A novel strategy for community screening of SARS-CoV-2 (COVID-19): Sample pooling method

Abstract

The rapid global spread of the coronavirus disease (COVID-19) has inflicted significant health and socioeconomic burden on affected countries. As positive cases continued to rise in Malaysia, public health laboratories experienced an overwhelming demand for COVID-19 screening. The confirmation of positive cases of COVID-19 has solely been based on the detection of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) using real-time reverse transcription polymerase chain reaction (qRT-PCR). In efforts to increase the cost-effectiveness and efficiency of COVID-19 screening, we evaluated the feasibility of pooling clinical Nasopharyngeal/Oropharyngeal (NP/OP) swab specimens during nucleic acid extraction without a reduction in sensitivity of qRT-PCR. Pools of 10 specimens were extracted and subsequently tested by qRT-PCR according to the WHO-Charité protocol. We demonstrated that the sample pooling method showed no loss of sensitivity. The effectiveness of the pooled testing strategy was evaluated on both retrospective and prospective samples, and the results showed a similar detection sensitivity compared to testing individual sample alone. This study demonstrates the feasibility of using a pooled testing strategy to increase testing capacity and conserve resources, especially when there is a high demand for disease testing.

Fig 1. Number of clinical specimens tested for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).

Testing was performed by pooled sample screening at the IMU Advanced Microbiology Collaborative Research Laboratory since April 13, 2020 (S1 Dataset). Each pool included 10 clinical NP/OP swab specimens. A total of 195 pools comprising of 1,745 clinical specimens was screened; * There was no specimen received for testing on Day 8 (April 20, 2020) and Day 14 (April 26, 2020).