A Central Government-run institute of medical sciences has developed a new multiplex RT-PCR kit which has a higher accuracy of detecting Covid-19 across various mutant strains of coronavirus than the existing tests, according to a statement issued by the Ministry of Science and Technology.
The Indian Council of Medical Research (ICMR) has validated this kit at the National Institute of Virology, Pune, and found that it has 97.3% sensitivity and 100% specificity in Covid-19 detection, the statement said.
The new multiplex RT-PCR kit developed by the Government’s Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST) targets two SARS CoV2 genes: RdRp and ORFb-nsp14, and the human RNAse P gene as the internal control to help detect a range of mutant strains.
Various studies have shown that RdRp and ORF1b-nsp14 genes are more sensitive in detecting Covid-19. In order to target the multiple variants in the second wave, using two highly accurate confirmatory genes like RdRp and ORF-nsp14, can give precise results. The ORFb-nsp14 is one of the least mutated genes in Covid-19 and currently, there are no kits in the market with ORF-nsp14 as the target, according to the government statement.
The new kit is based on multiplex Taqman chemistry, amplifying all three genes in a single reaction. The amplification time for the assay is 45 minutes, apart from the time required for the RNA isolation from nasopharyngeal swab samples. Multiplexing two confirmatory genes will help shortlist possible new variants if one of the genes fails to amplify and can be marked for sequence analysis, the statement added.
SCTIMST has signed a non-exclusive license MoU with Huwel Lifesciences, Hyderabad, on 14th May 2021 to commercialize the kit.
As the pandemic is going through a second wave with multiple variants, the selection of target genes in multiplex RT-PCR assay is becoming critical for accurate detection of the virus.
Even though coronaviruses make far fewer errors than other RNA viruses, the mutations in S, R, and N genes often interfere with RT-PCR assay. For example, the “variant of concern” B1.1.7 (also known as the UK variant) has a 69-70del, due to deletion of 6 bases in the RNA, which resulted in S gene drop out from RT-PCR assay.
“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,” said Secretary, DST, Prof Ashutosh Sharma.
