Optimal size of Sample Pooling for RNA Pool Testing: An Avant-Garde for Scaling up Severe Acute Respiratory Syndrome Coronavirus-2 Testing

Abstract

Background and Objectives: Timely diagnosis is essential for the containment of the disease and breaks in the chain of transmission of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The present situation demands the countries to scale up their testing and design innovative strategies to conserve diagnostic kits and reagents. The pooling of samples saves time, workforce and most importantly diagnostic kits and reagents. In the present study, we tried to define the pool size that could be applied with acceptable confidence for testing. Materials and Methods: We used repeatedly tested positive clinical sample elutes having different levels of SARS CoV 2 RNA and negative sample elutes to prepare seven series of 11 pools each, having pool sizes ranging from 2 to 48 samples to estimate the optimal pool size. Each pool had one positive sample elute in different compositions. All the pools were tested by SARS CoV 2 reverse transcriptase quantitative polymerase chain reaction. Results: Out of the 77 pools, only 53 (68.8%) were found positive. The sensitivity of pools of 2–48 samples was decreased from 100% (95% confidence interval [CL]; 98.4–100) to 41.41% (95% CL; 34.9–48.1). The maximum size of the pool with acceptable sensitivity (>95%) was found to be of six samples. For the pool size of six samples, the sensitivity was 97.8% and the efficiency of pooling was 0.38. Conclusions: The pooling of samples is a practical way for scaling up testing and ultimately containing the further spread of the CoV disease 2019 pandemic.

Sample pooling, a population screening strategy for SARS-CoV2 to prevent future outbreak and mitigate the “second-wave” of infection of the virus

“…Several countries have been using pool testing as a successful strategy for the population wide screen of SARS-CoV-2 infection (Khodare et al , 2020). Recently, attempts been made to understand the sensitivities of the SARS-CoV-2 detection real time kits in pool testing set up and feasibility.…”

Test Groups, Not Individuals: A Review of the Pooling Approaches for SARS-CoV-2 Diagnosis

“…Evaluation of efficiency gain is performed differently in the analyzed research studies. Many of them discuss thoroughly the sensitivity of pools, but report efficiency data only about a single clinical application [ 9 , 10 , 19 , 20 , 21 , 22 ,]. Other papers evaluate, at least approximately, the probability of obtaining a negative pool or the expected number of tests required, as a function of N , vf , and pool size, s [ 11 , 12 , 15 , 16 , 22 ].…”

“…The dilution effect due to pooling was considered to be of varying importance among the studies, which is likely because, in the different experimental settings, samples with different viral loads were pooled. Arvind and colleagues [ 20 ] investigated the pool size in depth on the basis of different viral loads. Clinical samples previously tested as positive but with a different range of Ct values of the E gene target were chosen, serially diluted with negative sample elutes, and tested by RT-PCR to determine whether they remained detectable.…”

Group testing as a strategy for COVID-19 epidemiological monitoring and community surveillance

“…Late April, a report from Saarland University, Germany, indicated that positive sample with a relatively mild viral load from asymptomatic patients could still be detected within pools of 30 [21]. Further works suggest that RT-qPCR viral detection can been achieved in pools with a number of samples ranging from 5 to 64 [22][23][24][25][26][27][28][29][30][31][32][33][34][35][36].…”