BENGALURU: The new SARS-CoV-2 virus variant discovered in the United Kingdom and which has slipped into India has people worried in Karnataka. That is understandable as ten Covid-19-positive patients have been detected in Karnataka, the highest in the country. Of these, six are in Bengaluru (three in Bommanahalli, two in Rajajinagar and one in JP Nagar), while four are in Shivamogga.
The UK variant — also referred to as “SARS-CoV-2 VOC 202012/01” (the first ‘Variant Of Concern’ from 2020 December), or “B.1.1.7” — was identified early December by UK health officials through genome sequencing of two samples collected on September 20. The tests, confirming the new variant, estimated it to have up to 70 per cent higher transmissibility than its original version.
While the Indian government took quick interventions, including banning all UK flights into the country, a question remains: Is it just this variant present in the country or others which have not been identified yet? A Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB) study points at 5,879 variants of Covid virus currently in India. This is out of 6,370 genomes that have been analysed so far.
However, it is important to know which variant is associated with a function that can make it more transmissible, as many genomic variations do not make it more virulent, explains Dr Vinod Scaria, genomic scientist, CSIR-IGIB. “Only variants that have more infectivity, or can escape the antibodies, are what everyone is worried about. Some variants can escape specific antibodies and are hence more important. The genetic lineage with the UK variant, for instance, is believed to be more infectious, although there is only limited scientific evidence to substantiate that,” Dr Scaria says.
The study by CSIR-IGIB and Kurnool Medical College on SARS-CoV-2 genomes from Andhra Pradesh and across India detected 19 such variants. One of them is said to have emerged in larger numbers in Andhra Pradesh and in smaller numbers in other states, including Maharashtra and Telangana.
Dr Giridhar Babu, member, Karnataka State Expert Committee, says, “Population diversity, genetic makeup, environment — including proportion of the people infected — will definitely influence the way a virus changes. The virus has to survive and it won’t, if it kills more people. It can survive only when the host (human) survives.”
Panel to track new variants
It is to tackle these issues that the Centre on December 30 constituted a high-level inter-ministerial steering Committee. Its role is to guide the Indian SARS-CoV-2 Genomic (INSACOG) consortia, which has been formed to identify new variants of SARS-CoV-2 virus, says Renu Swarup, Secretary, Department of Biotechnology (DBT).
INSACOG will monitor genomic variations in the virus on a regular basis through a network of 10 laboratories and keep track of the status of the new variant in India. It will establish a sentinel surveillance system for early detection of variants and determine the genomic variants in case of unusual events and trends (super-spreader events, high mortality/morbidity trend areas). The consortium will be involved in developing potential vaccines too, the DBT said.
DBT-National Institute of BioMedical Genomics (NIBMG), which is the coordinating unit of the consortium, will work with a nodal unit of National Centre for Disease Control (NCDC) on SOPs, data annotation, data analysis, and data release.
NCDC will maintain a database of all samples of the variants. The data will be epidemiologically analysed, interpreted and shared with states/districts for investigation, contact tracing and response strategies. All the genomic sequencing data will be maintained in a national database at two sites, DBT-NIBMG, Kalyani and CSIR-IGIB, New Delhi. The isolated virus will be deposited at the Regional Centre for Biotechnology, Faridabad and National Institute of Virology, Pune.
Efficacy of vaccines on new strain
Retired professor of Neurovirology, NIMHANS and Nodal Officer for genetic confirmation for SARS COV-2 in Karnataka, Dr V Ravi, says, “The vaccines are definitely going to be effective even with the new variant, while some vaccine companies are modifying their vaccines for the UK variant. The people who get vaccines will be safe from Covid for one or two years. What is required now is to continue genome sequencing on a regular basis to monitor and detect emergence of new variants.”
Should we worry?
On December 29, the Ministry of Health confirmed that Karnataka had its first three cases of the UK variant. Till January 1, it went up to 10. The state government, however, has been taking quick steps to identify their contacts and isolate them. Experts say one needs to be cautious. “If you were to ask Covid19 its mantra, it would say, ‘Unlike my cousins Ebola and Zika, I don’t go for the kill straight away. I spread far and wide, and then seek out the meek to kill.’ The new variants are emerging from Nigeria, South Africa and other countries, are the result of a combination of lineage-defining mutations in the spike protein of SARS-CoV-2. Should we be worried? Well, certainly yes, enough to get our guard up again, literally in the form of physical distance, masks, and hand-hygiene,” says Dr Vishal Rao, member, Covid Consultative Group.
The mutation
The “B.1.1.7” variant of SARS-CoV-2 virus has a mutation in the receptor binding domain of the spike protein at position 501, where amino acid asparagine (N) has been replaced with tyrosine (Y). The shorthand for this mutation is N501Y, sometimes noted as S:N501Y to specify that it is in the spike protein.
Implications
(GFX source: Centre for Disease Control & Prevention)