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Coronavirus | Labs grapple with shortage of reagents, funds hits genome sequencing

Not conducting enough tests runs risk of not detecting future variants of concern.

Not conducting enough tests runs risk of not detecting future variants of concern.

Amidst the third wave of COVID-19, several laboratories tasked with genome sequencing are limiting the number of coronavirus samples they analyse for a variety of reasons, The Hindu has learnt, including a paucity of necessary reagents, a fund shortage or a deluge of sampling requests.

Some of these labs are part of the INSACOG network, the pan-India consortium of 38 laboratories tasked with monitoring the genomic variations in SARS-CoV-2.

An internal note by the Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, for instance says the “reagent shipment is highly impacted” and only limited number of samples would be taken up for sequencing. The institute however said it expected the shortage to resolve within a week.

The Delhi-based National Centre for Disease Control (NCDC) refused to analyse cases (determining the variant) involving “adverse outcomes” and directed that they be sent to the Institute of Liver and Biliary Sciences, also in Delhi. “No samples to be sent to NCDC as they have run out of [test] kits,” said another note to labs viewed by The Hindu .

Both the RGCB and the NCDC are part of the INSACOG network. A January 10 note by the INSACOG made public on January 23 said India was now in “community transmission”, the first time a government body has conceded so. It said Omicron and its related variant, BA.2, was the dominant variant driving infections across the country.

That the true extent of the spread of the Omicron variant is unknown is apparent from the same INSACOG note, which says only 517 instances (as of Jan 10) have been confirmed to be Omicron. This, when India had started to report over 1,00,000 cases every day.

One scientist, connected to the genome sequencing effort, said on condition of anonymity that genome sequencing relied almost entirely on imported chemicals, and the case surge in Europe meant that supply shortages were inevitable. “NCDC is a blackhole with little data sharing.”

Some labs were not getting the necessary funds promised by the government and therefore unable to keep pace with demand, The Hindu has learnt.

Rakesh Mishra, former Director of the Centre for Cellular and Molecular Biology, Hyderabad, also an INSACOG lab, said not conducting enough tests ran the risk of not detecting future variants of concern.

Some laboratories relied on a genome sequencing technology from Nanopore, a United Kingdom-based company, that could be causing disruptions in supply. He said most of the labs with dedicted expertise in genome sequencing weren’t facing a problem but many of the “newer labs” roped in as part of INSACOG for whom molecular biology wasn’t their core function, could be facing challenges.

“Omicron is driving the surge, undoubtedly, but a lab’s capabilities depend on whether they regularly receive samples from hospitals or healthcare facilities in their States to assess the threat. So not all places will work equally,” he said.


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Printable version | May 18, 2022 10:10:44 am | https://www.thehindu.com/news/national/coronavirus-labs-grapple-with-shortage-of-reagents-funds-hits-genome-sequencing/article38325933.ece