Coronavirus Infection Dynamics and Cross-species Transmission in Bats

ABSTRACT Coronavirus Infection Dynamics and Cross-species Transmission in Bats Prevention of future zoonotic disease emergence, including pandemic threats, is only possible with a thorough understanding of infection dynamics in reservoir host populations. The emergence of SARS-CoV, MERS, and SARS-CoV-2 highlight the need to examine bat-borne coronaviruses in their natural environments. Disease dynamics and cross-species transmission events in bat populations are complex and remain poorly understood, despite evidence suggesting that cross-species transmission has shaped coronavirus diversity and evolution and that viruses with broad host ranges may have increased pandemic potential. Understanding the longitudinal infection dynamics and the ecological conditions under which coronavirus cross-species transmission events occur will characterize the processes underlying virus emergence in bats. I hypothesize that coronavirus cross-species transmission dynamics are driven by host ecology and environmental conditions. In Aim 1, I will assess ecological drivers of cross-species transmission of coronaviruses in bats. Using viral surveillance data standardized across 30 countries with over 50,000 individual bats sampled, I will assess the likelihood of coronavirus cross-species transmission using an evolutionary Bayesian phylogenetic approach. Covariates examined will include host-genetic similarity, roost-type, reproductive characteristics, conservation status, and geographical home-range overlap. Cross-species transmission of bat-borne coronaviruses may play an important role in increasing the distribution of viruses and pandemic potential. In Aim 2, I will characterize longitudinal dynamics of coronavirus infections in bats in diverse roost locations. I will lead local fieldwork in California (USA) to characterize seasonality and diversity of coronavirus infections in primarily single-species roosts. In Myanmar, I will collaborate with an international team to examine longitudinal dynamics and additionally assess risk factors for coronavirus positivity. The coronavirus and ecological data generated will help parameterize models to understand the role of cross-species transmission in outbreak thresholds, thereby revealing mechanism underpinning viral emergence. My proposed work has specific relevance towards understanding the dynamics underlying the origins of SARS- CoV-2 and could inform on future pandemic threats. This study will provide actionable insights into public health risks, especially for local communities that are most likely to be first exposed to emerging diseases.