India to begin sequencing of genes of 5% Covid +ve samples

India will soon begin sequencing the genes of at least 5% of all Covid-19 positive samples in an attempt to better track mutations, officials in the Union health ministry have said, detailing a new genomic surveillance exercise to be able to better detect if there are any worrying variants of the virus.

The moves comes weeks after the UK found a variant with an unusually high number of changes, including some that are believed to make the virus 56%-70% more transmissible. The new strain is as yet not known to cause more severe disease or make the current class of vaccines ineffective.

With India reporting 22,383 case a day on average over the last week, it would mean sequencing1,120genomes a day. To do this, the government has set-up a genomic surveillance consortium under the National Centre for Disease Control (NCDC), the union health ministry said.

Currently, laboratories under the consortium have 50 samples of people who returned from the UK.

Separately, the National Task Force on Covid-19 that met on Saturday recommended that whole genome sequencing be also done in cases where the S gene does not show up in an RT-PCR or other molecular testing.

Eight of the 23 mutations that have been identified in the new UK variant are on the S gene, including one on the receptor binding domain that is used by the virus to enter the human cells.

All molecular tests – such as RT PCR, CBNAAT, and TrueNat — amplify the genetic material of the virus present the in the swab samples and match it against two or three genes of Sars-CoV-2 to give a positive result. With the new mutations, some tests might fail to recognise the S gene in a patient sample.

The NTF has also recommended that the sequencing be done if there is a proven case of re-infection.

“The United Kingdom does whole genome sequencing for about 10% of their positive samples, which is one of the highest in the world. That is how they were able to detect the new variant that was spreading quickly in London and some other regions. Sequencing 5% of the total sample will be a very big exercise, but it will be very helpful in giving us information on which variant is in circulation, where should we implement restrictions to stop the spread of a particular variant, and whether the vaccines in development will continue to work against the variant,” said Dr Rakesh Mishra, director of Centre for Cellular and Molecular Biology. Experts have said that the vaccines and natural immunity is likely to work against the new UK variant.

To quickly detect and isolate people who might be carrying the mutant variant that is thought to spread 70% faster, the NCDC had already directed all agencies to send positive samples of UK returnees for whole genome sequencing. Whole genome sequencing was also mandated for anyone who tested positive in the community after returning from UK in the last 28 days.

The consortium will comprise of laboratories of the National Institute of Virology-Pune, Institute of Genomics and Integrative Biology- Delhi, Centre for Cellular and Molecular Biology-Hyderabad, National Institute of Mental Health & Neurosciences-Bangalore among others.

“A genomic surveillance consortium – INSACOG — has been formed under the leadership of NCDC, New Delhi for laboratory and epidemiological surveillance of circulating strains of SARS-CoV-2 in the country,” said a release from the union health ministry. Most of these laboratories were already sequencing genomes of Sars-CoV-2, however, it is likely to increase the scale and coordinate the efforts.

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