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

doi:10.3390/v15081711

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

Viruses. 2023 Aug 9;15(8):1711. doi: 10.3390/v15081711.

Authors

Maria Concetta Bellocchi¹, Rossana Scutari², Luca Carioti¹, Marco Iannetta³, Greta Marchegiani¹, Lorenzo Piermatteo⁴, Luigi Coppola³, Simona Tedde³, Leonardo Duca¹, Vincenzo Malagnino³, Lorenzo Ansaldo³, Neva Braccialarghe³, Stefano D Anna¹, Maria Mercedes Santoro¹, Andrea Di Lorenzo³, Romina Salpini¹, Elisabetta Teti³, Valentina Svicher⁴, Massimo Andreoni³, Loredana Sarmati³, Francesca Ceccherini-Silberstein¹, On Behalf Of The Ptv-Utv-Id-Covid Group

Affiliations

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.

Keywords: COVID-19; N-glycosylation; SARS-CoV-2; epidemiology; spike; variants of concern.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19* / epidemiology
Glycoproteins
High-Throughput Nucleotide Sequencing
Humans
Italy / epidemiology
Mutation
Retrospective Studies
SARS-CoV-2 / genetics
Spike Glycoprotein, Coronavirus* / genetics

Substances

spike protein, SARS-CoV-2
Spike Glycoprotein, Coronavirus
Glycoproteins

Supplementary concepts

SARS-CoV-2 variants

Grants and funding

This project has received the contribution of the EuCARE Project funded by the European Union’s Horizon Europe Research and Innovation Programme under Grant Agreement No 101046016 and on behalf of SARS-CoV-2 ITALIAN RESEARCH ENTERPRISE-(SCIRE) Collaborative Group from the Ministero dell’Università e della Ricerca (PRIN 202022GZEHE_01).