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. 2023 Jan 18;15(2):277.
doi: 10.3390/v15020277.

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  1 , Luca Ferretti  2 , Alice Ledda  3 , Antonello Di Nardo  4 , Matteo Floris  5 , Piero Bonelli  1 , Federica Loi  6 , Maria Laura Idda  7 , Pier Paolo Angioi  1 , Susanna Zinellu  1 , Mariangela Stefania Fiori  1 , Roberto Bechere  1 , Paola Capitta  1 , Annamaria Coccollone  1 , Elisabetta Coradduzza  1 , Maria Antonietta Dettori  1 , Maria Caterina Fattaccio  1 , Elena Gallisai  1 , Caterina Maestrale  1 , Daniela Manunta  1 , Aureliana Pedditzi  1 , Ivana Piredda  1 , Bruna Palmas  1 , Sara Salza  1 , Anna Maria Sechi  1 , Barbara Tanda  1 , Maria Paola Madrau  1 , Maria Luisa Sanna  1 , Simonetta Cherchi  1 , Nicoletta Ponti  1 , Giovanna Masala  1 , Roberto Sirica  8 , Eloisa Evangelista  8 , Annalisa Oggiano  1 , Giantonella Puggioni  1 , Ciriaco Ligios  1 , Silvia Dei Giudici  1
Affiliations

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 et al. Viruses. .

Abstract

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.

Keywords: SARS-CoV-2; genetic diversity; molecular epidemiology; spike (S) protein; whole genome sequencing.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Weekly Italian trends of COVID-19 confirmed cases (A) and deaths (B).
Figure 2
Figure 2
Daily Sardinian COVID-19 confirmed cases and reported deaths.
Figure 3
Figure 3
Frequency of amino acid mutations found in Sardinian samples (n = 55). Only mutations detected in more than 5% of samples were illustrated in this figure.
Figure 4
Figure 4
Maximum-likelihood phylogeny reconstructed using the Sardinian SARS-CoV-2 strains generated in this study. The tree is rooted to the SARS-CoV-2 reference genome Wuhan-Hu NC 045512.2. Purple triangles and red circles indicate sequences belonging to the first and second waves, respectively. SARS-CoV-2 clades and lineages are annotated using brackets.
Figure 5
Figure 5
Assignment of the 55 Sardinian samples (large black circles) within the global SARS-CoV-2 phylogeny generated from Auspice/NextStrain. Most samples belong to the B.1.177 lineage and correspond to the NextStrain clade 20E (EU1).
Figure 6
Figure 6
Local subtree generated from Auspice/NextStrain containing 28 out of the 55 Sardinian sequences presented in this wok (white circles). Note how most of the sequences in this subtree, including the most basal one, originate from continental Italy.
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