Fukasawa Lucila Okuyama, Sacchi Cláudio Tavares, Gonçalves Maria Gisele, Lemos Ana Paula Silva, Almeida Samanta Cristine Grassi, Caterino-de-Araujo Adele
Centro de Imunologia, Instituto Adolfo Lutz, Coordenadoria de Controle de Doenças, Secretaria de Estado da Saúde de São Paulo, SP 01246-902, Brazil.
Laboratório Estratégico, Instituto Adolfo Lutz, Coordenadoria de Controle de Doenças, Secretaria de Estado da Saúde de São Paulo, SP, Brazil.
J Clin Virol Plus. 2021 Jun;1(1):100012. doi: 10.1016/j.jcvp.2021.100012. Epub 2021 Apr 5.
Brazil is the second largest country with COVID-19 positive cases worldwide. Due to the potent spread of the virus and the scarcity of kits and supplies, the Brazilian Ministry of Health has granted authorization for the use of kits available during this emergency, without an accurate evaluation of their performance. This study compared the performance and cost-effectiveness of seven molecular assays/kits available in São Paulo, Brazil, for SARS-CoV-2 diagnosis.
A total of 205 nasopharyngeal/oropharyngeal samples from suspected cases of COVID-19, were tested using the following assays: (i) GeneFinder COVID-19 plus RealAmp kit; (ii) 2019-nCoV RNA PCR-Fluorescence Probing, Da An Gene Co.; (iii) in-house RT-qPCR SARS-CoV-2 IAL; (iv) 2019-nCoV kit, IDT; (v) molecular SARS-CoV-2 (E) kit, Bio-Manguinhos; (vi) Allplex 2019-nCoV modified Assay, Seegene Inc, and (vii) Biomol one-step COVID-19 kit, IBMP. The criteria for determining a SARS-CoV-2 true positive result included the cycle threshold cut-off values, the characteristics of exponential/linear curves, the gene target diversity, and a positive result in at least two assays.
The overall sensitivity of the assays listed were GeneFinder 83.6%, Da An Gene 100.0%, IAL 90.4%, IDT 94.6%, Bio-Manguinhos 87.7%, Allplex 97.3%, and IBMP 87.7%. The minor sensitive gene target was RdRP. Although all assays had a Cohen's Kappa index ≥0.893, the best tests used multiplex assays identifying -gene and/or -gene targets.
All assays tested accurate for diagnosis, but considering cost-effectiveness (cost, time consumption, number of samples tested, and performance), the in-house IAL assay was ideal for COVID-19 diagnosis in São Paulo, Brazil.
巴西是全球新冠肺炎确诊病例第二多的国家。由于病毒传播迅猛且检测试剂盒和物资短缺，巴西卫生部已批准在此次紧急情况下使用现有试剂盒，而未对其性能进行准确评估。本研究比较了巴西圣保罗市可用于严重急性呼吸综合征冠状病毒2（SARS-CoV-2）诊断的七种分子检测方法/试剂盒的性能和成本效益。
使用以下检测方法对总共205份来自新冠肺炎疑似病例的鼻咽/口咽样本进行检测：（i）GeneFinder COVID-19 plus RealAmp试剂盒；（ii）2019新型冠状病毒核糖核酸聚合酶链式反应-荧光探针法，达安基因股份有限公司；（iii）内部逆转录定量聚合酶链式反应SARS-CoV-2 IAL法；（iv）2019新型冠状病毒试剂盒，IDT公司；（v）分子SARS-CoV-2（E）试剂盒，Bio-Manguinhos公司；（vi）Allplex 2019新型冠状病毒改良检测法，Seegene公司；以及（vii）Biomol一步法新冠肺炎试剂盒，IBMP公司。确定SARS-CoV-2真阳性结果的标准包括循环阈值截断值、指数/线性曲线特征、基因靶点多样性以及至少两种检测方法呈阳性结果。
所列检测方法的总体灵敏度分别为：GeneFinder 83.6%、达安基因100.0%、IAL 90.4%、IDT 94.6%、Bio-Manguinhos 87.7%、Allplex 97.3%以及IBMP 87.7%。最不敏感的基因靶点是核糖核酸依赖的RNA聚合酶（RdRP）。尽管所有检测方法的科恩卡帕指数均≥0.893，但最佳检测方法采用了可识别-基因和/或-基因靶点的多重检测法。
所有检测方法对诊断而言均准确，但考虑到成本效益（成本、耗时、检测样本数量和性能），内部IAL检测法对巴西圣保罗市的新冠肺炎诊断而言是理想选择。
