Covid 19: Augmenting Traditional Clinical Genomic Surveillance of SARS-CoV-2 with Wastewater Data to Provide Valuable Complementary Insights for Public Health

The nature of the threat of the COVID-19 pandemic has evolved from a race to develop an effective vaccine against a strain of SARS-CoV-2 that afflicted the elderly disproportionately to a race to deliver that vaccination in an environment of shifting variants of SARS-CoV-2. Disturbingly, the current variant (Delta) has overwhelmed hospital systems and has driven a large number of children into acute care. Most state and national governments are operating very low resolution clinical genomic surveillance programs due to the great cost and complexity of full sequencing of clinical swabs. Public heath agencies would benefit from a lower cost, higher scale genomic screening approach to complement the clinical case-based methods. This submission proposes a pilot project utilizing clinical genomic sequencing data in conjunction with wastewater variant surveillance data to identify early warning signals for new or emerging variant spread that could then serve as a template for resource limited setting across the globe. Vaneet Arora, M.D, MPH is Associate Director in Clinical Microbiology at the University of Kentucky (UK) and also serves as the Medical Director of State Public Health Laboratory. He will collaborate with University of Louisville Envirome Institute to corroborate/overlay genomic data on variants from clinical specimens and wastewater samples to anticipate/predict the emergence of newer variants. For the prospective part of this study, as he analyzes the data coming out of the Genomic Laboratory to assess the distribution, location, and proportions of known or new variants/mutations of concern/interest employing GISAID, Pangolin lineages and NextStrain builds, he, with assistance from his team at the State and UK will share information on emerging, reemerging, or novel mutation or variants of concern/interest with the collaborators at the UofL. Similarly, he will receive data on mutations and putative variants of concern/interest identified in wastewater surveillance that will enable identification of geographic locations for existing sequencing data or additional targeted surveillance sequencing of clinical specimens working with State, Regional and Local epidemiologists, and clinical labs.