Evaluation of sample pooling for diagnosis of COVID-19 by real time-PCR: A resource-saving combat strategy

Although about 80% of coronavirus disease-2019 (COVID-19) cases are reported to be mild, the remaining 20% of cases often result in severe disease with the potential of crushing already overstrained health care services. There has been sustainable growth of COVID-19 cases worldwide since mid-May 2020. To keep tabs on community transmission of COVID-19 infection screening of the samples from a large population is needed which includes asymptomatic/symptomatic individuals along with the migrant population. This requires extra resources, man power, and time for detection of severe acute respiratory syndrome coronavirus 2 by real-time polymerase chain reaction (RT-PCR). In the current scenario, the pooled sample testing strategy advocated by the Indian Council of Medical Research, New Delhi is a new approach that is very promising in resource-limited settings. In this study, we have evaluated the pooled strategy in terms of accurate testing results, utilization of consumables, and identification of borderline positive cases.

Between April and June 2020, we performed COVID-19 testing by RT-PCR from areas with varying prevalence of population referred to COVID laboratory, Dr Ram Manohar Lohia Institute of Medical Sciences, Lucknow. In the first step, the samples are collated into pools of 5 or 10. These pools are tested by RT-PCR. Negative pools were reported as negative whereas positive pools of 5 and 10 are then deconvoluted and each sample is tested individually.

In the present study, we tested 4620 samples in 462 pools of 10 and 14 940 samples in 2990 pools of 5. Among 10 samples pool, 61 (13%) pools flagged positive in the first step. In the second step, among 61 pools (610 samples) deconvoluted strategy was followed in which 72 individual samples came positive. The pooled-sample testing strategy helps saves substantial resources and time during surge testing and enhanced pandemic surveillance. This approach requires around 76% to 93% fewer tests done in low to moderate prevalence settings and group sizes up to 5-10 in a population, compared to individual testing.

Pooled-sample PCR analysis strategies can save substantial resources and time for COVID-19 mass testing in comparison with individual testing without compromising the resulting outcome of the test. In particular, the pooled-sample approach can facilitate mass screening in the early coming stages of COVID-19 outbreaks, especially in low- and middle-income settings, and control the spread by meticulous testing of all risk groups.