New COVID Variant: India Forms Genomic Surveillance Consortium

In the backdrop of new and potentially more transmissible COVID-19 variants discovered in the United Kingdom, South Africa and Nigeria, the Indian government has set up a genomic surveillance consortium - Indian SARS-CoV-2 Genomics Consortium (INSACOG) - under National Centre for Disease Control to detect the any circulating variants in the country.

“Against this background, the sudden outbreak of a new SARS-CoV-2 variant in the UK requires India to increase viral genomic surveillance in order to understand the spread of the virus in a rapid and robust manner. The proposed Indian SARS-CoV-2 Genomics Consortium will help 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, can be observed in the samples.”

Union Health Ministry

The Central government said on Saturday that more than 50 samples of returnees from the UK, are currently undergoing genome sequencing at the designated laboratories across the country, reported IANS.

Genome sequencing refers to sequencing the entire genome of an organism.

It involves taking a “genetic fingerprint” of an organism and maps how the DNA or RNA inside it is ordered. Looking at the genetic sequence of different cases, we can detect differences in each new infection and detect variations or mutations, according to an article in The Conversation.

The overall aim of the proposed consortium is to monitor the genomic variations in the SARS-CoV-2 on a regular basis through a multi-laboratory network.

The health ministry lays down three pertinent objectives of the consortium:

1. To ascertain the current status of new variant of SARS-CoV-2 (SARS-CoV-2 VUI 202012/01) in the country
2. To establish a sentinel surveillance for early detection of genomic variants with public health implication
3. To determine the genomic variants in the unusual events/trends (super-spreader events, high mortality/morbidity trend areas etc.)

India’s Action Plan

• The country has ten regional genome sequencing laboratories, which will cater to their nearest states.
• The states will send 5% of the positive samples to these labs for genome sequencing.
• The data generated would then be analyzed by the respective centres and sent to the National Centre for Disease Control (NCDC), Delhi for collation and integration.

The data from the genome sequencing laboratories will be analyzed to study the linkages (if any) between the genomic variants and epidemiological trends. This will help to understand super spreader events, outbreaks and strengthen public health interventions across the country to help in breaking the chains of transmission.

What happens when the UK COVID-19 variant or any other variant mutation is detected in a sample?

• The ministry guidelines state that the virus will then be sent to any of the two notified COVID Virus Repositories at RCB Faridabad or NIV, Pune for isolating and further culturing. This can then be shared as per notified Guidelines for development of assays, which will help in validation of diagnostics and also testing of the vaccines under development.
• The molecular surveillance will be closely linked with the epidemiological surveillance and clinical specimens will also be collected for relevant clinical correlations. The SOPs, which have been developed for the SARS-CoV-2 Genome Sequencing sample collection, deposit and sharing in May, 2020 will be adopted.
• The relevant case details, travel details, of any sample detected with the new UK variant (or any other found to be of significant from public health perspective) will be communicated to NCDC (Director) Nodal Unit. No details shall be revealed before due approval by the competent authority.
• NCDC Nodal Unit will maintain a database of all samples of the new variants (of public health significance). The data will be epidemiologically analysed, interpreted and shared with state/district for investigation, contact tracing and planning response strategies.
• All the genomic sequencing data will be maintained in a National database at two sites, NIBMG, Kalyani and IGIB, New Delhi

The designated laboratories where samples of UK returnees are currently under sequencing include - NCDC, Delhi; CSIR-Institute of Genomics and Integrative Biology, Delhi; CSIR- Centre for Cellular and Molecular Biology, Hyderabad, DBT- Institute of Life Sciences, Bhubaneshwar, DBT-National Institute of Biomedical Genomics, Kalyani; DBT-InStem-National Centre for Biological Sciences, Bengaluru; National Institute of Mental Health & Neurosciences (NIMHANS), Bengaluru and National Institute of Virology, Pune, according to a PTI report.