THE FIRST report in India on the genome of SARS-CoV-2 has found that a particular variant of the virus brought in mainly by travellers from Europe has become the most prominent across the country, giving rise to the hope that it may be easier to deal with a more “homogenous’’ entity than those with different lineages.
According to scientists involved in the study, the finding also suggests that the stringent nationwide lockdown that was in place between March and May “has actually worked’’ since the ban on international and inter-state travel “prevented the entry of new lineages of the virus”.
The report, which was tabled before Union Health Minister Dr Harsh Vardhan by the Department of Biotechnology Saturday, states that the A2a haplotype has rooted out any other haplotypes that existed before. A haplotype is a group of genes, which is inherited together by an organism from a single parent.
“Initial results indicate that multiple lineages of SARS-CoV-2 are circulating in India, probably introduced by travel from Europe, USA and East Asia. In particular, there is a predominance of the A2a haplotype (20A/B/C) with D614G (gene) mutation, which is found to be emerging in almost all regions of the country. This particular haplotype is globally reported to be associated with enhanced transmission efficiency,’’ says the study.
“The findings show that the predominant haplotype strain in India has come from the cluster in Europe, and the entry of this lineage happened through travellers from Europe and Saudi Arabia. In the earlier months from January, there were cases of 19A and 19B, the original Wuhan strain, which indicated that these were through travel from China. But these cases were less and the A2a haplotype strain took over entirely. Now, it exists in all areas of the country and is the most prominent strain,’’ says Dr Arindam Mitra, one of the study’s lead scientists from the National Institute of Biomedical Genomics (NIBMG) in Kalyani, West Bengal.
Hope, fingers crossed | Sharp dip in Delhi cases and spread of infection
The study found that haplotype diversions peaked between March and May, before the A2a haplotype emerged as predominant by June. “This has also shown us that the lockdown imposed by the government between March and May has worked. The complete ban of international as well as inter-state travel prevented the entry of new lineages of the virus as well as the spread of these lineages across the country,’’ says Mitra.
The study also found that the D164G gene variant, a global characteristic of the SARS-Cov-2 virus, is on the decline in Delhi, which may have possibly resulted in a “decline in transmission” in the capital.
“But we cannot conclusively say anything until this is studied further. The D164G is known to make the virus efficient in transmission. There is a probability that a decline in this variant could result or has resulted in a decline in transmission in Delhi. It is also possible that the government managed to contain the spread in the early months,’’ says Dr Saumitra Das, director, NIBMG, who was part of the research team.
NIBMG was the coordinating institute for the genome sequencing project. The report is based on the findings of a consortium of science agencies and institutes, which concluded the sequencing of 1,000 genomes from nose and throat swabs collected from those who tested positive across 10 states through Real Time PCR tests.
The study further found that the haplotype groups are similar in the east and north where 20 A is prominent, while the west and south have witnessed a prevalence of 20 B.
“We will not know which haplotype is more virulent until there is further investigation and in-vitro research. The strength of the virus doesn’t just depend on the virus itself or the mutation, but also the host. India is a vast country with different socio-economic nature and customs, which determine our diet, for instance, and also our immunity. The viral load also depends on the host,’’ says Das of NIBMG.
Some of the other premier institutes involved in the study were National Centre for Biological Sciences in IISc-Bangalore, National Centre for Cell Science (NCCS) in Pune and the Indian Council of Medical Research (ICMR) in Delhi, apart from a number of top hospitals and institutions from across the country.
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