Pooled Testing Strategies for SARS-CoV-2 diagnosis: A comprehensive review

Abstract

SARS-CoV-2 has surged across the globe causing the ongoing COVID-19 pandemic. Systematic testing to facilitate index case isolation and contact tracing is needed for efficient containment of viral spread. The major bottleneck in leveraging testing capacity has been the lack of diagnostic resources. Pooled testing is a potential approach that could reduce cost and usage of test kits. This method involves pooling individual samples and testing them 'en bloc'. Only if the pool tests positive, retesting of individual samples is performed. Upon reviewing recent articles on this strategy employed in various SARS-CoV-2 testing scenarios, we found substantial diversity emphasizing the requirement of a common protocol. In this article, we review various theoretically simulated and clinically validated pooled testing models and propose practical guidelines on applying this strategy for large scale screening. If implemented properly, the proposed approach could contribute to proper utilization of testing resources and flattening of infection curve.

Keywords: COVID-19; Diagnosis; Pooled testing; RT-PCR; SARS-CoV-2; Sensitivity.

Fig. 1

Adaptive pooled testing strategies: (A) Dorfman Pooling: Population is divided into two pools of optimum size 8 and tested. The positively tested pool is then deconvoluted to identify the individual infected sample. (B) Column and row pooling: On a 96-well plate, rows and columns are pooled separately. The negative rows and columns are excluded. The individuals from positive rows and columns are then tested individually. In the above illustration, 5 positive samples are identified with 45 tests, compared to 96 tests if tested individually. (C) Household grouping: Pools are formed from each household in a locality and tested. Positive groups undergo individual testing.

Fig. 2

Adaptive pooled testing strategy: Sample pooling based on Hypercube algorithm. For this example, the three sets of slices are shown in blue, red and green. If one infected individual is present, tests on each set of slices identify their coordinate in that direction. Hence only nine tests would uniquely identify them. (Colour version of figure is available online)

Fig. 3

Pooling methods employed in clinical setups: (A) Sample pooling before RNA extraction (B) Pooling of extracted RNA (C) Sample pooling at the time of collection (D) Sample collected directly into the lysis buffer; VTM= viral transport media.

Fig. 4

Diagnostic accuracy utilising pooled testing strategy: The size of the bubble depicts pool size, while the different colours code for different studies. The purple-shaded area represents areas with sensitivity and specificity combinations that meet the acceptable levels of Target Product Profile (TPP) put forth by WHO for COVID-19 diagnostics. The dashed square box within the purple-shaded area portrays the desirable level. Study bubbles clustered within the acceptable limits infer efficient diagnostic capability in detecting SARS-CoV-2 by pooling samples. (Colour version of figure is available online)