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

被引:2
|
作者
Rocchigiani, Angela Maria [1 ]
Ferretti, Luca [2 ]
Ledda, Alice [3 ]
Di Nardo, Antonello [4 ]
Floris, Matteo [5 ]
Bonelli, Piero [1 ]
Loi, Federica [6 ]
Idda, Maria Laura [7 ]
Angioi, Pier Paolo [1 ]
Zinellu, Susanna [1 ]
Fiori, Mariangela Stefania [1 ]
Bechere, Roberto [1 ]
Capitta, Paola [1 ]
Coccollone, Annamaria [1 ]
Coradduzza, Elisabetta [1 ]
Dettori, Maria Antonietta [1 ]
Fattaccio, Maria Caterina [1 ]
Gallisai, Elena [1 ]
Maestrale, Caterina [1 ]
Manunta, Daniela [1 ]
Pedditzi, Aureliana [1 ]
Piredda, Ivana [1 ]
Palmas, Bruna [1 ]
Salza, Sara [1 ]
Sechi, Anna Maria [1 ]
Tanda, Barbara [1 ]
Madrau, Maria Paola [1 ]
Sanna, Maria Luisa [1 ]
Cherchi, Simonetta [1 ]
Ponti, Nicoletta [1 ]
Masala, Giovanna [1 ]
Sirica, Roberto [8 ]
Evangelista, Eloisa [8 ]
Oggiano, Annalisa [1 ]
Puggioni, Giantonella [1 ]
Ligios, Ciriaco [1 ]
Dei Giudici, Silvia [1 ]
机构
[1] Ist Zooprofilatt Sperimentale Sardegna, I-07100 Sassari, Italy
[2] Univ Oxford, Pandem Sci Inst, Li Ka Shing Ctr Hlth Informat & Discovery, Nuffield Dept Med, Oxford OX1 2JD, England
[3] UK Hlth Secur Agcy, London NW9 5EQ, England
[4] Pirbright Inst, Ash Rd, Woking GU24 0NF, England
[5] Univ Sassari, Dept Biomed Sci, I-07100 Sassari, Italy
[6] Ist Zooprofilatt Sperimentale Sardegna, Osservatorio Epidemiol Vet Regionale, I-09125 Cagliari, Italy
[7] Natl Res Council CNR, Inst Genet & Biomed Res IRGB, I-07100 Sassari, Italy
[8] Ames Polydiagnost Grp Ctr SRL, I-80013 Naples, Italy
来源
VIRUSES-BASEL | 2023年 / 15卷 / 02期
关键词
SARS-CoV-2; spike (S) protein; whole genome sequencing; molecular epidemiology; genetic diversity; ALIGNMENT; ACCURATE;
D O I
10.3390/v15020277
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
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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页数:16
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