Frequency of Atypical Mutations in the Spike Glycoprotein in SARS-CoV-2 Circulating from July 2020 to July 2022 in Central Italy : A Refined Analysis by Next Generation Sequencing
In this study, we provided a retrospective overview in order to better define SARS-CoV-2 variants circulating in Italy during the first two years of the pandemic, by characterizing the spike mutational profiles and their association with viral load (expressed as ct values), N-glycosylation pattern, hospitalization and vaccination. Next-generation sequencing (NGS) data were obtained from 607 individuals (among them, 298 vaccinated and/or 199 hospitalized). Different rates of hospitalization were observed over time and among variants of concern (VOCs), both in the overall population and in vaccinated individuals (Alpha: 40.7% and 31.3%, Beta: 0%, Gamma: 36.5% and 44.4%, Delta: 37.8% and 40.2% and Omicron: 11.2% and 7.1%, respectively, both p-values < 0.001). Approximately 32% of VOC-infected individuals showed at least one atypical major spike mutation (intra-prevalence > 90%), with a distribution differing among the strains (22.9% in Alpha, 14.3% in Beta, 41.8% in Gamma, 46.5% in Delta and 15.4% in Omicron, p-value < 0.001). Overall, significantly less atypical variability was observed in vaccinated individuals than unvaccinated individuals; nevertheless, vaccinated people who needed hospitalization showed an increase in atypical variability compared to vaccinated people that did not need hospitalization. Only 5/607 samples showed a different putative N-glycosylation pattern, four within the Delta VOC and one within the Omicron BA.2.52 sublineage. Interestingly, atypical minor mutations (intra-prevalence < 20%) were associated with higher Ct values and a longer duration of infection. Our study reports updated information on the temporal circulation of SARS-CoV-2 variants circulating in Central Italy and their association with hospitalization and vaccination. The results underline how SARS-CoV-2 has changed over time and how the vaccination strategy has contributed to reducing severity and hospitalization for this infection in Italy.
Medienart: |
E-Artikel |
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Erscheinungsjahr: |
2023 |
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Erschienen: |
2023 |
Enthalten in: |
Zur Gesamtaufnahme - volume:15 |
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Enthalten in: |
Viruses - 15(2023), 8 vom: 09. Aug. |
Sprache: |
Englisch |
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Beteiligte Personen: |
Bellocchi, Maria Concetta [VerfasserIn] |
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Links: |
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Themen: |
COVID-19 |
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Anmerkungen: |
Date Completed 28.08.2023 Date Revised 07.09.2023 published: Electronic Citation Status MEDLINE |
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doi: |
10.3390/v15081711 |
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funding: |
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Förderinstitution / Projekttitel: |
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PPN (Katalog-ID): |
NLM361302371 |
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245 | 1 | 0 | |a Frequency of Atypical Mutations in the Spike Glycoprotein in SARS-CoV-2 Circulating from July 2020 to July 2022 in Central Italy |b A Refined Analysis by Next Generation Sequencing |
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520 | |a In this study, we provided a retrospective overview in order to better define SARS-CoV-2 variants circulating in Italy during the first two years of the pandemic, by characterizing the spike mutational profiles and their association with viral load (expressed as ct values), N-glycosylation pattern, hospitalization and vaccination. Next-generation sequencing (NGS) data were obtained from 607 individuals (among them, 298 vaccinated and/or 199 hospitalized). Different rates of hospitalization were observed over time and among variants of concern (VOCs), both in the overall population and in vaccinated individuals (Alpha: 40.7% and 31.3%, Beta: 0%, Gamma: 36.5% and 44.4%, Delta: 37.8% and 40.2% and Omicron: 11.2% and 7.1%, respectively, both p-values < 0.001). Approximately 32% of VOC-infected individuals showed at least one atypical major spike mutation (intra-prevalence > 90%), with a distribution differing among the strains (22.9% in Alpha, 14.3% in Beta, 41.8% in Gamma, 46.5% in Delta and 15.4% in Omicron, p-value < 0.001). Overall, significantly less atypical variability was observed in vaccinated individuals than unvaccinated individuals; nevertheless, vaccinated people who needed hospitalization showed an increase in atypical variability compared to vaccinated people that did not need hospitalization. Only 5/607 samples showed a different putative N-glycosylation pattern, four within the Delta VOC and one within the Omicron BA.2.52 sublineage. Interestingly, atypical minor mutations (intra-prevalence < 20%) were associated with higher Ct values and a longer duration of infection. Our study reports updated information on the temporal circulation of SARS-CoV-2 variants circulating in Central Italy and their association with hospitalization and vaccination. The results underline how SARS-CoV-2 has changed over time and how the vaccination strategy has contributed to reducing severity and hospitalization for this infection in Italy | ||
650 | 4 | |a Journal Article | |
650 | 4 | |a Research Support, Non-U.S. Gov't | |
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700 | 1 | |a Iannetta, Marco |e verfasserin |4 aut | |
700 | 1 | |a Marchegiani, Greta |e verfasserin |4 aut | |
700 | 1 | |a Piermatteo, Lorenzo |e verfasserin |4 aut | |
700 | 1 | |a Coppola, Luigi |e verfasserin |4 aut | |
700 | 1 | |a Tedde, Simona |e verfasserin |4 aut | |
700 | 1 | |a Duca, Leonardo |e verfasserin |4 aut | |
700 | 1 | |a Malagnino, Vincenzo |e verfasserin |4 aut | |
700 | 1 | |a Ansaldo, Lorenzo |e verfasserin |4 aut | |
700 | 1 | |a Braccialarghe, Neva |e verfasserin |4 aut | |
700 | 1 | |a D Anna, Stefano |e verfasserin |4 aut | |
700 | 1 | |a Santoro, Maria Mercedes |e verfasserin |4 aut | |
700 | 1 | |a Di Lorenzo, Andrea |e verfasserin |4 aut | |
700 | 1 | |a Salpini, Romina |e verfasserin |4 aut | |
700 | 1 | |a Teti, Elisabetta |e verfasserin |4 aut | |
700 | 1 | |a Svicher, Valentina |e verfasserin |4 aut | |
700 | 1 | |a Andreoni, Massimo |e verfasserin |4 aut | |
700 | 1 | |a Sarmati, Loredana |e verfasserin |4 aut | |
700 | 1 | |a Ceccherini-Silberstein, Francesca |e verfasserin |4 aut | |
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