The genomic surveillance consortium, INSACOG, has been formed under the leadership of the National Centre for Disease Control (NCDC), New Delhi. Further, more than 50 samples of UK returnees are currently under sequencing at the designated laboratories.
Five percent of the positive cases of COVID-19 from all states and UTs will be tested for Whole Genome Sequencing (WGS) as part of the strategy that has been put in place to detect and contain the mutant variant, the Union Health Ministry said after a meeting of the National Task Force (NTF) on COVID-19 on the issue.
“It is proposed to continue enhanced genomic surveillance for early detection and containment of the UK variant SARS-CoV-2 strains. However, it is important to understand that like all other RNA viruses, SARS-CoV-2 will continue to mutate,” the ministry said.
The mutated virus can also be contained by measures like social distancing, hand hygiene, wearing masks and also by an effective vaccine, as and when available, the ministry said.
The meeting of the NTF was convened on Saturday by ICMR under co-chairpersonship of Dr Vinod Paul, Member NITI Aayog and Dr Balram Bhargava, Secretary, Director General ICMR.
The main objective of the meeting was to discuss evidence-based modifications in testing, treatment and surveillance strategies for SARS-CoV-2 in view of the recent reports of the emergence of a new variant strain of the virus from the UK.
It was emphasized that since the UK variant strain is implicated to cause increased transmissibility of the virus, it is critical to identify individuals infected with this strain and adequately contain them to prevent its transmission in India, the statement stated.
The NTF concluded that there is no need to change the existing Treatment Protocol in view of mutations emerging in the strain.
Further, 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 the existing surveillance strategies, it is critical to conduct enhanced genomic surveillance for SARS-CoV-2 especially in incoming passengers from the UK.
The meeting was also attended by Prof. Randeep Guleria, Director, AIIMS; Director General Health Services (DGHS); Drug Controller General of India (DCGI); Director, National Center for Disease Control (NCDC); other representatives from Ministry of Health and ICMR as well as independent subject experts.
“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,” the ministry said in its statement.
The NTF deliberated in detail on aspects related to the current National Treatment Protocol, testing strategy and surveillance of SARS-CoV-2 vis- -vis the UK variant strain.
The NTF 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 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.
The NCDC informed that the Centre has taken cognizance of the reports of mutant variant and the response of other countries to these reports.
The situation is being monitored proactively.
A strategy has been put under place under which all passengers who had arrived from the UK between December 21n and 23 have been tested at the airports and only after the-PCR test result are available, the negative passengers are permitted to exit the airports
All positively tested passengers are put under institutional isolation and their samples sent for Whole Genome Sequencing (WGS)
Only after the confirmation of the non-mutant variant upon WGS result, the positive cases are permitted to leave institutional isolation as per the existing management protocol
All the 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 the UK between 25th November – 20th December 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 and these contacts are also put under facility quarantine.