Department of Biomedical Sciences, Division of Microbiology and Virology, University of Sassari, 07100 Sassari, Italy.
Microbiologia e Virologia, Azienda Ospedaliera Universitaria, 07100 Sassari, Italy.
J Infect Dev Ctries. 2021 Mar 7;15(2):242-246. doi: 10.3855/jidc.14972.
The spread of new SARS-CoV-2 variants represents a serious threat worldwide, thus rapid and cost-effective methods are required for their identification. Since November 2020, the TaqPath COVID-19 assay (Thermo Fisher Scientific) has been used to identify viral strains of the new lineage B.1.1.7, since it fails to detect the S-gene with the ∆69/70 deletion. Here, we proposed S-gene mutations screening with the Allplex SARS-CoV-2 assay (Seegene), another widely used RT-PCR test that targets Sarbecovirus E, SARS-CoV-2 N, and RdRp/S genes. Accordingly, we evaluated the S gene amplification curve pattern compared to those of the other genes. Exploiting an Allplex assay-generated dataset, we screened 663 RT-PCR digital records, including all SARS-CoV-2 respiratory samples tested in our laboratory with the Allplex assay between January 1st and February 25th, 2021. This approach enabled us to detect 64 samples with peculiar non-sigmoidal amplification curves. Sequencing a selected group of 4 RNA viral genomes demonstrated that those curves were associated with B.1.1.7 variant strains. Our results strongly suggest that B.1.1.7 variant spread has begun in this area at least since January and imply the potential of these analytical methods to track and characterize the spread of B.1.1.7 strains in those areas where Allplex SARS-CoV-2 datasets have been previously recorded.
新的 SARS-CoV-2 变体的传播在全球范围内构成了严重威胁，因此需要快速且具有成本效益的方法来识别它们。自 2020 年 11 月以来，TaqPath COVID-19 检测（赛默飞世尔科技）已用于鉴定新谱系 B.1.1.7 的病毒株，因为它无法检测到具有 ∆69/70 缺失的 S 基因。在这里，我们提出了使用另一种广泛使用的 RT-PCR 检测方法 Allplex SARS-CoV-2 检测（Seegene）进行 S 基因突变筛查，该检测方法针对 Sarbecovirus E、SARS-CoV-2 N 和 RdRp/S 基因。因此，我们评估了与其他基因相比的 S 基因扩增曲线模式。利用 Allplex 检测产生的数据集，我们筛选了 663 个 RT-PCR 数字记录，包括 2021 年 1 月 1 日至 2 月 25 日期间我们实验室用 Allplex 检测进行的所有 SARS-CoV-2 呼吸道样本。这种方法使我们能够检测到 64 个具有特殊非正弦扩增曲线的样本。对一组 4 个 RNA 病毒基因组进行测序表明，这些曲线与 B.1.1.7 变体株有关。我们的结果强烈表明，至少从 1 月开始，该变体在该地区已经开始传播，并且这些分析方法有可能在先前记录有 Allplex SARS-CoV-2 数据集的地区跟踪和表征 B.1.1.7 株的传播。
