The risk of SARS-2 establishing itself in animal reservoirs

The current SARS-2 pandemic is primarily driven by human to human spread, yet its origins began in wildlife and the virus displays a propensity for repeated spill over from humans to other animal species. The establishment of infection spreading from animal to animal in farmed mink in Europe has highlighted that the virus is quite capable of establishing itself in new animal reservoirs. Should the species it establishes in be a wild animal rather than an easily culled domestic one this creates a permanent re-infection risk for the human population, greatly complicating efforts to minimise COVID-19s impact Southern India is a prime hotspot for zoonotic spillovers with a dense human population and a tropical climate with high species diversity and density in the animal population. Ample opportunity exists for human/wildlife interactions and the sharing of pathogens. This project will focus on identifying whether SARS-2 spill over is occurring into the wild animal population in the Indian State of Kerala. The project will use established pan-coronavirus PCR and deep sequencing methods used successfully to identify coronaviruses in wild animals to determine whether animals in this location are contracting SARS-2 from the human population and whether it is establishing independent circulation. This project will in addition identify any other coronaviruses present filling a crucial knowledge gap in preparation for the next pandemic. The sheer variety of wildlife present in Kerala means that it is not feasible to sample all species, this project will focus on those groups (bats and small carnivores) with a known propensity for SARS-2 infection , those likely to carry SARs like viruses (the sarbecovirus genus) naturally and those in close contact with the human population