In silico analysis of mismatches in RT-qPCR assays of 177 SARS-CoV-2 sequences from Brazil

Abstract INTRODUCTION: Quantitative reverse transcription polymerase chain reaction (RT-qPCR) can detect the severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) in a highly specific manner. However, a decrease in the specificity of PCR assays for their targets may lead to false negative results. METHODS: Here, 177 high-coverage complete SARS-CoV-2 genome sequences from 13 Brazilian states were aligned with 15 WHO recommended PCR assays. RESULTS: Only 3 of the 15 completely aligned to all Brazilian sequences. Ten assays had mismatches in up to 3 sequences and two in many sequences. CONCLUSION: These results should be taken into consideration when using PCR-based diagnostics in Brazil.

摘要

引言：定量逆转录聚合酶链反应（Quantitative reverse transcription polymerase chain reaction，RT-qPCR）可实现高特异性检测严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）。但针对靶标的PCR检测体系特异性降低可能引发假阴性结果。

方法：本研究将来自巴西13个州的177条高覆盖度完整SARS-CoV-2基因组序列，与世界卫生组织（WHO）推荐的15种PCR检测体系进行序列比对。

结果：15种检测体系中仅3种可与所有巴西来源的病毒基因组序列完全匹配；10种检测体系在至多3条序列中存在碱基错配，另有2种检测体系在大量序列中存在错配。

结论：在巴西使用基于PCR的诊断方法时，应将本研究结果纳入考量。