New strain: Scientists find a dominant virus genome among Indian samples

A distinct cluster of Covid virus population prevalent in India comprises 41 per cent of all SARS-CoV2 genomes of Indian samples and 3.5 per cent of global genomes submitted in public domain.
Health workers collect swab sample of a doctor for the COVID-19 test at a government dispensary during the nationwide lockdown in Patiala Monday June 1 2020. (Photo | PTI)
Health workers collect swab sample of a doctor for the COVID-19 test at a government dispensary during the nationwide lockdown in Patiala Monday June 1 2020. (Photo | PTI)

NEW DELHI: A distinct cluster of COVID virus population prevalent in India comprises 41 per cent of all SARS-CoV2 genomes of Indian samples and 3.5 per cent of global genomes submitted in public domain.

Called Clade A3i, this cluster, uncharacterized so far, seems to have originated from an outbreak in February and spread through India, said scientists of the CSIR-Centre for Cellular and Molecular Biology.

The genomes isolated from India were classified under five clusters — Clades A2a, A3, A3i, B, and B4. A fresh preprint on genome analysis of SARS-CoV2 shows that considering all the genomic data available from India, the Clade A3i is represented in 145 genomes (41.2 per cent) and represented 6 of 19 states from which the genomes originated.

The geographical distribution and the proportion of the Clade A3i isolates shows the highest prevalence in Tamil Nadu, Telangana, Maharashtra and Delhi followed by Bihar, Karnataka, UP, West Bengal, Gujarat and Madhya Pradesh.

Haryana, Jammu and Kashmir, Madhya Pradesh, Odisha, and Rajasthan have one genome each under Clade A3i.

“The cluster suggests a potential single introduction in February, followed by a country-wide spread, mostly affecting the South as evidenced by the most recent common ancestor (tMRCA) as well as the short cluster. Our analysis suggests that the Clade A3i was represented in almost all states from which genomes are available, barring a few,” said a scientist.

Constantly evolving

The virus has differentiated into at least 10 Clades and is evolving.

This has implications in genetic epidemiology, surveillance, contact tracing, development of long term strategies.

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