New technology to make COVID testing more accurate

SHILLONG: Undergoing COVID tests can at times cause immense tension oscillating as they do between negative-positive-negative. Looks like, this is soon going to be a thing of the past.
“India will soon have better and more accurate testing facilities and which can also be used as a confirmatory test,” according to Sridhar Sivasubbu, senior Scientist at the CSIR-Institute of Genomics and Integrative Biology (IGIB).
In a phone conversation with The Shillong Times on Thursday, he said that to speed up testing as well as improve the accuracy of testing for coronavirus (COVID-19) positive cases, CSIR is working on developing “mega labs” where large machines, called Next Generation Sequencing machines (NGS), which are also used for sequencing human genomes, will be repurposed to sequence 1,500-3,000 viral genomes at a go for detecting the SARS-CoV-2 novel coronavirus.
Used optimally and with appropriate modifications, these genome sequencing machines can substantially detect the possible presence of the virus even in several instances where the traditional RT-PCR (reverse transcription polymerase chain reaction) tests miss out on them. This is primarily because the RT-PCR test identifies the SARS-CoV-2 virus by exploring only specific sections of the virus whereas the genome method can read a bigger chunk of virus genome and thereby provide more certainty that the virus in question is indeed the particular coronavirus of interest.
The test, he said, is more credible and can also trace the evolutionary history of the virus and track mutations more reliably. Unlike the RT-PCR that needs primers and probes — a key hurdle in operationalising such tests on a mass scale early on in the pandemic — the NGS does not need primers and probes, and only needs custom reagents.
The CSIR has partnered with the U.S.-based Illumina, a company that specialises in the manufacture of NGS machines. Five such sequencers, costing ?4 crore each, are currently available in India.
“From our pilot tests so far, we found that 99% of confirmed RT-PCR positive samples were identified so by the NGS method. More importantly, nearly half of the samples that the RT-PCR termed ‘inconclusive’ were identified as either positive or negative,” informed Dr Sivasubbu.
) Researchers in CSIR have also published the results of their analysis on Monday last, on bioRxiv, a preprint server where scientific results are up for public viewing. These, however, have not been peer-reviewed.
Though India has tested 24 million samples so far, that only works out to about 17,000 per million. With about 7.5 lakh tests per day, the Indian Council of Medical Research (ICMR) says it aims to scale up testing to at least a million per day. NGS could help with that, said Dr. Sivasubbu, but would serve a larger purpose of continuous surveillance.
“While RTPCR is 70%-80% accurate and antigen tests 50% so, it implies that there would be a sizeable population that is falsely negative. Regular surveillance of a large pool in, say industrial hubs, commercial establishments or places where an outbreak is likely would help catch new infections,” he said in a phone conversation.
More effective RT-PCR method
Dr. Anurag Agrawal, Director, CSIR-IGIB, said that establishing “hubs” capable of whole genome sequencing would help track significant mutations in the virus and can be repurposed for any kind of outbreak, be they of viral or bacterial origin.
The NGS approach took 11 hours for sequencing 1,536 samples, and using methods such as “pooling”, where batches of samples are optimally chosen and analysed, a single run could be used to double the number of analysed samples.
In July this year, Prime Minister Narendra Modi announced the launch of three centres that would be able to sequence 10,000 samples a day, but these would be traditional RT-PCR units.

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