Kocaeli University, Research and Education Hospital, PCR Unit, 41380, Kocaeli, Turkey.
Near East University, DESAM Research Institute, 99138, Nicosia, Northern Cyprus.
New Microbiol. 2023 May;46(2):133-140.
The study's objective was to assess whether the performance of the DIAGNOVITAL SARS-CoV-2 Mutation Detection Assays is affected by Omicron mutations. In silico evaluation of 67,717 Variant of Concern, Variant of Interest sequences and 6,612 sequences of the Omicron variants involving BA1., BA2., BA3 sub-lineages downloaded from the GISAID database by 17 December 2021, were performed. The sequences were aligned according to the reference genome MN908947.3 using MAFFT multiple sequence alignment software version 7. Our findings showed that among 6,612 Omicron, 41 Spike gene mutations with a frequency of ≥70% were identified. Some of the Omicron mutations (R408S, N440K, G446S, Q493S, Q498R) could affect the diagnostic performance of K417N, L452R, and E484K assays against the Omicron sub-lineages. However, L452R and K417N mutation tests allow differentiation of the Delta and Omicron variants mutation profile. The COVID-19 pandemic lasted longer than expected, and the rapid modification of diagnostic kits seems necessary to combat the pandemic.
本研究旨在评估 DIAGNOVITAL SARS-CoV-2 Mutation Detection Assays 的性能是否受到奥密克戎突变的影响。通过对 2021 年 12 月 17 日之前从 GISAID 数据库下载的 67717 个关注变异、感兴趣变异序列和涉及 BA1、BA2、BA3 亚谱系的 6612 个奥密克戎变异序列进行了计算机模拟评估。使用 MAFFT 多序列比对软件版本 7 根据参考基因组 MN908947.3 进行序列比对。我们的研究结果表明，在 6612 个奥密克戎中，有 41 个棘突蛋白突变的频率≥70%。奥密克戎的一些突变（R408S、N440K、G446S、Q493S、Q498R）可能会影响针对奥密克戎亚谱系的 K417N、L452R 和 E484K 检测的诊断性能。然而，L452R 和 K417N 突变测试可以区分德尔塔和奥密克戎变异的突变谱。COVID-19 大流行持续的时间比预期的要长，因此似乎有必要快速修改诊断试剂盒以对抗大流行。
