ICMR approves dry-swab RT-PCR method to ramp up Covid testing

The method also skips over the step of RNA extraction, with the samples being directly set up for RT-PCR following a simple processing.

The Indian Council of Medical Research (ICMR) has approved the “dry swab-direct” RT-PCR method for Covid-19 testing, after finding it to be 96.9% in concordance with the current sample collection method. The process developed by researchers from the Centre for Cellular and Molecular Biology-Hyderabad (CCMB-H) skips a few steps done before performing the gold standard RT-PCR test, meaning it can help in scaling up Covid-19 testing two to three times at no additional cost.

The organisation had been collecting and testing patient samples since April 2020 and had been able to identify the bottlenecks. (HT Photo)

Under the new method, nasal swab samples can be directly put in a dry test tube for transportation instead of using a viral transport media (VTM), which is a solution that can keep the live virus stable for 72 hours without refrigeration. Using a dry tube instead of VTM also prevents spillage and contamination of samples that can result in the test throwing up false positives.

The method also skips over the step of RNA extraction, with the samples being directly set up for RT-PCR following a simple processing.

“Handling of the dry swab becomes extremely easy because there is no risk of spillage and the vials do not need to be sealed. In addition, we also skip the step of RNA extraction, which even with automation takes 4 hours for roughly 500 samples. This cuts down the time and the cost of an RT-PCR test by half. For example, for each test the VTM costs about ₹100, the RNA extraction kit about ₹200 to 250, and the additional steps also consumes a lot of plastic ware that will be eliminated,” said Dr Rakesh Mishra, director, CCMB.

The organisation had been collecting and testing patient samples since April 2020 and had been able to identify the bottlenecks. The process was submitted for approval to the ICMR in June but the delay in approval had prompted the director of Council of Scientific and Industrial Research, which runs CCMB, had said, “What we needed in the country is to get science rid of the bureaucracy. In fact one thing that hinders science in India is our bureaucracy. We had announced dry swab in June and yet on today’s date, we don’t have regulatory approval for one reason or the other. It’s a shame.” He was speaking at a lecture in Pune International Centre (PIC) in September.

Following this, ICMR had tweeted, “Scientific evaluation proved that despite initial promises, swabs collected from clinic attendees & transported in a dry test tube environment w/o VTM for RT-PCR & skipping RNA extraction in the laboratory, is not effective for diagnosis of SARS-CoV-2.”

This prompted the researchers to add an enzyme to the process, making it more robust, and in concordance to the results given by the existing method even for samples with low viral load.

“At our end, the results were similar to the traditional RT PCR method. However, in some settings and depending on people running and reading the tests, the samples where the CT value was high – meaning low viral load – the results could be interpreted as this way or that. As we do not do RNA extraction, we need to get an efficient amount of virus even from such samples. For that, we have added a cheap enzyme Proteinase K to the sample before putting it in RT PCR. This helps in getting more viral particles and proteins for the test to detect,” said Dr Mishra.