The availability of new technologies for deep sequencing, including next-generation sequencing (NGS), allows for the detection of viral genome variations. The epidemiological determination of SARS-CoV-2 viral genome changes during the pandemic waves displayed the genome evolution and subsequent onset of variants over time. These variants were often associated with a different impact on viral transmission and disease severity. We investigated, in a retrospective study, the trend of SARS-CoV-2-positive samples collected from the start of the Italian pandemic (January 2020) to June 2023. In addition, viral RNAs extracted from 938 nasopharyngeal swab samples were analyzed using NGS between February 2022 and June 2023. Sequences were analyzed with bioinformatic tools to identify lineages and mutations and for phylogenetic studies. Six pandemic waves were detected. In our samples, we predominantly detected BA.2, BQ.1, BA.5.1, BA.5.2, and, more recently, XBB.1 and its subvariants. The data describe the SARS-CoV-2 genome evolution involved in viral interactions with the host and the dynamics of specific genome mutations and deletions.

中文翻译：

---

乘风破浪 SARS-CoV-2：利用意大利维罗纳的 NGS 调查分析病毒基因组变异

深度测序新技术的出现，包括下一代测序（NGS），可以检测病毒基因组变异。大流行期间 SARS-CoV-2 病毒基因组变化的流行病学测定显示了随着时间的推移基因组进化和随后变异的发生。这些变异通常与对病毒传播和疾病严重程度的不同影响有关。我们在一项回顾性研究中调查了从意大利大流行开始（2020 年 1 月）到 2023 年 6 月期间收集的 SARS-CoV-2 阳性样本的趋势。此外，还使用 ​​NGS 分析了从 938 份鼻咽拭子样本中提取的病毒 RNA 2022 年 2 月至 2023 年 6 月之间。使用生物信息学工具对序列进行分析，以识别谱系和突变并进行系统发育研究。检测到六次大流行浪潮。在我们的样本中，我们主要检测到 BA.2、BQ.1、BA.5.1、BA.5.2，以及最近的 XBB.1 及其子变体。这些数据描述了病毒与宿主相互作用所涉及的 SARS-CoV-2 基因组进化以及特定基因组突变和缺失的动态。