Book Description

Pathogenic RNA viruses emerging from zoonotic reservoirs are among the highest threats for global infectious disease control. Every single major epidemic or pandemic in the 21st century has resulted from an emerging or re-emerging zoonotic RNA virus. Severe Acute Respiratory Syndrome virus 1 (SARS-CoV) emerged in 2003, a novel pandemic H1N1 influenza virus in 2009, Middle East Respiratory Syndrome virus (MERS-CoV) in 2012 and 2015, Ebola in 2014, Zika virus in 2015, Yellow fever virus in 2016, and SARS-CoV-2 in 2019. It is clear the primary drivers of the emergence of these zoonotic RNA viruses are increasing globalization, habitat fragmentation, and encroachment of a continuously growing human population into wildlife habitats 1. It is notable that this increased interaction between humans and animals likely increases the risk of interspecies transmission among a large number of potential pathogens, yet RNA viruses are the dominant source of emerging human pathogens 2. The capacity for RNA viruses to rapidly adapt to new host environments and to respond to shifting selective pressures is not completely understood. Current dogma suggests this trait is tied to short generation times and high mutation rates resulting from error-prone viral replication. RNA virus mutability creates diverse viral populations which are more capable than homogenous populations of adapting to new hosts and host environments 3. However, the generation of viral variation is only the first step. Individual mutations that confer fitness benefits in particular environments must then increase in frequency and/or make their way out of individual hosts and into populations. This stage presents several obstacles that the virus must overcome and is therefore likely to be rate-limiting for the overall pace of viral evolution and host-switching. The first three chapters (chapters 2-4) of this dissertation focus on investigating the evolutionary processes by which zoonotic RNA viruses adapt to mammalian hosts. The results of this work call attention to several significant obstacles that zoonotic RNA viruses must overcome in order to successfully and efficiently emerge in and adapt to human hosts. I suggest these obstacles all derive from the effects of randomness on viral systems. The cumulative impact of these obstacles has critical implications in assessing the pandemic potential of viruses that have already caused human epidemics, like avian influenza viruses, and the adaptive potential of the current pandemic virus, SARS-CoV-2. The final two chapters (chapters 5-6) of this dissertation discuss our work combining principles of viral evolution with epidemiology and population health to investigate the early patterns of SARS-CoV-2 spread in the state of Wisconsin. Taken together, this work suggests the effects of randomness on viral populations within and between individual hosts are a previously underappreciated brake to the pace of viral adaptation and host-switching for influenza A virus (IAV) and SARS-CoV-2. Additionally, this work underscores the value of genomic epidemiology early in a pandemic to understand patterns of viral transmission in different populations and to assess the impact of public health guidelines and interventions on a rolling basis.