Bioinformatics Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.
The Cyprus School of Molecular Medicine, Nicosia, Cyprus.
BMC Genom Data. 2021 Nov 13;22(1):48. doi: 10.1186/s12863-021-01007-9.
This study aims to characterize SARS-CoV-2 mutations which are primarily prevalent in the Cypriot population. Moreover, using computational approaches, we assess whether these mutations are associated with changes in viral virulence.
We utilize genetic data from 144 sequences of SARS-CoV-2 strains from the Cypriot population obtained between March 2020 and January 2021, as well as all data available from GISAID. We combine this with countries' regional information, such as deaths and cases per million, as well as COVID-19-related public health austerity measure response times. Initial indications of selective advantage of Cyprus-specific mutations are obtained by mutation tracking analysis. This entails calculating specific mutation frequencies within the Cypriot population and comparing these with their prevalence world-wide throughout the course of the pandemic. We further make use of linear regression models to extrapolate additional information that may be missed through standard statistical analysis.
We report a single mutation found in the ORF1ab gene (nucleotide position 18,440) that appears to be significantly enriched within the Cypriot population. The amino acid change is denoted as S6059F, which maps to the SARS-CoV-2 NSP14 protein. We further analyse this mutation using regression models to investigate possible associations with increased deaths and cases per million. Moreover, protein structure prediction tools show that the mutation infers a conformational change to the protein that significantly alters its structure when compared to the reference protein.
Investigating Cyprus-specific mutations for SARS-CoV-2 can lead to a better understanding of viral pathogenicity. Researching these mutations can generate potential links between viral-specific mutations and the unique genomics of the Cypriot population. This can not only lead to important findings from which to battle the pandemic on a national level, but also provide insights into viral virulence worldwide.
本研究旨在描述主要在塞浦路斯人群中流行的 SARS-CoV-2 突变。此外，我们还利用计算方法评估这些突变是否与病毒毒力的变化有关。
我们利用了 2020 年 3 月至 2021 年 1 月期间从塞浦路斯人群中获得的 144 个 SARS-CoV-2 毒株的遗传数据，以及 GISAID 上提供的所有数据。我们将这些数据与国家的区域信息（如每百万人口的死亡和病例数，以及与 COVID-19 相关的公共卫生紧缩措施的反应时间）相结合。通过突变跟踪分析获得塞浦路斯特定突变具有选择优势的初步迹象。这需要计算塞浦路斯人群中特定突变的频率，并将其与大流行期间全球的流行率进行比较。我们还进一步利用线性回归模型来推断通过标准统计分析可能遗漏的其他信息。
我们报告了一个在 ORF1ab 基因（核苷酸位置 18440）中发现的单一突变，该突变似乎在塞浦路斯人群中明显富集。氨基酸变化被标记为 S6059F，它映射到 SARS-CoV-2 的 NSP14 蛋白上。我们进一步使用回归模型分析该突变，以研究其与每百万人口死亡和病例数增加的可能关联。此外，蛋白质结构预测工具表明，该突变导致蛋白质构象发生变化，与参考蛋白相比，其结构发生了显著改变。
研究 SARS-CoV-2 的塞浦路斯特有突变可以更好地了解病毒的致病性。研究这些突变可以发现病毒特异性突变与塞浦路斯人群独特基因组之间的潜在联系。这不仅可以在国家层面上为抗击大流行提供重要的发现，还可以为全球的病毒毒力提供新的认识。
