INSACOG and India's strategy for Covid-19 surveillance, sequencing. All you need to know

The objective of the INSACOG is to ascertain the status of variants of interest (VOI) and variants of concern (VOC) in the country and to establish sentinel surveillance and surge surveillance mechanisms for the early detection of genomic variants.

The Indian SARS-CoV-2 Genomics Consortium (INSACOG) is a national multi-agency consortium of Genome Sequencing Laboratories (RGSLs), established by the Centre on December 30 last year for sequencing and analysis of genome data.

The scope of laboratories under INSACOG has been expanded from the initial 10 labs in the country to 28 at present.(HT Photo)

All you need to know about INSACOG:

The scope of laboratories under INSACOG has been expanded from the initial 10 labs in the country to 28 at present. RGSLs are responsible for genome sequencing and identification of variants of concern/variants of interest, potential variants of interest, and other mutations.

The consortium was established to expand whole genome sequencing of SARS-CoV-2 virus, commonly known as Covid-19, across the nation to aid the understanding of how the virus spreads and evolves.

The objective of the consortium is to ascertain the status of variants of interest (VOI) and variants of concern (VOC) in the country and to establish sentinel surveillance and surge surveillance mechanisms for the early detection of genomic variants.

So far, VOC has been found in 174 districts in 35 states of the country. The highest number of VOCs have been detected from districts in Maharashtra, Delhi, Punjab, Telangana, West Bengal and Gujarat. Variants of Concern of public health importance detected in community samples in India are, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1) and Delta, stated ministry of health and family welfare.

"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," the ministry said.

B.1.617.2.1 (AY.1) or commonly known as Delta Plus variant signifies Delta variant with an additional mutation, according to the ministry.

Initially, the National Institute of Virology (NIV) and the Indian Council for Medical Research (ICMR) sequenced samples of international passengers who arrived in India from the UK, Brazil or South Africa or travelled through these countries, as these countries reported a surge in Covid cases.

RT-PCR positive test samples from states reporting sudden hikes in cases were sequenced in priority, this was further expanded by efforts of Council of Scientific and Industrial Research (CSIR), Department of Biotechnology (DBT) and National Centre for Disease Control (NCDC), as well as individual institutions.

The country first focussed on controlling the spread of global variants in the country with a high transmissibility rate. Subsequently, Delta and Delta Plus variants were also identified based on genome sequencing analysis conducted by the consortium laboratories.

India's strategy for Covid surveillance:

Earlier genomic surveillance was focussed on the variants carried by international travelers and their contacts through sequencing 3-5% of the total positive samples.

Sentinel surveillance strategy was subsequently communicated to states and Union territories in April 2021. Under the strategy, multiple sentinel sites were identified to adequately represent the geographic spread of a region, and RTPCR positive samples are sent from each site for sequencing.

Surge surveillance strategy for districts with Covid-19 clusters or those reporting surge in cases was also undertaken under which a representative number of samples are collected and sent to RGSLs.

The detailed SOPs for sending samples from identified sentinel sites regularly to the designated Regional Genome Sequencing Laboratories (RGSLs) were shared with states/UTs, the ministry said.

The SOPs for sending samples for sequencing are:

The Integrated Disease Surveillance Programme (IDSP) machinery coordinates sample collection and transportation from the districts/sentinel sites to RGSLs.

The information obtained on VOCs and VOIs is submitted to Central Surveillance Unit, IDSP for establishing a clinico-epidemiological correlation in coordination with state surveillance officers.

Upon identification of a genomic mutation of public health relevance, RGSL is required to submit the same to the Scientific and Clinical Advisory Group (SCAG). After discussion, The SCAG, if felt appropriate, recommends VOIs and other potential mutations to the Central Surveillance Unit for further investigation.