The Indian Genome Sequencing Initiative for SARS CoV 2

Dr Renu Swarup
Dr Renu Swarup

15 May, 2021

Dr Renu Swarup

Secretary Department of Biotechnology, Govt of India

A major impetus in biomedical science, beyond curiosity alone, is to find solutions for problems and to better face challenges. The biggest challenge before all of us – people, government, scientists and health care professionals –right now is to deal with the second surge of this rapidly changing virus. The current wave, is more severe, especially in terms of the ferocity of the rise. I see three clear factors for this. First, and foremost public laxity has been greater than expected and non-compliance with Covid Appropriate Behaviour. Early this year, as the new cases subsided, people started interacting as if there was no threat of the virus. Then there have been cases of some reinfections and breakthrough infections, the variants have exhibited data that shows that they can be more transmissible and, in some cases, capable of escaping prior immunity. This is not unusual in the case of respiratory infections; any immunity is transient.

When the pandemic started in 2020, it was essential to study the virus and understand the characteristics. For that a Pan India Genome sequencing initiative was launched, sentinel sites were selected and collectively till December 2020 Institutes of Department of Biotechnology, ICMR, CSIR and other State and National Institutes sequenced around 6000 sequences. The data revealed that there were mutations however they were not found on regions of the sequence which would have any likely impact and these did not show any major impact clinically.

Then around December 2020, there was information that one variant was reported in the UK which was clinically correlated and notified as Variant of Concern (VOC). It was important to then bring all research groups with expertise together to sequence samples from across the country. INSACOG -Indian SARS-CoV-2 Consortium on Genome sequencing (a consortium of national laboratories) was set up with a specific mandate to sequence samples from across the country and identify the VoC and any new variants.  The Consortium has over the last three months collected samples from different States and after sequencing identified the presence of the VoC (Variants of Concern) and also new variants.

The UK variant, B.1.1.7, was first noted in the sequences in September last year in the Kent region of the UK. It took the scientists two months to know its behaviour, complete the analysis and correlate it clinically, and only in November did they declare it as a variant of concern.  Tracking a variant, sequencing and analysing its epidemiology and understanding its clinical manifestation is a time-taking process. Our scientists have done a commendable job in tracking known variants of concern B1.1 7, B1351, and identifying a new one BI 617 within a couple of months of the start of INSACOG, several other mutations have been identified but they have shown no relevance with regard to the specific sequence impacted. These were then correlated with clinical data and based on that it was noted that there was a Variant of Interest B1.617. While there are indications of increased transmission rates, we do not have sufficient data to confirm increased severity and mortality due to this variant. However, it is important to note that with these variants there is no change to the treatment or public health action.


We are also studying the effect of vaccines on these variants, the virus has been cultured, the neutralising assays developed and all vaccines –Covishield, Covaxin and Sputnik being tested

While our scientists are tracking mutants and the threat they pose, it is equally important that all citizens make it a habit to follow COVID Appropriate Behaviour.