The genomic surveillance consortium, INSACOG, was formed under the leadership of the National Center for Disease Control (NCDC), New Delhi. In addition, more than 50 samples of returnees in the UK are currently being sequenced at designated laboratories.
Five percent of positive Covid-19 cases from all states and UTs will be tested for Complete Genome Sequencing (WGS) as part of the strategy that was implemented to detect and contain the mutant variant, said the Union Ministry of Health after a meeting of the National Task Force (NTF) at Covid-19 on the subject.
“It is proposed to continue enhanced genomic surveillance for early detection and containment of strains of SARS-CoV-2 variants in the UK. However, it is important to understand that, like all other RNA viruses, SARS-CoV-2 will continue to mutate, “the ministry said.
The mutant virus can also be contained by measures such as social detachment, hand hygiene, wearing masks and also by an effective vaccine, when available, the ministry said.
The NTF meeting was convened on Saturday by ICMR under the co-chairmanship of Dr. Vinod Paul, NITI Aayog Member and Dr. Balram Bhargava, ICMR Secretary and Director General.
The main objective of the meeting was to discuss evidence-based changes in the tests, treatment and surveillance strategies for SARS-CoV-2, in view of recent reports on the emergence of a new variant strain of the virus in the United Kingdom.
It was emphasized that, since the variant strain in the United Kingdom is implicated in causing the increase in the transmissibility of the virus, it is essential to identify individuals infected with this strain and contain them properly to prevent its transmission in India, the statement said.
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NTF concluded that there is no need to change the existing Treatment Protocol in view of the emerging mutations in the strain.
In addition, since the ICMR has always advocated the use of two or more genetic assays to test SARS-CoV-2, it is unlikely that there will be no cases of infection 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 for SARS-CoV-2, especially for passengers arriving from the UK.
The meeting was also attended by Professor Randeep Guleria, Director, AIIMS; General Director of Health Services (DGHS); General Controller of Medicines of India (DCGI); Director, National Center for Disease Control (NCDC); other representatives of the Ministry of Health and the ICMR, as well as independent experts on the subject.
“The variant strain has 14 non-synonymous mutations (amino acid changes), 6 synonymous mutations (non-amino acid changes) and 3 deletions.
“Eight mutations are present in the Spike (S) gene, which carries the binding site (Receptor Binding Domain) of ACE2 receptors, which are the point of entry of the virus into human respiratory cells,” the ministry said in its statement.
The NTF deliberated in detail on aspects related to the current National Treatment Protocol, test strategy and surveillance of SARS-CoV-2 in relation to the variant strain of the United Kingdom.
The NTF was of the opinion that it will also be critical to conduct genome sequencing in samples where there is a loss of the S gene in the laboratory diagnosis, proven cases of reinfections, etc. Routine genomic surveillance of SARS-CoV-2 by the representative Samples in all samples must be a continuous and well-planned activity, according to the statement.
Designated laboratories where samples from returnees from the UK are currently being sequenced include -NCDC, Delhi; CSIR-Institute of Genomics and Integrative Biology, Delhi; CSIR- Center 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 Center for Biological Sciences, Bengaluru; National Institute of Mental Health and Neuroscience (NIMHANS), Bengaluru and National Institute of Virology, Pune.
The NCDC reported that the Center became aware of the reports of the mutant variant and the response of other countries to those reports.
The situation is being proactively monitored.
A strategy has been put in place whereby all passengers arriving from the UK between 21 and 23 December have been tested at airports and only after the PCR test result is available, negative passengers are allowed to leave the airports
All positively tested passengers are placed in institutional isolation and their samples sent for Complete Genome Sequencing (WGS)
Only after confirmation of the non-mutant variant in the WGS result, positive cases can leave institutional isolation in accordance with the existing management protocol
All positive case contacts are also quarantined at the facility and are tested according to ICMR guidelines
In addition, the list of all arrivals to the UK during the past 28 days has been shared by the Bureau of Immigration with the states involved.
All passengers arriving from the UK between 25 November and 20 December 2020 are being tracked by IDSP State Surveillance Units (SSUs) and District Surveillance Units (DSUs)
Samples of all positive cases are being sent to WGS and improved contact tracking of these positive cases is being carried out and these contacts are also quarantined at the facility.