Origin, Genetic Variation and Molecular Epidemiology of SARS-CoV-2 Strains Circulating in Sardinia (Italy) during the First and Second COVID-19 Epidemic Waves

• Published in: Viruses 2023-01, Vol.15 (2), p.277
• Main Authors: Rocchigiani, Angela Maria, Ferretti, Luca, Ledda, Alice, Di Nardo, Antonello, Floris, Matteo, Bonelli, Piero, Loi, Federica, Idda, Maria Laura, Angioi, Pier Paolo, Zinellu, Susanna, Fiori, Mariangela Stefania, Bechere, Roberto, Capitta, Paola, Coccollone, Annamaria, Coradduzza, Elisabetta, Dettori, Maria Antonietta, Fattaccio, Maria Caterina, Gallisai, Elena, Maestrale, Caterina, Manunta, Daniela, Pedditzi, Aureliana, Piredda, Ivana, Palmas, Bruna, Salza, Sara, Sechi, Anna Maria, Tanda, Barbara, Madrau, Maria Paola, Sanna, Maria Luisa, Cherchi, Simonetta, Ponti, Nicoletta, Masala, Giovanna, Sirica, Roberto, Evangelista, Eloisa, Oggiano, Annalisa, Puggioni, Giantonella, Ligios, Ciriaco, Dei Giudici, Silvia
• Format: Article
• Language: English
• Subjects: Coronaviruses; COVID-19; COVID-19 - epidemiology; COVID-19 vaccines; Disease transmission; Epidemics; Epidemiology; Fatalities; Genetic diversity; Genetic Variation; Genomes; Health surveillance; Humans; Immunization; Infections; Infectious diseases; Influenza; Italy - epidemiology; Methods; Molecular Epidemiology; Mortality; Next-generation sequencing; Pandemics; Phylogeography; SARS-CoV-2; SARS-CoV-2 - genetics; Seasons; Severe acute respiratory syndrome coronavirus 2; Software; spike (S) protein; Strains (organisms); Viruses; whole genome sequencing; Zoonoses
• ISSN: 1999-4915; 1999-4915
• DOI: 10.3390/v15020277

Understanding how geography and human mobility shape the patterns and spread of infectious diseases such as COVID-19 is key to control future epidemics. An interesting example is provided by the second wave of the COVID-19 epidemic in Europe, which was facilitated by the intense movement of tourists around the Mediterranean coast in summer 2020. The Italian island of Sardinia is a major tourist destination and is widely believed to be the origin of the second Italian wave. In this study, we characterize the genetic variation among SARS-CoV-2 strains circulating in northern Sardinia during the first and second Italian waves using both Illumina and Oxford Nanopore Technologies Next Generation Sequencing methods. Most viruses were placed into a single clade, implying that despite substantial virus inflow, most outbreaks did not spread widely. The second epidemic wave on the island was actually driven by local transmission of a single B.1.177 subclade. Phylogeographic analyses further suggest that those viral strains circulating on the island were not a relevant source for the second epidemic wave in Italy. This result, however, does not rule out the possibility of intense mixing and transmission of the virus among tourists as a major contributor to the second Italian wave.