Department of Medicine, Aga Khan University, Karachi, Pakistan.
Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan.
BMC Res Notes. 2021 Aug 17;14(1):316. doi: 10.1186/s13104-021-05722-5.
We investigated the discrepancy between clinical and PCR-based diagnosis of COVID-19. We compared results of ten patients with mild to severe COVID-19. Respiratory samples from all cases were tested on the Roche SARS-CoV-2 (Cobas) assay, Filmarray RP2.1 (bioMereiux) and TaqPath™ COVID19 (Thermofisher) PCR assays.
Laboratory records of ten patients with mild to severe COVID-19 were examined. Initially, respiratory samples from the patients were tested as negative on the SARS-CoV-2 Roche assay. Further investigation using the BIOFIRE Filmarray RP2.1 assay identified SARS-CoV-2 as the pathogen in all ten cases. To investigate possible discrepancies between PCR assays, additional testing was conducted using the TaqPath™ COVID19 PCR. Eight of ten samples were positive for SARS-CoV-2 on the TaqPath assay. Further, Spike gene target failures (SGTF) were identified in three of these eight cases. Discrepancy between the three PCR assays could be due to variation in PCR efficiencies of the amplification reactions or, variation at primer binding sites. Strains with SGTF indicate the presence of new SARS-CoV-2 variant strains. Regular modification of gene targets in diagnostic assays may be necessary to maintain robustness and accuracy of SARS-CoV-2 diagnostic assays to avoid reduced case detection, under-surveillance, and missed opportunities for control.
我们调查了 COVID-19 的临床诊断与基于 PCR 的诊断之间的差异。我们比较了 10 例轻度至重度 COVID-19 患者的结果。所有病例的呼吸道样本均在罗氏 SARS-CoV-2（Cobas）检测、Filmarray RP2.1（bioMeriux）和 TaqPath™ COVID19（Thermofisher）PCR 检测上进行了检测。
对 10 例轻度至重度 COVID-19 患者的实验室记录进行了检查。最初，患者的呼吸道样本在罗氏 SARS-CoV-2 检测上呈阴性。进一步使用 BIOFIRE Filmarray RP2.1 检测发现，所有 10 例均为 SARS-CoV-2 病原体。为了调查 PCR 检测之间可能存在的差异，使用 TaqPath™ COVID19 PCR 进行了额外的检测。10 个样本中有 8 个在 TaqPath 检测上呈 SARS-CoV-2 阳性。此外，在这 8 个病例中的 3 个中鉴定出 Spike 基因靶标失败（SGTF）。这三种 PCR 检测之间的差异可能是由于扩增反应的 PCR 效率不同或引物结合位点的差异造成的。具有 SGTF 的菌株表明存在新的 SARS-CoV-2 变异株。为了保持 SARS-CoV-2 诊断检测的稳健性和准确性，以避免减少病例检测、监测不足和错失控制机会，可能需要定期修改基因靶标。
