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All you need to know on how India is keeping track of mutations in Coronavirus

All you need to know on how India is keeping track of mutations in Coronavirus

The government has set up a consortium of 38 genome sequencing laboratories across the country that are closely studying changes and mutations in the deadly coronavirus and identifying variants of concern. India Narrative brings to its readers a Q & A presentation based on how the system operates based on facts provided by the Health Ministry.     

What is INSACOG?

A- The Indian SARS-CoV-2 Genomics Consortium (INSACOG) is a national multi-agency consortium of 38 Genome Sequencing Laboratories (RGSLs) established by the Government of India for genome sequencing of SARS-CoV-2. Any changes to the genetic code, or mutations in the virus, can be observed based on the analysis and sequencing of samples done in the laboratories under INSACOG. This helps us track  how the virus spreads and evolves.

INSACOG has the following specific objectives:


·         To ascertain the status of Variants of Interest (VoI) and Variants of Concern (VoC) in the country

·         To establish sentinel surveillance and surge surveillance mechanisms for early detection of genomic variants and assist in formulating effective public health response

·         To determine the presence of genomic variants in samples collected during super-spreader events and in areas reporting increasing trend of cases/deaths etc.   

Q- What is the strategy for SARS CoV-2 surveillance in India?

Initially, genomic surveillance was focused on the variants carried by international travellers and their contacts in the community through sequencing 3-5% of the total RTPCR positive samples.

Subsequently, the sentinel surveillance strategy was also communicated to the States/UTs in April 2021. Under this strategy, multiple sentinel sites are identified to adequately represent the geographic spread of a region, and RTPCR positive samples are sent from each sentinel site for Whole Genome Sequencing. Detailed SOPs for sending samples from the identified sentinel sites regularly to the designated Regional Genome Sequencing Laboratories (RGSLs) were shared with States/UTs. The list of INSACOG RGSLs tagged to States was also communicated to the States.  A dedicated Nodal Officer was also designated by all States/UTs for coordinating the activity of Whole Genome Sequencing.

Sentinel Surveillance (for all States/UTs/): This is an ongoing surveillance activity across India. Each State/UT has identified sentinel sites (including RT-PCR labs and tertiary health care facilities) from where RT-PCR positive samples are sent for Whole Genome Sequencing.

Surge Surveillance (for districts with COVID19 clusters or those reporting a surge in cases):  A representative nos. of samples (as per the sampling strategy finalized by State Surveillance Officer/Central Surveillance Unit) are collected from the districts which show a surge in the number of cases and are sent to RGSLs.

Q- What is the current status of Variants of Concern (VOC)?

A. Variants of Concern have been found in 174 districts in 35 States in India. Highest numbers of VOCs have been reported from districts in Maharashtra, Delhi, Punjab, Telangana, West Bengal & Gujarat. Variants of Concern of public health importance detected in community samples in India are: Alpha, Beta, Gamma and Delta.

The B.1.617 lineage, first observed in Maharashtra, was associated with the unusual rise observed in several districts of the State. It is now found in many States in India.

Q- What is Delta Plus variant?

A. B.1.617.2.1 (AY.1) or commonly known as Delta Plus variant signifies Delta variant with an additional mutation.

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