Govt mulling testing of random Covid-19 samples for UK virus

The government is considering genetically sequencing random Covid-19 samples from the public from January in a bid to check whether the new UK novel coronavirus has spread beyond international passengers.

The proposal comes as the state potentially faces the challenges of contending with two variants of the virus. It also comes in the wake of the central government calling for 5% of all Covid-19 swabs in the country to be genomically processed to reveal the mutational fingerprint of virus samples.

So far, genomic sequencing of 31 Covid-19 positive individuals among air passengers in Karnataka has found initially seven people infected with the new UK variant of the Sars-CoV-2 virus, titled B.1.1.1.7.

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Sources told DH that random sequencing was likely to be introduced after genomic sequencing centres in Karnataka finish processing a backlog of samples collected from the nearly 2,000 international passengers.

Sources added that the backlog is due to the limited capacity for sequencing in Bengaluru. Nimhans, which has been carrying out genomic sequencing of Covid-19 samples within weeks of the start of the outbreak, has a capacity of 12 samples per day.

Meantime, InStem and the National Centre of Biological Sciences (NCBS), together have a capacity to test 50 samples per day, according to Professor Satyajit Mayor, Director of NCBS.

“The capacity can be and should be increased if Karnataka is to test more samples,” Dr Mayor said.

While reports suggested that the Indian Institute of Science (IISc) had been roped in to help with sequencing, two senior scientists there said they had been given no such information.

At the same time, the Minister of Health, Dr K Sudhakar, said that there was no plan to physically increase the number of testing centers. “We have one in Nimhans. If need be, we will think of equipping other centres to conduct genome sequencing,” he said.

While scaling up will eventually happen, it will not be on a mass scale, added Dr C N Manjunath, nodal officer for testing in Karnataka. “Any scaling up would be done by Nimhans and NCBS,” he said.

Mayor confirmed that NCBS-Instem had the capacity to increase sequencing by a factor of five if it could employ “multiplexing.” In this method, DNA fragments from different samples are pooled and sequenced all together. This increases sample throughput while reducing time and cost.

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At present, the cost to sequence a single sample in a government lab comes to about Rs 20,000 per sample, explained Dr Manjunath. Dr Mayor added that multiplexing could further slash prices per sample.

Dr Manjunath clarified that the primary effort of the government would still be on strengthening surveillance measures. “We have understood this virus. The clinical outlook for both variants is the same. However, since an alert has come that the UK variant is present in Karnataka, we are taking precautions,” he said.