ICMR okays new RT-PCR kit with ‘high accuracy’

Using a gene that is least likely to mutate, the Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST) in Kerala have developed a new RT-PCR kit that they say has a higher accuracy in detecting Covid-19.

The kit has been approved by the Indian Council of Medical Research (ICMR) for use.

When tested at the National Institute of Virology-Pune, it was found to be 97.3% sensitive and 100% specific, meaning it is unlikely to throw up any false positives and has only a 2.7% chance of showing a false negative.

SCTIMST has already signed a non-exclusive license deal with biotech company Huwel Lifesciences for scaling up production.

RT-PCR tests amplify the genetic material of the virus found on swab samples, extract it and check for specific fragments to give a positive or negative report; the probe in the RT-PCR kit targets these specific fragments or genes and attach with it to detect it. The test developed by SCTIMST uses probes against RdRp and ORFb-nsp14 genes of Sars-CoV-2 virus that causes Covid-19.

The mutations on the commonly used S, R and N gene of the virus interfere with the result of an RT-PCR test. For example, the changes in the spike protein of B.1.1.7 (first found in the UK) resulted in failure of probes for the S gene.

According to researchers from the institute, “various studies have shown that RdRp and ORF1b-nsp14 genes are more sensitive in detecting Covid-19”.

The ORFb-nsp14 is one of the least mutated genes of the virus but currently there are no kits available in the market with probes for the gene.

The turnaround time using the kit developed by SCTIMST is also faster. The kit amplifies all three genes – two Sars-CoV-2 genes and one human gene used as control to see whether the reaction happened properly – in a single reaction, taking 45 minutes in addition to approximately 30 minutes it takes to extract the RNA from the patient’s swab sample. A normal RT-PCR takes about five to six hours to be completed.

“This unique RT-PCR kit will be a significant weapon in our fight against Covid-19 by a facile detection of SARS-CoV-2 mutations which are becoming increasingly important,” Prof Ashutosh Sharma, secretary, department of science and technology, said in a release.