(GIST OF YOJANA) Indian SARS-CoV-2 Genomics Consortium

(GIST OF YOJANA) Indian SARS-CoV-2 Genomics Consortium


Indian SARS-CoV-2 Genomics Consortium

What is INSACOG?

  • The Indian SARS-CoV-2 Genomics Consortium (INSACOG) is a national multi-agency consortium of Genome Sequencing Laboratories (RGSLs) laboratories established by the Government of India on 30th December 2020. Initially, this consortium had 10 laboratories. Subsequently, the scope of laboratories under INSACOG was expanded and at present, there are 28 laboratories under this Consortium that monitor the genomic variations in SARS-CoV-2.

What is the objective of INSACOG?

  • The SARS-CoV-2 virus, commonly known as Covid-19 virus posed unprecedented public health challenges globally.
  • To fully understand the spread and evolution of the SARS CoV-2 virus, its mutations, and resulting Variants, the need for in-depth sequencing and analysis of the genomic data was felt against this backdrop.
  • INSACOG was established to expand whole-genome sequencing of SARS-CoV-2 virus across the nation, aiding our understanding of how the virus spreads and evolves. 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.

INSACOG has the following specific objectives:

  • To ascertain the status of Variants of Interest (Vol) 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.

When did India start SARS COV-2 viral sequencing?

  • India started sequencing SARS-CoV-2 viral genomes in 2020. Initially, NTV and ICMR sequenced samples of international passengers who arrived in India from the UK,
  • Brazil, or South Africa or transited through these countries, as these countries reported a sudden surge in cases. 
  • RTPCR positive samples from States reporting sudden surges in cases were sequenced on priority. This was further expanded through efforts of the Council of Scientific and Industrial Research (CSIR), Department of Biotechnology (DBT), and National Centre for Disease Control (NCDC), as well as individual Institutions.
  • The initial focus of India was on restricting the spread of global variants of concern in the country - Alpha (B.l.1.7), Beta (B.1.351), and Gamma (P.1), which had high transmissibility.
  • The entry of these variants was carefully tracked by INSACOG. Subsequently, the Delta and Delta Plus variants were also identified based on Whole Genome Sequencing analysis conducted in the INSACOG laboratories.

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.
  • 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 COVID-19 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.

What is the Standard Operating Procedure (SOP) for sending samples to INSACOG laboratories?

  • The Standard operating procedure for sending samples to INSACOG laboratories and subsequent action based on genome sequencing analysis is as follows:
  • The Integrated Disease Surveillance Programme (IDSP) machinery coordinates sample collection and transportation from the districts/sentinel sites to Regional Genome Sequencing Laboratories. The RGSLs are responsible for Genome sequencing and identification of Variants of Concern/Variants of Interest, potential Variants of Interest, and other mutations. Information on Variants of Concern (VOC)/Variants of Interest (VOI) is submitted to Central Surveillance Unit, IDSP for establishing a clinico-epidemiological correlation in coordination with State Surveillance Officers.
  • Based on discussions in the Scientific and Clinical Advisory Group (SCAG) established to support the INSACOG, it was decided that upon identification of a genomic mutation that could be of public health relevance, RGSL will submit the same to SCAG. SCAG discusses the Potential Variants of Interest and other mutations and, if felt appropriate, recommends to Central Surveillance Unit for further investigation.
  • The genome sequencing analysis and clinic-epidemiological correlation established by IDSP is shared with MOHFW, ICMR. DBT, CSIR, and States/UTs for formulating and implementing requisite public health measures.
  • The new mutations/variants of concern are cultured and genomic studies are undertaken to see the impact on vaccine efficacy and immune escape properties.

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

  • Variants of Concern have been found in 174 districts in 35 states in India. The 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.1.61 7 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.

What is the Delta Plus variant?

  • 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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    • India is known as the “World’s Pharmacy” as it is the largest producer of generic medicines accounting for 20 percent of global production and also manufactures more than 60 percent of all vaccines sold across the globe. 
    • India is the world’s second-largest exporter of Ayurvedic & Alternative Medicines with a Compound Annual Growth Rate (CACTR) of 22% during 2015-20 in the healthcare sector. India had launched the world’s largest Covid-19 vaccination drive in January 2021 and has supplied millions of doses to various countries. Till now, around 38 crore people have been vaccinated in India and 342 crore people globally.
    • Ensured timely lockdown and saved lakhs of lives.
    • Creation of extensive support system through setting up of COVID-19 warriors’ network and a national taskforce.
    • Aatmanirbhar Bharat economic stimulus relief package of 20 lakh crore amounting to 10% of GDP.
    • 80 crore people being given free food grains under PM Garib Kalyan Yojana.
    • 20 crore women Jan Dhan holders being given ?500 per month for three months.
    • MGNREGA wage rate was increased to Rs. 202 per person per day and is benefiting 13.62 crore families.
    • Support to Indian vaccine manufacturing companies.
    • It was launched by the PM on India’s 74th Independence Day in August 2020. It is being implemented by National Health Authority (NHA) under the Ministry of Health and Family Welfare, Gol. The plan is to create a digital health ecosystem for India featuring health ID, personal health records, Digi Doctor, and health facility registry. E-pharmacy and telemedicine services are planned to be included later. 
    • NDHM syncs with Ayushman Bharat, a flagship scheme launched by PM in 2018 through the recommendation by the National Health Policy 2017, to achieve the vision of Universal Health Coverage (UHC) by covering 50 crore beneficiaries. Ayushman Bharat is the world’s largest government-funded healthcare programme.
    • India offers affordable healthcare services for all and is a famous destination for medical tourism. It is estimated to be worth 5 to 6 billion USD with over 500,000 patient visits annually. 
    • Chennai city of Tamil Nadu state has famous Multi and super-specialty hospitals with the inflow of the greatest number of international patients. India offers a smooth process for the issue of medical visas and provides the best healthcare facilities, frontier technologies, finest doctors, financial savings with the lowest waiting time. 
    • The Indian government had launched a single-window portal in 2017 to promote medical and wellness tourism in the country.