Table_2_The Impact of Accumulated Mutations in SARS-CoV-2 Variants on the qPCR Detection Efficiency.pdf

SARS-CoV-2 is evolving with mutations throughout the genome all the time and a number of major variants emerged, including several variants of concern (VOC), such as Delta and Omicron variants. In this study, we demonstrated that mutations in the regions corresponding to the sequences of the probes and 3’-end of primers have a significant impact on qPCR detection efficiency. We also found that the G28916T mutation of the N gene accounts for 78.78% sequenced genomes of Delta variant. It was found that detection sensitivity of G28916T mutant was 2.35 and 1.74 times less than that of the wt sequence and detection limit was reduced from 1 copy/μl to 10 copies/μl for the commercially available CP3 and CP4 primer/probe sets. These results indicate that the detection probes and primers should be optimized to keep maximal detection efficiency in response to the emergence of new variants.

严重急性呼吸综合征冠状病毒2（SARS-CoV-2）始终通过基因组范围内的突变持续进化，目前已出现多种主流变异株，其中包括若干值得关注的变异株（Variant of Concern，VOC），例如德尔塔（Delta）与奥密克戎（Omicron）变异株。本研究证实，探针序列对应区域及引物3'端发生的突变，会对定量实时聚合酶链反应（qPCR）的检测效率产生显著影响。研究同时发现，德尔塔变异株的测序基因组中，78.78%的序列携带N基因的G28916T突变。针对市售的CP3与CP4引物/探针组合，G28916T突变株的检测灵敏度分别较野生型序列低2.35倍与1.74倍，且其检测限从1拷贝/微升降至10拷贝/微升。上述结果表明，为应对新变异株的出现，需对检测用探针与引物进行优化，以维持最优的检测效率。