Omicron surge stretches a Central genome lab

National Centres for Disease Control has asked States to restrict samples sent for analyses.

December 31, 2021 09:36 pm | Updated 10:44 pm IST - NEW DELHI:

The National Centres for Disease Control, along with being a sequencing laboratory, is also a hub that coordinates with all regional labs as well as the India SARS-CoV2 Genome Consortium (INSACOG). Photo:

The National Centres for Disease Control, along with being a sequencing laboratory, is also a hub that coordinates with all regional labs as well as the India SARS-CoV2 Genome Consortium (INSACOG). Photo:

The surge in coronavirus cases appears to be stretching the organisational capacity of labs tasked with sequencing virus genomes.

The Delhi-based National Centres for Disease Control (NCDC), a Union Health Ministry laboratory and a key lab in India's genome sequencing network, has asked States to temporarily pause sending COIVD positive samples to it. For the past year, labs have been sending the NCDC samples to check for the presence of key variants of concern and since December Omicron.

Also read | Tamil Nadu lab gets INSACOG recognition

In a note sent on Thursday to labs of State health departments seen by The Hindu , an NCDC official says: “Keeping in view the surge in number of COVID-19 cases and increased flow of samples for next generation sequencing (genome sequencing) to NCDC has resulted in a situation wherein they (NCDC) are not in a position to accommodate samples further (for the time being). ... All labs are requested to store all positive samples as per established protocol till further directions. However positive samples of individuals arriving at IGI Airport (New Delhi international airport) with a history of travel to country of concern/their contacts will continue to be sent to NCDC for sequencing.”

NCDC, along with being a sequencing laboratory, is also a hub that coordinates with all regional labs as well as the India SARS-CoV2 Genome Consortium (INSACOG), an all-India group of 10 labs and 18 satellite labs that analyses a certain percentage of all coronavirus positive samples for their genetic makeup to determine evolutionary changes in the coronavirus, whether variants of concern are present in India and, if coronavirus samples in India are displaying signs of mutational changes that may forewarn future surges. The Delta variant, for instance, was first validated in India by INSACOG labs and was later linked to be the main culprit behind the lethal second wave. NCDC is also an INSACOG lab.

NCDC Director Sujeet Kumar Singh told The Hindu that this was a “partial” message and the request was that Delhi samples be diverted to other labs for quicker analysis to avoid delay.

“The message is samples of Delhi may be kindly diverted to other genome sequencing laboratories for the time being as most samples are from Delhi to avoid delay in processing and reporting. Further, some States have been asked to send the samples to other nearby labs which have the capacity,” he told The Hindu in a text message.

The NCDC has an estimated sequencing capacity of 3,000 samples per month and Mr. Singh didn't clarify to The Hindu if the samples from Delhi exceeded this capacity.

On Thursday, The Hindu had reported that Delhi government officials were contemplating reducing the COVID-19 samples sent for genome sequencing as over half of a batch of 125 samples collected from people in the city, who did not have a travel history, had been confirmed to be Omicron.

“These 125 samples are from different labs in the city and not from the airport. This shows that there is transmission of the Omicron variant in the community and there is no point in sending all positive samples to check whether they are Omicron variant,” a Delhi government official had said. These samples were sent to another lab, the Institute of Liver and Biliary Sciences, which too is part of the INSACOG network.

The States and Union Territories that send samples to NCDC include eastern Madhya Pradesh, Uttarakhand, Chandigarh, Delhi, Haryana, Himachal Pradesh, Ladakh, Jammu and Kashmir and Punjab. Designated hospitals and laboratories in these states are expected to send at least 15 COVID positive samples every fortnight.

Delhi, notably, has seen a rapid surge in cases with over 1,000 cases being reported since Thursday and 320 of them confirmed to be of the Omicron variant. The other States under the purview of the NCDC have reported fewer cases: Himachal Pradesh, Punjab, Ladakh have each reported one Omicron case. J&K and Chandigarh three cases, Uttarakhand four cases, Haryana 14 cases and Eastern Madhya Pradesh nine cases.

An INSACOG scientist, who declined to be identified, said NCDC’s predicament stemmed from having too few labs able to reliably test genomes at scale. Moreover, the person said, it was bewildering that despite the strain NCDC chose to continue expending effort in testing international travellers when the Omicron strain was clearly far widespread in the community.

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