Transmission and adaptation of SARS-CoV-2 across different hosts and environments

I aim to study various aspects of the transmission, adaptation, and surveillance of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) across different hosts species and environments. SARS-CoV-2 is a generalist virus, and through jumping species barriers can easily infect a wide range of mammalian species. Several animal species including mink and white-tailed deer have been heavily affected by the virus, in some cases leading to extensive culling of these animals. Due to this characteristic of the virus, animal reservoirs become involved in the evolutionary course of the virus by allowing for the selection of novel variants. If transmitted back to humans, these variants can have effects on transmissibility, disease severity, and vaccine efficacy. Furthermore, In response to the COVID-19 pandemic, many institutes tracked the presence of SARS-CoV-2, in wastewater (WW) samples. Clinical surveillance of SARS-CoV-2 is expensive, inefficient, and has sampling bias due to systemic healthcare disparities. WW surveillance on the other hand, is unaffected by such biases, and is a novel, promising source for the prediction and tracking of infected cases in a community. To this end we defined our research aims as follows: First, we quantified transmission rates of SARS-CoV-2 from and back to animal species in a comparative manner. Second, we identified species-specific mutations that have possibly been adapted to animal species with a high incidence of SARS-CoV-2 infection. Third, we compared the levels of within-host diversity of SARS-CoV-2 in different animal species and used statistical and mathematical models to identify factors that contribute to varying levels of diversity found within an individual host. Finally, we aim to analyze wastewater sequences of SARS-CoV-2 and assess the ability of such data to forecast case counts, and compare the utility of sequencing-based approaches in such predictions with existing methods.