Pooling five COVID-19 samples may not lead to much loss of sensitivity even for low viral loads: ICMR scientist
Sep 05, 2020
By Priyanka Sharma
New Delhi [India], September 5 : A study done by the Indian Council of Medical Research (ICMR) has revealed that pooling five samples to detect coronavirus by RT-PCR may be an acceptable strategy without much loss of sensitivity even for low viral loads, while with 10-sample pools there could be considerably higher numbers of false negatives.
The study was done to understand comparative analysis of pooled testing for five- and 10-sample pools by RT-PCR at ten different laboratories conducting COVID-19 testing across the country.
The findings of the study have now been published in the latest edition of the Indian Journal of Medical Research (IJMR).
Dr Nivedita Gupta, a scientist at ICMR and author of the study, said that the laboratories are facing huge sample loads for COVID-19 diagnosis by RT-PCR.
"The high sensitivity of optimized real-time RT-PCR assays makes pooled testing a potentially efficient strategy for resource utilization when positivity rates for particular regions or groups of individuals are low. We conducted a comparative analysis of pooled testing for 5- and 10-sample pools by real-time RT-PCR across 10 COVID-19 testing laboratories in India," she said.
At least ten virus research and diagnostic laboratories (VRDLs) testing COVID-19 by RT-PCR participated in this evaluation.
"At each laboratory, 100 nasopharyngeal swab samples including 10 positive samples were used to create 5- and 10-sample pools with one positive sample in each pool. RNA extraction and real-time RT-PCR for SARS-CoV-2-specific E gene targets were performed for individual positive samples as well as pooled samples," Dr Gupta said.
The scientist said that concordance between individual sample testing and testing in the 5- or 10-sample pools was calculated and the variation across sites and by sample cycle threshold (Ct ) values was analyzed.
"Results from this multi-site assessment suggest that pooling five samples for SARS-CoV-2 detection by RT-PCR may be an acceptable strategy without much loss of sensitivity even for low viral loads, while with 10-sample pools, there may be considerably higher numbers of false negatives. However, testing laboratories should perform validations with the specific RNA extraction and RT-PCR kits in use at their centres before initiating pooled testing," she said.
