Rapid Public Health Genomics Capacity Building During The COVID-19 Delta Crisis Driven By A Transnational Private, Public And Social Alliance

Mehul Champakala Mehta^1,2*Gayatri Nair Lobo³Gretchen Weightman⁴Jayanthi S Shastri^5,6,7

• ¹School of Public Health, Yale University, New Haven, United States
• ²Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States
• ³ATE Chandra Foundation, Mumabi, India
• ⁴Illumina (United States), San Diego, California, United States
• ⁵Brihanmumbai Municipal Corporation, Mumbai, Maharashtra, India
• ⁶Topiwala National Medical College and BYL Nair Charitable Hospital, Mumbai, Maharashtra, India
• ⁷Maharashtra University of Health Sciences,, Maharashtra, India

When COVID-19’s Delta variant spread globally during late 2020, Public Health Genomics (PHG) capabilities were missing in several cities, significantly impairing the ability of policymakers and public health systems to rapidly identify COVID-19 variants and effectively respond, with tragic human and economic consequences. In this community case study, we retrospectively studied the dire situation during the Delta wave five years ago when we rapidly constituted a transnational public, private, and social, pro-bono alliance to establish PHG capabilities in Mumbai, a mega metropolis that lacked this capacity. The Albright Stonebridge Group - a renowned global commercial diplomacy entity, Illumina - a genomic sequencing equipment leader, a leading Mumbai non-governmental organization - the ATE Chandra Foundation, and the Municipal Corporation of Greater Mumbai, came together in an alliance, to rapidly establish PHG capabilities in Mumbai. This effort was coordinated across multiple countries, with distributed decision-making and defined responsibilities. An optimal site for a PHG center in Mumbai was identified and the operational requirements, governance structures, and resource and sustainability requirements were defined. In three months, the Genome Sequencing Centre for Outbreak Preparedness & Epidemiology (GeSCOPE) was successfully established in Mumbai’s public infectious disease hospital, Kasturba. The percentage of samples sequenced increased from less than 1% to over 30%, including all the known RT-PCR positive cases, the sequencing time dropped to under 72 hours, and public health policy and responses were enhanced. Currently, GeSCOPE has established itself as the epidemiological hub for Mumbai and western India at large, identifying infectious disease threats like Dengue, Chikungunya, and resistance genes in Mycobacterium tuberculosis strains. This has transformed Mumbai’s ability to expeditiously identify and contain infectious outbreaks thus better protecting its citizens. Our experience has generalizable lessons, that we hope will inform other communities seeking to establish and strengthen their PHG capabilities.