Officials are checking if the variant, where two mutations come together in the same virus, may be more infectious or less affected by vaccines.
Some 10,787 samples from 18 Indian states also showed up 771 cases of known variants - 736 of the UK, 34 of the South African and one Brazilian.
Officials say the variants are not linked to a spike in cases in India.
India reported 47,262 cases and 275 deaths on Wednesday - the sharpest daily rise this year.
The Indian SARS-CoV-2 Consortium on Genomics (INSACOG), a group of 10 national laboratories under India's health ministry, carried out genomic sequencing on the latest samples. Genomic sequencing is a testing process to map the entire genetic code of an organism - in this case, the virus.
The genetic code of the virus works like its instruction manual. Mutations in viruses are common but most of them are insignificant and do not cause any change in its ability to transmit or cause serious infection. But some mutations, like the ones in the UK or South Africa variant lineages, can make the virus more infectious and in some cases even deadlier.
Virologist Shahid Jameel explained that a "double mutation in key areas of the virus's spike protein may increase these risks and allow the virus to escape the immune system".
The spike protein is the part of the virus that it uses to penetrate human cells.