Genomic landscape of COVID in India changing, say CCMB scientists

Hyderabad: Scientists at the CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, have found that SARS-CoV-2 virus genomes have undergone change since June. According to the study, there is an increase in A2a clade of the virus since June.

CCMB analysed more than 2,000 SARS-CoV-2 genomes from India available in the public domain to understand the various strains in circulation.

In June, the team had revealed the presence of a distinct virus population among Indians. This was named the clade I/A3i which is recognised by the presence of four specific variations in their genetic makeup (genomes). At the time, 41 per cent of all Indian SARS-CoV-2 genomes belonged to this clade.

The current analysis shows that the proportion of A3i clade has now dropped to 18 per cent. “One of the four distinct variations that define the A3i clade is present in a key viral enzyme called RDRP, involved in making new copies of the viral RNA. This variant was predicted to be deleterious or bad for the virus, and if the prediction is indeed correct, we expected A3i clade to slowly disappear with time, and other clades without this variation to prevail. This is exactly what we see now,” said Dr. Divya Tej Sowpati, a scientist at the CCMB who is leading the genome study.

The decrease in the proportion of A3i clade is accompanied by an increase in the A2a clade, also referred to as the G clade or the 20A/B/C clades in other nomenclatures. Viruses of the A2a or the G clade carry the D614G mutation in their spike protein which is shown to be associated with increased infectivity. At present, approximately 70 per cent of all Indians, as well as global SARS-CoV-2 genomes, fall into this clade.

“As expected, for a strain which is more infectious, A2a clade quickly became the dominant clade in India just like everywhere else. There is no evidence to state that this mutation is clinically a more difficult one. The similarity in viral genome globally should be considered positive news because a vaccine or a drug targeting this mutation will work with the same effect all over the world,” said Dr Rakesh K. Mishra, the director of CCMB and co-author of the study.

It is, however, important to note that no clade at present has been conclusively shown to be associated with a more severe form of COVID-19 or an increased risk of death.