Sree Chitra Institute develops multiplex RT-PCR kit that can detect new strains of Wuhan virus

A new multiplex RT-PCR kit developed by Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), an institute under the Department of Science and Technology (DST), has a higher accuracy of detecting Wuhan virus or the new coronavirus across its various mutant strains now spreading the pandemic.

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.
“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,” secretary, DST,  Ashutosh Sharma, said.
Even though the Wuhan virus makes 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.
The new multiplex RT-PCR kit developed by Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), an institute of national importance under the Department of Science and Technology, 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 the new coronavirus. 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 the new coronavirus and currently, there are no kits in the market with ORF-nsp14 as the target, says a DST release.
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.
ICMR has validated this kit at the National Institute of Virology, Pune, and found that it has 97.3 per cent sensitivity and 100 per cent specificity in coronavirus detection.
SCTIMST has signed a non-exclusive license MoU with Huwel Lifesciences, Hyderabad, to commercialise the kit.