Top scientists from leading research institutes in the country have estimated that the ancestor of the novel coronavirus strain from Wuhan was in circulation by December 11, 2019. Using a scientific technique called “time to most recent common ancestor”, MRCA, scientists estimated the viral strain now circulating in Telangana and other states had originated between November 26 and December 25, the median being December 11.
Whether the virus was introduced to India by passengers from China prior to January 30 is not clear as Covid-19 tests were not carried out on a large scale in the country then.
Researchers, including from the city-based Centre for Cellular and Molecular Biology (CCMB), have not only estimated the age of the most recent common ancestor of various strains of the novel coronavirus but also discovered a new strain, or clade, that’s different from the existing ones. They have named this Clade I/A3i.
A “clade” is defined as “a group of organisms believed to comprise all the evolutionary descendants of a common ancestor”.
The viral strain found in India’s first Covid-19 case in Kerala belonged to the Wuhan ancestor, while the one discovered from Hyderabad (Clade I/A3i) is unique as it originated not in China but somewhere in Southeast Asia. The exact country of origin of this new clade is not known, said the CCMB director, Dr Rakesh K Mishra.
As far as the most recent common ancestor of the new strain (Clade I/A3i) is concerned, it was in circulation between January 17 and February 25, with the median being February 8. Another clade, A2a, which is the predominant clade in India, had a tMRCA of January 2, with the period of its likely emergence lying between December 13, 2019 and January 22, 2020.
The team, which included researchers from the Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, and the Academy of Scientific and Innovative Research, Ghaziabad, noted that the new clade is not found anywhere else in the world. This is also different from the other 10 known clades discovered earlier.
The new clade was introduced in India from a single point. It was also from a single outbreak. It later saw a rapid spread, spanning multiple regions across the country. As part of the study, the team performed whole-genome sequencing for 64 genomes, making a total of 361 genomes from India. They also did the dating for the different clusters of viral genomes.
Dr Mishra said Clade I/A3i encompasses 41% of all genomes sequenced and deposited in the public domain from multiple states in India. Globally, 3.5% of genomes, which till date could not be mapped to any distinct known cluster, fall in this newly defined clade. The I/A3i clade is represented in 145 genomes (41.2%) and represented from 16 of the 19 states from which the genomes originated.
Tamil Nadu, Telangana, Maharashtra, and Delhi have the highest proportions of this new clade, followed by Bihar, Karnataka, UP, West Bengal, Gujarat and Madhya Pradesh. Haryana, Jammu & Kashmir, Madhya Pradesh, Odisha, and Rajasthan have one genome each under Clade I/A3i.