Genetically unique strain makes 40% of coronavirus in India

A genetically unique strain of novel coronavirus 2019 - introduced in India in February - has silently spread to the majority of the states to emerge as the second most dominant types of the pandemic virus sweeping the country.

The discovery by CSIR scientists is set to expand the understanding of scores of researchers who are trying to figure out a way to fight the virus with drugs and vaccines.

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Known as Clade A3i, this group of virus now consists of nearly 41% of the pathogens circulating in India. The dominant strain, however, is Clade A2a that comprises more than 50% of the strains.

"While Clade A2a is seen around the world, Clade A3i is found mostly in India. Singapore is the only other country where 8% presence of such a clade has been," said a member of the CSIR research team.

In a research paper, the scientists demonstrated that a single introduction in February was followed by a country-wide spread mostly affecting the South Indian states. The first detection of this group took place in March at a hospital in Hyderabad.

From the analysis of more than 200 genetic sequences, they reported that Clade A3i was the predominant class of the COVID-19 in Tamil Nadu, Telengana, Maharashtra and Delhi. It is the second most dominant group in Bihar, Karnataka, Uttar Pradesh, West Bengal, Gujarat and Madhya Pradesh.

This group is characterised by four specific genetic signatures unique to the strain.

"Put together, the cluster of genomes forms a distinct cluster, predominantly found among Indian COVID-19 genomes with limited representation outside the region," the scientists reported in the paper, which is not yet peer-reviewed but released in the academic circle.

The two CSIR laboratories that conducted the study are Centre for Cellular and Molecular Biology, Hyderabad and Institute of Genomics and Integrative Biology, Delhi.

The causative virus behind the epidemic, SARS-CoV-2, is a member of the genus betacoronavirus. It has differentiated into at least 10 clades globally and is continuously evolving.

"For insurance, the Clade A3i mutates less than the Clade A2a," said the CSIR scientist.

"The discovery of the new clade is important as it shows a group, which can now be connected to disease severity (if any) and the spread route (in geographical and temporal context). This will have large implications," CCMB director Rakesh Mishra told DH.

The discovery comes a month after two Indian geneticists at the National Institute of Biomedical Genomics, Kalyani showed to the world that Clade A2a was the dominating type of the virus almost all over the globe.

"The discovery of A3i is very interesting. Investigation of the geographical spread of the 62 coronavirus isolates in India that belong to A3i and the travel histories of the hosts, especially to Iran where A3 is prevalent, will be instructive," commented Partha Majumder, a veteran population geneticist and one of the NIBG scientists who was the lead scientist for the A2a research.

The new discovery from Team CSIR has implications in genetic epidemiology, surveillance, contact tracing and the development of long term strategies for mitigation of this disease, the scientists reported.