Page 65 - Covid 2021 June 2021

of national investment in such an endeavour. This is particularly true in the context of vaccination. While vaccine breakthrough is now recognized as most significant, the genomic characteristics of the viras that allows it to breakthrough depend on adequate genomic surveillance. The proposal address the genomics and immunology of vaccine breakthrough, correlated with disease severity in multiple geographies in India -- Vellore in Tamil Nadu and Bengaluru in Karnataka -- by creating and building on existing infrastructure and cohorts set up during this on-going pandemic. This will be coordinated and executed by some of the best hospitals (CMC, Vellore; Baptist Hospital and St Johns Research institute) and most accomplished institutes like DBT’s inStem and TIFR-NCBS in the country.
Contact Info: secy@psa.gov.in, sapna.poti@gov.in
A pan-national effort on enhanced viral surveillance to better track COVID-19 and vaccinations in India: The second wave and beyond – an initiative supported by Office of PSA
Pathogens like viruses have short generation times and high reproductive rates. This allows them to evolve or change very rapidly. SARS-CoV-2, the virus responsible for the on-going pandemic of COVID-19, mutates and changes continuously as it transmits from person to person. While most new mutations or changes are of little to no consequence, others are able to transmit better, escape existing immunity, dodge detection by diagnostic kits, or have serious clinical impacts. Continuous and on-going genome sequencing of the virus and genomic surveillance help better understand how SARS-CoV-2 is evolving. Such sequencing will eventually allow us to mitigate the risks posed by the ever-changing genomic landscape of the virus, particularly making course correction to vaccination strategies. Furthermore, genomics coupled with host serum analyses can help to explain why people respond to COVID-19 in different ways, therefore helping to identify and better protect those at greater risk of severe disease.
Genomic surveillance for both retrospective and prospective (future infections), when coupled with clinical data, allow us to infer correlations between viral mutations and patient outcomes. All centres will work with their respective states and clinical partners, who have access to epidemiological clinical data on disease outcomes. Such analyses will allow understanding the role of virus evolution in disease burden. Patient genomics can help identify individual-specific responses and correlates.
From a practical perspective, the only way forward is vaccination. Vaccine breakthrough, when vaccinated people get infected, is now recognized as significant. The genomic characteristics of the virus that allow it to breakthrough also require adequate genomic surveillance.
Objectives:
1. Retrospective genomic surveillance: Genome sequencing of archived samples representing dynamics of the pandemic (high vs. low incidence zones; asymptomatic/mild vs. severe symptoms/mortality; paediatric/young age vs. old age infections etc.).
2. Prospective genomic surveillance: Genome sequencing to i) track variant emergence and transmission using sampling strategies defined by sociodemographics; ii) reconstruct epidemiologic history using both phylogenetic analysis and gene genealogy; iii) characterize and draw inferences from clinical phenotypes including vaccine breakthroughs, re- infections, and others; and iv) conduct environmental surveillance (of sewage and waste water), potential to complement human surveillance and support of early interventions (considering large proportion of infected people are asymptomatic).
3. Build human resource: Bioinformatics and genomic epidemiology training for pathogen genomics across institutions and platforms. Adopt evolving technology for sequencing,
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