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

Angela Maria Rocchigiani; Luca Ferretti; Alice Ledda; Antonello Di Nardo; Matteo Floris; Piero Bonelli; Federica Loi; Maria Laura Idda; Pier Paolo Angioi; Susanna Zinellu; Mariangela Stefania Fiori; Roberto Bechere; Paola Capitta; Annamaria Coccollone; Elisabetta Coradduzza; Maria Antonietta Dettori; Maria Caterina Fattaccio; Elena Gallisai; Caterina Maestrale; Daniela Manunta; Aureliana Pedditzi; Ivana Piredda; Bruna Palmas; Sara Salza; Anna Maria Sechi; Barbara Tanda; Maria Paola Madrau; Maria Luisa Sanna; Simonetta Cherchi; Nicoletta Ponti; Giovanna Masala; Roberto Sirica; Eloisa Evangelista; Annalisa Oggiano; Giantonella Puggioni; Ciriaco Ligios; Silvia Dei Giudici

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

2023

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.

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