The Spread of SARS-CoV-2 Omicron Variant in CALABRIA: A Spatio-Temporal Report of Viral Genome Evolution

Claudia Veneziano; Nadia Marascio; Carmela De Marco; Barbara Quaresima; Flavia Biamonte; Enrico Maria Trecarichi; Gianluca Santamaria; Angela Quirino; Daniele Torella; Aldo Quattrone; Giovanni Matera; Carlo Torti; Caterina De Filippo; Francesco Saverio Costanzo; Giuseppe Viglietto

doi:10.3390/v15020408

The Spread of SARS-CoV-2 Omicron Variant in CALABRIA: A Spatio-Temporal Report of Viral Genome Evolution

Viruses. 2023 Jan 31;15(2):408. doi: 10.3390/v15020408.

Authors

Claudia Veneziano^{1

2}, Nadia Marascio³, Carmela De Marco^{1

2}, Barbara Quaresima^{1

2}, Flavia Biamonte^{1

2}, Enrico Maria Trecarichi^{4

5}, Gianluca Santamaria¹, Angela Quirino^{3

5}, Daniele Torella^{1

5}, Aldo Quattrone⁶, Giovanni Matera^{3

5}, Carlo Torti^{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 of Catanzaro, 88100 Catanzaro, Italy.
² Interdepartmental Center of Services (CIS), Molecular Genomics and Pathology, "Magna Græcia" University of Catanzaro, 88100 Catanzaro, Italy.
³ Department of Health Sciences, "Magna Graecia" University of Catanzaro, 88100 Catanzaro, Italy.
⁴ Department of Medical and Surgical Sciences, "Magna Graecia" University of Catanzaro, 88100 Catanzaro, Italy.
⁵ "Mater Domini" University Hospital of Catanzaro, 88100 Catanzaro, Italy.
⁶ Neuroscience Research Center, "Magna Graecia" University of Catanzaro, 88100 Catanzaro, Italy.

Abstract

We investigated the evolution of SARS-CoV-2 spread in Calabria, Southern Italy, in 2022. A total of 272 RNA isolates from nasopharyngeal swabs of individuals infected with SARS-CoV-2 were sequenced by whole genome sequencing (N = 172) and/or Sanger sequencing (N = 100). Analysis of diffusion of Omicron variants in Calabria revealed the prevalence of 10 different sub-lineages (recombinant BA.1/BA.2, BA.1, BA.1.1, BA.2, BA.2.9, BA.2.10, BA.2.12.1, BA.4, BA.5, BE.1). We observed that Omicron spread in Calabria presented a similar trend as in Italy, with some notable exceptions: BA.1 disappeared in April in Calabria but not in the rest of Italy; recombinant BA.1/BA.2 showed higher frequency in Calabria (13%) than in the rest of Italy (0.02%); BA.2.9, BA.4 and BA.5 emerged in Calabria later than in other Italian regions. In addition, Calabria Omicron presented 16 non-canonical mutations in the S protein and 151 non-canonical mutations in non-structural proteins. Most non-canonical mutations in the S protein occurred mainly in BA.5 whereas non-canonical mutations in non-structural or accessory proteins (ORF1ab, ORF3a, ORF8 and N) were identified in BA.2 and BA.5 sub-lineages. In conclusion, the data reported here underscore the importance of monitoring the entire SARS-CoV-2 genome.

Keywords: Italy; NGS; SARS-CoV-2; surveillance; variants; viral genomics.

Publication types

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

MeSH terms

COVID-19* / epidemiology
Evolution, Molecular
Genome, Viral
Humans
Italy / epidemiology
SARS-CoV-2 / genetics

Supplementary concepts

SARS-CoV-2 variants

Grants and funding

This research received specific financial support from University Magna Graecia, Department of Experimental and Clinical Medicine (COVID19-DMSC) and Interdepartmental Center of Services (CIS), Molecular Genomics and Pathology, Magna Græcia University of Catanzaro, Italy. This work was also supported by Regione Calabria (noCOVID19@UMG POR Calabria–FESR/FSE 2014-2020 D.D.R.C. n. 4584 del 4/5/2021-Azione 10.5.12).