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
Maria Concetta Bellocchi,
Rossana Scutari,
Luca Carioti,
Marco Iannetta,
Greta Marchegiani,
Lorenzo Piermatteo,
Luigi Coppola,
Simona Tedde,
Leonardo Duca,
Vincenzo Malagnino,
Lorenzo Ansaldo,
Neva Braccialarghe,
Stefano D′Anna,
Maria Mercedes Santoro,
Andrea Di Lorenzo,
Romina Salpini,
Elisabetta Teti,
Valentina Svicher,
Massimo Andreoni,
Loredana Sarmati,
Francesca Ceccherini-Silberstein,
on behalf of the PTV-UTV-ID-COVID Group
Affiliations
Maria Concetta Bellocchi
Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
Rossana Scutari
Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
Luca Carioti
Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
Marco Iannetta
Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
Greta Marchegiani
Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
Lorenzo Piermatteo
Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
Luigi Coppola
Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
Simona Tedde
Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
Leonardo Duca
Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
Vincenzo Malagnino
Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
Lorenzo Ansaldo
Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
Neva Braccialarghe
Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
Stefano D′Anna
Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
Maria Mercedes Santoro
Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
Andrea Di Lorenzo
Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
Romina Salpini
Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
Elisabetta Teti
Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
Valentina Svicher
Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
Massimo Andreoni
Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
Loredana Sarmati
Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
Francesca Ceccherini-Silberstein
Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
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 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.
