A new pooling method for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic testing that uses standard protocols, reagents and equipment can be applied immediately in current clinical testing laboratories, according to data published in Clinical Infectious Diseases.
The substantial need for diagnostic testing brought on by the coronavirus disease 2019 (COVID-19) pandemic has led to shortages in reagents associated with these tests. To help address the shortages, investigators aimed to develop a lean immediately-applicable protocol.
To test their method RNA extracts of positive samples were tested for the presence of SARS-CoV-2 using reverse transcriptase quantitative polymerase chain reaction (RT-qPCR), alone or in pools of 2, 4, 8, 16, 32 and 64, along with negative samples. Transport media of an additional 3 positive samples were also tested when mixed with transport media of negative samples in pools of 8.
Using standard kits and protocols a single positive could be detected in pools of up to 32 samples, with an estimated false negative rate of 10%. The detection of positive samples diluted in pools of up to 64 may also be possible, but may require additional amplification cycles. It was also shown that single positive samples can be detected when pooling either before or after RNA extraction.
Investigators hope that this proof-of-concept encourages further research that develops mathematical and computational tools tailored for pooled SARS-CoV-2 testing. They concluded that, “these results can be used not only for pooling, but also in multiplexing and any other signal compression techniques where samples are mixed to reduce the number of tests.” Pooling can be especially useful for routine community survey and for monitoring cohesive groups were a single positive typically requires quarantine of the entire group. It may also allow for more routine monitoring and detection of low frequency of carriage and therefore inform policy makers, reduce transmission, and alleviate strain on healthcare services.
Yelin I, Aharony N, Shaer Tamar E, et al. Evaluation of COVID-19 RT-qPCR test in multi-sample pools [published online May 2 2020]. Clin Infect Dis. doi:10.1093/cid/ciaa531