Hyderabad

COVID genome sequencing hit by sample shortage

Three months into the formation of the Indian SARS-CoV-2 Genomics Consortium (INSACOG) of top 10 regional labs of Council of Scientific & Industrial Research (CSIR), Department of Biotechnology (DBT) and Indian Council of Medical Research (ICMR) for genomic surveillance of SARS-CoV-2, they are yet to get sufficient number of samples from COVID-positive patients from both government and private healthcare centres.

“In the last few months, the funds have come by and necessary reagent purchases have been made. Coordination among the labs is improving too. However, we are not getting the required number of samples. It is about 50-60 samples a day when we can do genome sequence up to 1,000 samples. Efforts are being made for samples to be received by the labs to sequence the maximum and get the best outcome of that,” discloses CSIR-Centre for Cellular & Molecular Biology (CCMB) director Rakesh Mishra.

CCMB and Centre for DNA Fingerprinting and Diagnostics (CDFD) are among the 10 labs chosen by the Centre for genome sequencing of COVID-19 samples.

“We are supposed to get 5% of the new positive samples collected from various districts, mandals and even villages from across Telangana, Andhra Pradesh, parts of Karnataka and Goa. But, we have been receiving samples from limited geographical locations whereas the supply from the remote places is not there. It is also because the government health machinery has once again been stretched to the limit in the second wave,” he points out.

States like Karnataka and Goa seem to have preferred sending the COVID samples to the local labs. “Here, we need the help of governments and local bodies to secure more samples from those testing positive. We also need samples from private hospitals where people are getting admitted for effective and continuous monitoring,” says Dr. Mishra.

The consortium had, so far, genome sequenced up to 14,000 samples across the country finding “large number of variants of which 2,000 variants fall into the ‘concerned’ category”. “The very nature of the virus is to mutate and check into other nearby hosts. We have to continuously keep monitoring the variants to look for any potent strains which may make the available vaccines redundant or cause more rapid transmission. For that, we need to enhance our sample collection and also sequencing numbers,” he affirms.

The exercise is to ensure not a single variant arising from any remote corner escapes the notice of scientists. And, if one such dangerous variant is sighted, the particular area can be quarantined to keep it under check. “We are currently studying the double mutation variant and results should be out soon. Genome sequencing of the COVID samples will also establish whether the spike is due to superspreader events, look for high mortality, morbidity trends and co-relate with the associated symptoms. Reinfections, too, can be effectively monitored through this process,” says the CCMB director.

Other labs involved in genome sequencing are NIBMG Kalyani, ILS Bhubaneswar, ICMR-NIV Pune, NCCS Pune, InStem/NCBS Bengaluru, NIMHANS Bengaluru, CSIR-IGIB Delhi, and NCDC Delhi. Dr. Mishra had already stated that double mutation or ‘B.1.617’ variant is largely prevalent in Maharashtra (up to 50%) and UK variant in Punjab (up to 50%). These are found to be 5-10% prevalent in other places and it could mean the current spike is likely due to the commonly prevalent virus strains and lack of COVID-appropriate behaviour.

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Printable version | May 19, 2021 8:13:20 AM | https://www.thehindu.com/news/cities/Hyderabad/covid-genome-sequencing-hit-by-sample-shortage/article34380053.ece

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