Lo Presti Alessandra, Ambrosio Luigina, Di Martino Angela, Knijn Arnold, De Sabato Luca, Vaccari Gabriele, Di Bartolo Ilaria, Morabito Stefano, 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. 2024 Apr 30;12(5):908. doi: 10.3390/microorganisms12050908.
In this work, we studied the selective pressure and evolutionary analysis on the SARS-CoV-2 BF.7 and BQ.1.1 lineages circulating in Italy from July to December 2022. Two different datasets were constructed: the first comprised 694 SARS-CoV-2 BF.7 lineage sequences and the second comprised 734 BQ.1.1 sequences, available in the Italian COVID-19 Genomic (I-Co-Gen) platform and GISAID (last access date 15 December 2022). Alignments were performed with MAFFT v.7 under the Galaxy platform. The HYPHY software was used to study the selective pressure. Four positively selected sites (two in and two in the ) were identified in the BF.7 dataset, and two (one in ORF8 and one in the spike gene) were identified in the BQ.1.1 dataset. Mutation analysis revealed that R408S and N440K are very common in the of the BF.7 genomes, as well as L452R among BQ.1.1. N1329D and Q180H in were found, respectively, at low and rare frequencies in BF.7, while I121L and I121T were found to be rare in ORF8 for BQ.1.1. The positively selected sites may have been driven by the selection for increased viral fitness, under circumstances of defined selective pressure, as well by host genetic factors.
在这项研究中，我们对2022年7月至12月在意大利传播的新冠病毒SARS-CoV-2 BF.7和BQ.1.1谱系进行了选择压力和进化分析。构建了两个不同的数据集：第一个包含694个SARS-CoV-2 BF.7谱系序列，第二个包含734个BQ.1.1序列，这些序列可在意大利新冠病毒基因组（I-Co-Gen）平台和GISAID（最后访问日期为2022年12月15日）上获取。在Galaxy平台下使用MAFFT v.7进行序列比对。使用HYPHY软件研究选择压力。在BF.7数据集中鉴定出四个正选择位点（两个在 ，两个在 ），在BQ.1.1数据集中鉴定出两个（一个在ORF8，一个在刺突基因）。突变分析表明，R408S和N440K在BF.7基因组的 中非常常见，BQ.1.1中的L452R也很常见。在BF.7中， 中的N1329D和Q180H分别以低频率和罕见频率被发现，而I121L和I121T在BQ.1.1的ORF8中被发现为罕见。在特定选择压力的情况下，以及宿主遗传因素的作用下，正选择位点可能是由病毒适应性增强的选择驱动的。
