The Indian Institute of Technology (IIT), Delhi, has developed a method to detect COVID-19 that will bring down the cost of testing by one-fourth.
Approved by the Indian Council of Medical Research (ICMR) with 100% sensitivity and specificity, the IIT Delhi' s Kusuma School of Biological Sciences is perhaps the first academic institution in the country to get the nod for the diagnostic assay they have developed.
The test kits developed by the team would perhaps cost one-fourth of the rate of the existing real-time polymerase chair reaction (PCR) assay for detecting the SARS-CoV-2 virus. The institute is now in discussions to find reliable and suitable partners to transfer the technology that can help reach the masses.
Led by Associate professor Vivekanandan Perumal, the team comprised Bishwajit Kundu, professor; James Gomes, professor and head of the department; Manoj N. Menon, assistant professor; research scholars Prashant Pradhan, Ashutosh K. Pandy, and Praveen Tripati; post-doctoral scholars Akhilesh Mishra and Parul Gupta; and project consultant Sonam Dhamija.
Dr. Menon, who hails from Trippunithura, highlights some aspects of the procesure:
When did the team start with the research project?
We started around the end of January with designing the assay, when it was clear that the disease is on the rise.
Was there any direction from government?
No specific directions. The department broached the subject with the board of IIT-Delhi and it came up with schemes to support COVID-19 research and gave funding and special permissions for work during the lockdown.
What were the main roadblocks to the research?
The lockdown meant that students would not be there and that the reagents for research could not be procured easily. Moreover, safety regulations meant that viral RNA was not available easily. These were challenging situations
Availability of RNA would have made it much faster, but we had to create the RNA in vitro transcription. It was alright, but took time. What we made were shorter fragments of RNA. The full genome is too long. If we think of letters in a word, it is a 30,000-letter word.
The pros of this approach is safety and the fact that we could do real quantitative testing. We know how many copies of our target RNA can be picked up by the assay.
ICMR evaluation was done on real RNA samples and we fared 100/100 in sensitivity as well as specificity scales.
What was the turning point in your project?
The day we could generate the RNA in vitro was the main turning point. Unavailability of RNA was an issue, because of which we could initially standardise only the second part of the assay.
How long did your research take?
We had spent more time to design the best assay possible as these steps are crucial for specificity. After that came the lockdown. Then, we were working day and night to get the assay optimised, until we got the one-step assay that was submitted for evaluation by end of March.
Optimisation is the key in attaining specificity in probe-free assays, the reason why you do not see many even though it is cheaper.
Probe-based assay use a fluorescent labelled DNA to detect viral RNA, while in probe-free approach, unlabelled primer sequences alone are used to specifically amplify target RNA/DNA fragments. The amplified material is detected by a fluorescent dye which is cheaper and easier to procure than the custom-labelled probes.
Could you explain how your kits fared with ICMR’s evaluation?
The ICMR tests each kit on a pael of patient isolated RNA. They will have a set of negative samples, some low positives, and high positives. Our assay detected all positive and negative samples correctly. So our score was cent percent.
