New Delhi: An Institute of National Importance under the Ministry of Science and Technology has developed a new RT-PCR kit with novel gene which targets facilitating detection of Covid-19 across various mutant strains.
In a statement, the Ministry of Science and Technology said, "A newly developed multiplex RT-PCR kit has a higher accuracy of detecting Covid 19 across the various mutant strains of the virus responsible for the global 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."
"The new multiplex RT-PCR kit targets two SARS-CoV-2 genes: RdRp and ORFb-nsp14, and the human RNAse P gene as the internal control to help detect a range of mutant strains,"
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.
"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, Government of India targets two SARS-CoV-2 genes: RdRp and ORFb-nsp14, and the human RNAse P gene as the internal control to help detect a range of mutant strains," the Ministry said.
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.
"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 Ministry said.
The Indian Council of Medical Research (ICMR) has validated this kit at the National Institute of Virology (NIV) Pune, and found that it has 97.3 per cent sensitivity and 100 per cent specificity in Covid 19 detection.
The SCTIMST has signed a non-exclusive license MoU with Huwel Lifesciences, Hyderabad, on May 14 to commercialize the kit.
"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 Prof Ashutosh Sharma, Secretary, DST.
US Researchers Develop Portable, Low-Cost COVID-19 Test
Meanwhile, US researchers have developed a new portable Coronavirus test that can get accurate results from a saliva sample in less than 30 minutes.
Many of the components of the hand-held device used in this technology, called Scalable and Portable Testing (SPOT) , can be 3D-printed. The test can detect as little as one viral particle per 1-microlitre drop of fluid, researchers report in the journal Nature Communications.
"We developed a rapid, highly sensitive and accurate assay, and a portable, battery-powered device for Covid-19 testing that can be used anywhere at any time," said lead researcher Huimin Zhao, chemical and biomolecular engineering professor at the University of Illinois Urbana-Champaign, in the US.
Though it is still in the prototype stage, the device is estimated to cost less than $78 and the reagents and other materials needed for testing would amount to $6-$7 per test, the researchers said.
The new technology does away with the complicated process of heating and cooling each sample to get results, as many current testing protocols require. SPOT also can detect multiple genes per sample, making it more accurate than single-gene tests, which can yield incorrect or inconclusive results. Another advantage is that it utilises saliva, which is easier to collect and less invasive than a nasal swab.
The innovation was made possible by the recent discovery in Zhao's laboratory of a system for making artificial restriction enzymes that can be programmed to recognise and cleave specific genes in an organism's genome.
In the new device, enzymes carry DNA guides that tag the viral genes of interest. The enzyme cleaves the genes, which have been tagged with a dye that fluoresces only after the genes are cut. The resulting fluorescence signals that those genes are present -- a positive test result.
The team tested SPOT using 104 clinical saliva samples and found that it accurately identified 28 out of 30 SARS-CoV-2-positive samples and 73 of 74 SARS-CoV-2-negative samples.
The team also tested SPOT with samples containing -- or lacking -- the influenza virus, the new coronavirus and three other human coronaviruses. It accurately identified samples containing the new coronavirus, whether or not other viruses were present in the sample.