Rodríguez Flores Sofía N, Rodríguez-Martínez Luis Mario, Reyes-Berrones Bernardita L, Fernández-Santos Nadia A, Sierra-Moncada Elthon J, Rodríguez-Pérez Mario A
Instituto Politécnico Nacional, Centro de Biotecnologia Genomica, Reynosa, Mexico.
Laboratorio Estatal de Salud Pública de Tamaulipas, Secretaría de Salud de Tamaulipas, Ciudad Victoria, Mexico.
Front Bioeng Biotechnol. 2021 Mar 29;9:638902. doi: 10.3389/fbioe.2021.638902. eCollection 2021.
During the COVID-19 pandemic, a certified laboratory of Tamaulipas, Mexico has processed over 100,000 samples of COVID-19 suspected patients, working a minimum of 100 tests daily. Thus, it would be beneficial for such certified laboratories nationwide to reduce the time and cost involved in performing the diagnosis of COVID-19, from sample collection, transportation to local lab, processing of samples, and data acquisition. Here, 30 nasopharyngeal swab and saliva samples from the same COVID-19 individuals were assessed by a standard nucleic acid extraction protocol, including protein lysis with proteinase K followed by binding to column, washing, and elution, and by the SalivaDirect protocol based on protein lysis, skipping the other steps to reduce processing time and costs. The genomic RNA was amplified using a SARS-CoV-2 Real-Time PCR kit. A variation ( > 0.05) in the 95% CIs = 72.6%-96.7% was noted by using the SalivaDirect protocol and saliva samples (sensitivity of 88.2%) in comparison to those of standard protocol with oropharyngeal swab samples (95% CIs = 97.5%-100%; sensitivity of 100%) as reported elsewhere. However, when using nasopharyngeal swab samples in the SalivaDirect protocol (sensitivity of 93.6%; 95% CIs = 79.2%-99.2%), it was in concordance ( < 0.05) with those of the standard one. The logical explanation to this was that two samples with Ct values of 38, and 40 cycles for gene E produced two false negatives in the SalivaDirect protocol in relation to the standard one; thus, there was a reduction of the sensitivity of 6.4% in the overall assay performance.
在新冠疫情期间，墨西哥塔毛利帕斯州的一家认证实验室已处理了超过10万份新冠疑似患者样本，每天至少进行100次检测。因此，对于全国范围内的此类认证实验室来说，减少新冠诊断过程中从样本采集、运输到当地实验室、样本处理及数据采集所涉及的时间和成本将大有裨益。在此，我们采用标准核酸提取方案（包括用蛋白酶K进行蛋白质裂解，随后与柱子结合、洗涤和洗脱）以及基于蛋白质裂解的SalivaDirect方案（跳过其他步骤以减少处理时间和成本），对来自同一新冠患者的30份鼻咽拭子和唾液样本进行了评估。使用SARS-CoV-2实时PCR试剂盒对基因组RNA进行扩增。与其他地方报道的使用标准方案检测口咽拭子样本（95%置信区间=97.5%-100%；灵敏度为100%）相比，采用SalivaDirect方案检测唾液样本时（灵敏度为88.2%），95%置信区间出现了变化（>0.05），即72.6%-96.7%。然而，当在SalivaDirect方案中使用鼻咽拭子样本时（灵敏度为93.6%；95%置信区间=79.2%-99.2%），与标准方案的结果一致（<0.05）。对此合理的解释是，在SalivaDirect方案中，基因E的Ct值分别为38和40个循环的两个样本相对于标准方案产生了两个假阴性结果；因此，在整体检测性能中灵敏度降低了6.4%。
