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
Author:
Bellocchi Maria Concetta1ORCID, Scutari Rossana2, Carioti Luca1ORCID, Iannetta Marco3ORCID, Marchegiani Greta1, Piermatteo Lorenzo4ORCID, Coppola Luigi3, Tedde Simona3, Duca Leonardo1, Malagnino Vincenzo3ORCID, Ansaldo Lorenzo3ORCID, Braccialarghe Neva3ORCID, D′Anna Stefano1, Santoro Maria Mercedes1ORCID, Di Lorenzo Andrea3ORCID, Salpini Romina1, Teti Elisabetta3, Svicher Valentina4, Andreoni Massimo3, Sarmati Loredana3ORCID, Ceccherini-Silberstein Francesca1,
Affiliation:
1. Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy 2. Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy 3. Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy 4. Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
Abstract
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.
Funder
European Union’s Horizon Europe Research and Innovation Programme Ministero dell’Università e della Ricerca
Subject
Virology,Infectious Diseases
Cited by
1 articles.
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