背景:意大利是第一个处理SARS-CoV-2的欧洲国家,其在领土上的扩散并不均匀。在意大利地区,撒丁岛是发病率最低的地区之一,可能是由于其孤立的性质。尽管如此,孤立性对SARS-CoV-2遗传多样性的影响尚未得到全面描述。
方法:在本研究中,我们对撒丁岛前23个月收集的888个SARS-CoV-2基因组进行了高通量测序.此外,从GISAID下载了1439个在撒丁岛传播三年(2019年12月至2023年1月)的高覆盖率SARS-CoV-2基因组,总共有2327个病毒序列,这些序列以系统发育和基因组多样性为特征。
结果:总体而言,撒丁岛的COVID-19大流行在全国范围内显示出巨大的差异,感染的额外高峰和罕见的血统,反映了国家和地区的重新开放政策以及随后的旅游到来。撒丁岛对至少87个SARS-CoV-2谱系的流通感兴趣,包括一些在国家和欧洲层面代表性不足的国家,可能与多个进口事件有关。撒丁岛SARS-CoV-2谱系的相对频率已与其他地中海群岛进行了比较,揭示了独特的构图。
结论:撒丁岛SARS-CoV-2的基因组多样性是由岛屿地理的复杂相互作用决定的,人口密度低,和旅游到来,一方面导致在国家一级仍然罕见的血统进口,并在另一方面导致其他常见变体的延迟输入。
BACKGROUND: Italy has been the first European Country dealing with SARS-CoV-2, whose diffusion on the territory has not been homogeneous. Among Italian regions, Sardinia represented one of the lowest incidence areas, likely due to its insular nature. Despite this, the impact of insularity on SARS-CoV-2 genetic diversity has not been comprehensively described.
METHODS: In the present study, we performed the high throughput sequencing of 888 SARS-CoV-2 genomes collected in Sardinia during the first 23 months of pandemics. In addition, 1439 high-coverage SARS-CoV-2 genomes circulating in Sardinia along three years (December 2019 - January 2023) were downloaded from GISAID, for a total of 2327 viral sequences that were characterized in terms of phylogeny and genomic diversity.
RESULTS: Overall, COVID-19 pandemic in Sardinia showed substantial differences with respect to the national panorama, with additional peaks of infections and uncommon lineages that reflects the national and regional policies of re-opening and the subsequent touristic arrivals. Sardinia has been interested by the circulation of at least 87 SARS-CoV-2 lineages, including some that were poorly represented at national and European level, likely linked to multiple importation events. The relative frequency of Sardinian SARS-CoV-2 lineages has been compared to other Mediterranean Islands, revealing a unique composition.
CONCLUSIONS: The genomic diversity of SARS-CoV-2 in Sardinia has been shaped by a complex interplay of insular geography, low population density, and touristic arrivals, leading on the one side to the importation of lineages remaining rare at the national level, and resulting on the other side in the delayed entry of otherwise common variants.