Dynamics of Viral Infection and Evolution of SARS-CoV-2 Variants in the Calabria Area of Southern Italy

Carmela De Marco; Claudia Veneziano; Alice Massacci; Matteo Pallocca; Nadia Marascio; Angela Quirino; Giorgio Settimo Barreca; Aida Giancotti; Luigia Gallo; Angelo Giuseppe Lamberti; Barbara Quaresima; Gianluca Santamaria; Flavia Biamonte; Stefania Scicchitano; Enrico Maria Trecarichi; Alessandro Russo; Daniele Torella; Aldo Quattrone; Carlo Torti; Giovanni Matera; Caterina De Filippo; Francesco Saverio Costanzo; Giuseppe Viglietto

doi:10.3389/fmicb.2022.934993

Dynamics of Viral Infection and Evolution of SARS-CoV-2 Variants in the Calabria Area of Southern Italy

Front Microbiol. 2022 Jul 28:13:934993. doi: 10.3389/fmicb.2022.934993. eCollection 2022.

Authors

Carmela De Marco^{1

2}, Claudia Veneziano^{1

2}, Alice Massacci³, Matteo Pallocca³, Nadia Marascio⁴, Angela Quirino^{4

5}, Giorgio Settimo Barreca⁵, Aida Giancotti⁵, Luigia Gallo⁵, Angelo Giuseppe Lamberti⁵, Barbara Quaresima^{1

2}, Gianluca Santamaria¹, Flavia Biamonte^{1

2}, Stefania Scicchitano¹, Enrico Maria Trecarichi^{5

6}, Alessandro Russo^{5

6}, Daniele Torella^{1

5}, Aldo Quattrone⁷, Carlo Torti^{5

6}, Giovanni Matera^{4

5}, Caterina De Filippo⁵, Francesco Saverio Costanzo^{1

2

5}, Giuseppe Viglietto^{1

5}

Affiliations

¹ Department of Experimental and Clinical Medicine, "Magna Graecia" University, Catanzaro, Italy.
² Interdepartmental Center of Services, Molecular Genomics and Pathology, "Magna Graecia" University, Catanzaro, Italy.
³ UOSD Biostatistics, Bioinformatics, and Clinical Trial Center, IRCCS Regina Elena National Cancer Institute, Rome, Italy.
⁴ Department of Health Sciences, "Magna Graecia" University, Catanzaro, Italy.
⁵ "Mater Domini" University Hospital, Catanzaro, Italy.
⁶ Department of Medical and Surgical Sciences, "Magna Graecia" University, Catanzaro, Italy.
⁷ Neuroscience Research Center, "Magna Graecia" University, Catanzaro, Italy.

Abstract

In this study, we report on the results of SARS-CoV-2 surveillance performed in an area of Southern Italy for 12 months (from March 2021 to February 2022). To this study, we have sequenced RNA from 609 isolates. We have identified circulating VOCs by Sanger sequencing of the S gene and defined their genotypes by whole-genome NGS sequencing of 157 representative isolates. Our results indicated that B.1 and Alpha were the only circulating lineages in Calabria in March 2021; while Alpha remained the most common variant between April 2021 and May 2021 (90 and 73%, respectively), we observed a concomitant decrease in B.1 cases and appearance of Gamma cases (6 and 21%, respectively); C.36.3 and Delta appeared in June 2021 (6 and 3%, respectively); Delta became dominant in July 2021 while Alpha continued to reduce (46 and 48%, respectively). In August 2021, Delta became the only circulating variant until the end of December 2021. As of January 2022, Omicron emerged and took over Delta (72 and 28%, respectively). No patient carrying Beta, Iota, Mu, or Eta variants was identified in this survey. Among the genomes identified in this study, some were distributed all over Europe (B1_S477N, Alpha_L5F, Delta_T95, Delta_G181V, and Delta_A222V), some were distributed in the majority of Italian regions (B1_S477N, B1_Q675H, Delta_T95I and Delta_A222V), and some were present mainly in Calabria (B1_S477N_T29I, B1_S477N_T29I_E484Q, Alpha_A67S, Alpha_A701S, and Alpha_T724I). Prediction analysis of the effects of mutations on the immune response (i.e., binding to class I MHC and/or recognition of T cells) indicated that T29I in B.1 variant; A701S in Alpha variant; and T19R in Delta variant were predicted to impair binding to class I MHC whereas the mutations A67S identified in Alpha; E484K identified in Gamma; and E156G and ΔF157/R158 identified in Delta were predicted to impair recognition by T cells. In conclusion, we report on the results of SARS-CoV-2 surveillance in Regione Calabria in the period between March 2021 and February 2022, identified variants that were enriched mainly in Calabria, and predicted the effects of identified mutations on host immune response.

Keywords: NGS; SARS-CoV-2; immunogenomics; surveillance; variants.

Copyright © 2022 De Marco, Veneziano, Massacci, Pallocca, Marascio, Quirino, Barreca, Giancotti, Gallo, Lamberti, Quaresima, Santamaria, Biamonte, Scicchitano, Trecarichi, Russo, Torella, Quattrone, Torti, Matera, De Filippo, Costanzo and Viglietto.