Department of Microbiology, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, India.
Regional Virology Laboratory, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, India.
PLoS One. 2020 Sep 22;15(9):e0239492. doi: 10.1371/journal.pone.0239492. eCollection 2020.
Timely diagnosis of COVID-19 infected individuals and their prompt isolation are essential for controlling the transmission of SARS-CoV-2. Though quantitative reverse transcriptase PCR (qRT-PCR) is the method of choice for COVID-19 diagnostics, the resource-intensive and time-consuming nature of the technique impairs its wide applicability in resource-constrained settings and calls for novel strategies to meet the ever-growing demand for more testing. In this context, a pooled sample testing strategy was evaluated in the setting of emerging disease outbreak in 3 central Indian districts to assess if the cost of the test and turn-around time could be reduced without compromising its diagnostic characteristics and thus lead to early containment of the outbreak. From 545 nasopharyngeal and oropharyngeal samples received from the three emerging districts, a total of 109 pools were created with 5 consecutive samples in each pool. The diagnostic performance of qRT-PCR on pooled sample was compared with that of individual samples in a blinded manner. While pooling reduced the cost of diagnosis by 68% and the laboratory processing time by 66%, 5 of the 109 pools showed discordant results when compared with induvial samples. Four pools which tested negative contained 1 positive sample and 1 pool which was positive did not show any positive sample on deconvolution. Presence of a single infected sample with Ct value of 34 or higher, in a pool of 5, was likely to be missed in pooled sample analysis. At the reported point prevalence of 4.8% in this study, the negative predictive value of qRT-PCR on pooled samples was around 96% suggesting that the adoption of this strategy as an effective screening tool for COVID-19 needs to be carefully evaluated.
及时诊断 COVID-19 感染者并对其进行隔离对于控制 SARS-CoV-2 的传播至关重要。虽然实时荧光定量逆转录聚合酶链反应(qRT-PCR)是 COVID-19 诊断的首选方法，但该技术资源密集且耗时，限制了其在资源有限环境中的广泛适用性，并需要新的策略来满足不断增长的检测需求。在这种情况下，在印度中部三个地区的新发疾病爆发中评估了合并样本检测策略，以评估是否可以在不影响诊断特征的情况下降低检测成本和周转时间，从而实现对疫情的早期控制。从三个新发地区收到的 545 份鼻咽和口咽样本中，共创建了 109 个池，每个池有 5 个连续样本。以盲法方式比较了合并样本 qRT-PCR 的诊断性能与单个样本的诊断性能。虽然合并样本可以将诊断成本降低 68%，实验室处理时间降低 66%，但与个体样本相比，109 个池中有 5 个池的结果不一致。4 个检测结果为阴性的池中有 1 个阳性样本，1 个阳性池在去卷积后没有显示任何阳性样本。在合并样本分析中，很可能会漏掉 5 个样本中单个 Ct 值为 34 或更高的感染样本。在本研究中报告的 4.8%的点患病率下，合并样本 qRT-PCR 的阴性预测值约为 96%，这表明需要仔细评估采用这种策略作为 COVID-19 的有效筛查工具。
