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Researchers from the Institute of Genomics and Integrative Biology have modified their gene-editing technology-based FELUDA paper-strip diagnostic kit in such a manner that a simple PCR test can be used to detect mutated variants of the Sars-CoV-2 virus that causes coronavirus disease (Covid-19).
At present, to detect the UK, South Africa, or Brazilian variants, the entire genome of the virus has to be sequenced to look for specific mutations. This, however, adds cost and time to the process—three days in comparison to a few hours it takes to do a PCR.
After taking the name of the famous fictional Bengali detective for their first kit, the researchers have named the second one after the author of the detective series—RAY (Rapid variant AssaY).
“We have developed on the FELUDA platform to come up with a test that can tell us in a few hours whether an infected person has any of the three new variants of concern. This will make detecting the new variants simpler and eliminate the need for complete genetic sequencing for diagnosis, which costs many folds and takes about three days to do,” said Dr Debojyoti Chakraborty, senior scientist at IGIB and part of the team that developed both the tests.
He added, “This does not mean we can stop sequencing the viral genome. We will still have to sequence a proportion of our positive samples to detect whether new mutations are arising or any imported mutations are in circulation. Used along with the FELUDA strip, this test will just help in diagnosing whether a particular person has the mutated variant or not.”
Once a swab sample from the patient is collected, the viral RNA is extracted from it and amplified using a thermo-cycler machine. The FELUDA (FnCas9 Editor Linked Uniform Detection Assay) test then uses a paper strip barcoded with the Cas9 protein to recognise specific portions of the genetic material of the Sars-CoV-2 virus to give a positive result.
For RAY, the scientists have encoded the Cas9 protein to recognise the N501Y mutation, which is present in all the three new variants of concern.
“In theory, the Cas9 protein can be encoded to recognise any number of mutations as and when they arise. The high specificity of the Cas9 can be utilised to detect any point mismatch in the viral genome,” said Dr Chakraborty.
The lab is currently in talks with the industry to market the product. Tata Sons had manufactured and marketed the initial FELUDA test kits. The cost of the RAY test is likely to be the same as FELUDA. The scientists had earlier said that the lab cost of the test came up to R500 per sample, but the final cost decision depends on the company marketing it.