Cost-effective pool Testing qRT-PCR Method for early Detection and mass Screening of SARS-CoV-2 Infection
Author(s): Samiksha Sharma, Vaibhav K. Tamrakar, Nishant Burnase, Shailendra S. Parihar, Kirti Pagarware and Rekha Barapatre
The COVID-19 pandemic has affected millions of people all around the world. The molecular diagnostic method quantitative reverse transcriptase PCR (qRT-PCR) is considered the gold standard test for SARS-CoV-2 diagnostics. The current study focused on a pooled sample testing strategy and its evaluation in screening of SARS-CoV-2 clinical samples during a disease outbreak. In total, 1389 clinical samples were collected at the COVID-19 sample collection center, CIMS Bilaspur C.G. These samples were taken from the upper respiratory tract (Naso- and Oro-pharyngeal swabs) and kept in viral transport medium (VTM). Samples are randomly pooled in the desired cluster of samples during the lysis. All lysed samples are forwarded to extraction and then qRT-PCR is performed. Among 1389 samples, 600 were taken to make five pool simulations. Similarly, 789 samples were for three pool simulations and the results were compared to their individual test results. It has been found that both 3-sample and 5-sample pooling are almost equally accurate and showed a have a perfect agreement with individual sample testing. However, 3-sample pooling revealed low false negativity and had high concordance results with individual testing. Three pool simulations resulted in more précised and accurate diagnostic outcomes compared to 5 pool samples. Slightly false-negative results were seen in a few five pooled samples, which were further found positive upon retesting it in a single sample. It was observed that very minimal single positive samples with Ct values near 35-37 were likely to be missed in pooled sample analysis. This study concludes that the pool testing strategy should be considered an effective screening tool for mass sampling because this testing method also has less effect on the environment and reduces the cost of consumables.