In new strategy, 5% of all COVID cases to be tested for UK strain

Five per cent of COVID-19 positive cases from all states and union territories will be tested for Whole Genome Sequencing (WGS) as part of the Centre’s plan to detect and contain the new variant strain of the virus found in the UK, according to the Union health ministry.

The announcement was made after the National Task Force (NTF) on COVID-19 met on the issue on Saturday. The NTF concluded there is no need to change the existing Treatment Protocol in view of mutations emerging in the strain, the ministry said in a statement.

Moreover, the government has formed a genomic surveillance consortium, INSACOG, under the leadership of the National Centre for Disease Control (NCDC), New Delhi, for laboratory and epidemiological surveillance of circulating strains of SARS-CoV-2 in India.

Currently, more than 50 samples of UK returnees are under sequencing at the designated laboratories.

The ministry said that it is proposed to continue enhanced genomic surveillance for early detection and containment of the UK variant SARS-CoV-2 strains. But it is important to understand that like all other RNA viruses, SARS-CoV-2 will continue to mutate, it added.

It said that the mutated virus can be contained by measures like social distancing, hand hygiene, wearing masks and by an effective vaccine, as and when available.

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Since ICMR has always advocated the use of two or more gene assays for testing SARS-CoV-2, it is unlikely to miss infected cases using the current testing strategy, the ministry said. The NTF recommended that in addition to existing surveillance strategies, it is critical to conduct enhanced genomic surveillance especially in incoming passengers from the UK.

“The variant strain has 14 non-synonymous (amino acid altering) mutations, 6 synonymous (non amino-acid altering), and 3 deletions. Eight mutations are present in the Spike (S) gene which carries the binding site (Receptor Binding Domain) of the ACE2 receptors, which are the point of entry of the virus into the human respiratory cells,” said the ministry.

The NTF deliberated in detail on aspects related to the current National Treatment Protocol, testing strategy and surveillance of SARS-CoV-2 vis-à-vis the UK variant strain, and was of the view that it will also be critical to conduct genome sequencing in samples where there is a dropout of the S gene in lab diagnosis, proven cases of re-infections etc.

Routine genomic surveillance of SARS-CoV-2 from representative samples all across the samples needs to be a continuous and well-planned activity, according to the statement.

The designated laboratories where samples of UK returnees are currently under sequencing include NCDC, Delhi; CSIR-Institute of Genomics and Integrative Biology, Delhi; CSIR- Centre for Cellular and Molecular Biology, Hyderabad and DBT- Institute of Life Sciences, Bhubaneshwar. It is also being done at the DBT-National Institute of Biomedical Genomics, Kalyani; DBT-InStem-National Centre for Biological Sciences, Bengaluru; National Institute of Mental Health & Neurosciences (NIMHANS), Bengaluru and National Institute of Virology, Pune.

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A strategy has been put under place under which all passengers who had arrived from UK between December 21 and 23  have been tested at the airports and those testing negative allowed to exit the airports only after their RT-PCR test results are available. All positively tested passengers are put under institutional isolation and their samples sent for WGS.

Only after confirmation of the non-mutant variant upon WGS result, the positive cases are allowed to leave institutional isolation as per existing protocol. All contacts of the positive cases are also put under facility quarantine and are tested as per the ICMR guidelines.

Besides, the list of all UK arrivals during the last 28 days has been shared by the Bureau of Immigration with the states concerned. All passengers who had arrived from UK between November 25 and December 20, 2020 are being tracked by the IDSP State Surveillance Units (SSUs) and District Surveillance Units (DSUs).

Samples of all positive cases are being sent for WGS and enhanced contact tracing of these positive cases is being undertaken. These contacts are also put under facility quarantine.

(With inputs from agencies)