. This is fundamental to support the preparedness of the public health system, and the implementation preventive measures, such as vaccination campaigns to limit the number of infections caused by new variants.
La pandemia di COVID-19 ha rappresentato una grande sfida a livello globale per la salute pubblica. L’agente eziologico responsabile, ovvero il SARS-CoV-2, nel corso del tempo ha accumulato mutazioni che in molti casi hanno conferito un vantaggio evolutivo al virus; in particolare, dal 2020 ad oggi si sono susseguite diverse varianti virali scaturite dall’acquisizione di tali mutazioni che hanno fornito al virus maggior trasmissibilità, resistenza alle terapie, ma soprattutto la capacità di evadere le difese immunitarie maturate in seguito a precedenti infezioni o dalla vaccinazione. In occasione del monitoraggio mensile di SARS-CoV-2 indetto dall’Istituto Superiore di Sanità, sono stati sequenziati e analizzati diversi campioni risultati positivi per SARS-CoV-2, mediante tecnologia Next Generation Sequencing. Lo scopo dello studio è stato quello di stimare e analizzare le varianti che hanno circolato nella regione Marche nell’anno 2023, al fine di comprendere meglio l’andamento epidemiologico paragonandolo ai dati riferiti all’intero periodo pandemico. In particolare, nel mese di febbraio si è assistito alla comparsa delle varianti ricombinanti della Omicron, ossia il lineage XBB e le sue derivate, che hanno soppiantato le precedenti varianti della Omicron. In contrasto, i diversi ricombinanti hanno co-circolato senza sostituirsi l’un l’altro, fino alla comparsa, negli ultimi mesi del 2023, di una nuova variante, la BA.2.86. Questa variante, filogeneticamente correlata alle precedenti varianti Omicron 2, è risultata ipermutata nel gene S rispetto le altre varianti in circolazione, diventando rapidamente la variante predominante nella nostra regione. Inoltre, sono state analizzate le mutazioni riscontrate nei vari clades, al fine di caratterizzare le rispettive varianti e studiarne il potenziale impatto. La larga diffusione del virus e la comparsa di nuove varianti virali nel tempo, rendono SARS-CoV-2 un importante patogeno da studiare, sia in termini di patogenicità e di impatto clinico, ma anche da un punto di vista genetico-epidemiologico, affinché i risultati ottenuti possano essere di sostegno alla sanità pubblica per l’attuazione delle misure di prevenzione e di contenimento di eventuali nuove varianti virali, come campagne di vaccinazione.
ANALISI FILOGENETICA E CARATTERIZZAZIONE MOLECOLARE DELLE VARIANTI DI SARS-CoV-2 CIRCOLANTI NEL 2023 NELLA REGIONE MARCHE
PAPARONI, SILVIA
2022/2023
Abstract
The COVID-19 pandemic was a major challenge for global public health. The responsible etiological agent, namely SARS-CoV-2, has accumulated mutations over time which, in many cases, have given an evolutionary advantage to the virus. From 2020 to date have appeared several viral variants as a result of the acquisition of mutations which have provided the virus with greater transmissibility, resistance to therapies and the ability to evade the immune response developed with previous infections or vaccination. For the monthly monitoring of SARS-CoV-2 by the Istituto Superiore di Sanità, SARS-CoV-2 positive samples were sequenced and analysed using Next Generation Sequencing technology. The aim of the study was to estimate and analyse the variants circulating in the Marche region in the year 2023, to better understand the epidemiological trend, comparing it with the data referring to the entire pandemic period. Omicron recombinant variants, i.e. the XBB lineage and its sub-lineages, emerged in February and substituted the previous Omicron variants. By contrast, different recombinants co-circulated, without replacing each other, until the last months of 2023, when the new variant BA.2.86 was identified for the first time. This variant, phylogenetically linked to the previous Omicron 2 variants, is hypermutated in the S gene compared to the other circulating variants, and it became rapidly the predominant variant in our region. Furthermore, the mutations found in the various clades were analysed in order to characterize the SARS-CoV-2 variants and to study their potential impact viral evolution. The widespread diffusion of the virus and the rise of new viral variants over time, identify SARS-CoV-2 as an important pathogen to study, both in terms of pathogenicity and clinical impact, but also from a genetic-epidemiological point of view. This is fundamental to support the preparedness of the public health system, and the implementation preventive measures, such as vaccination campaigns to limit the number of infections caused by new variants.File | Dimensione | Formato | |
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https://hdl.handle.net/20.500.12075/16849