Lo Presti Alessandra, Di Martino Angela, Ambrosio Luigina, De Sabato Luca, Knijn Arnold, Vaccari Gabriele, Di Bartolo Ilaria, Morabito Stefano, Terregino Calogero, Fusaro Alice, Monne Isabella, Giussani Edoardo, Tramuto Fabio, Maida Carmelo Massimo, Mazzucco Walter, Costantino Claudio, Rueca Martina, Giombini Emanuela, Gruber Cesare Ernesto Maria, Capobianchi Maria Rosaria, Palamara Anna Teresa, Stefanelli Paola
Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy.
Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy.
Microorganisms. 2023 Oct 27;11(11):2644. doi: 10.3390/microorganisms11112644.
The SARS-CoV-2 Delta variant of concern (VOC) was often associated with serious clinical course of the COVID-19 disease. Herein, we investigated the selective pressure, gene flow and evaluation on the frequencies of mutations causing amino acid substitutions in the Delta variant in three Italian regions. A total of 1500 SARS-CoV-2 Delta genomes, collected in Italy from April to October 2021 were investigated, including a subset of 596 from three Italian regions. The selective pressure and the frequency of amino acid substitutions and the prediction of their possible impact on the stability of the proteins were investigated. Delta variant dataset, in this study, identified 68 sites under positive selection: 16 in the spike (23.5%), 11 in nsp2 (16.2%) and 10 in nsp12 (14.7%) genes. Three of the positive sites in the spike were located in the receptor-binding domain (RBD). In Delta genomes from the three regions, 6 changes were identified as very common (>83.7%), 4 as common (>64.0%), 21 at low frequency (2.1%-25.0%) and 29 rare (≤2.0%). The detection of positive selection on key mutations may represent a model to identify recurrent signature mutations of the virus.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）的Delta变异株（VOC）常与新冠肺炎疾病的严重临床病程相关。在此，我们研究了意大利三个地区Delta变异株中导致氨基酸替换的突变频率的选择压力、基因流动及评估。我们调查了2021年4月至10月在意大利收集的总共1500个SARS-CoV-2 Delta基因组，其中包括来自意大利三个地区的596个基因组子集。研究了选择压力、氨基酸替换频率及其对蛋白质稳定性可能影响的预测。在本研究中，Delta变异株数据集确定了68个处于正选择的位点：刺突蛋白（spike）中有16个（23.5%），非结构蛋白2（nsp2）中有11个（16.2%），非结构蛋白12（nsp12）中有10个（14.7%）。刺突蛋白中的三个正选择位点位于受体结合域（RBD）。在来自这三个地区的Delta基因组中，6个变化被确定为非常常见（>83.7%），4个为常见（>64.0%），21个为低频（2.1%-25.0%），29个为罕见（≤2.0%）。对关键突变的正选择检测可能代表一种识别该病毒反复出现的特征性突变的模型。
