Characterization of SARS-CoV-2 introduction and spread in southern Wisconsin

ABSTRACT

The rapid worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) took the world by storm in early 2020, amassing over 153 million con-firmed cases as of May 5, 2021. Whole-genome sequencing of confirmed SARS-CoV-2 cases has been used to infer patterns of viral transmission, identify putative introductions of the virus, and provide surveillance on established transmission chains. Aside from tracking the spread of SARS-CoV-2, sequencing data can provide insights into the efficacy of mitigation efforts and forecast the future trajectory of local outbreaks. In this dissertation I focus on exploring the factors that influenced SARS-CoV-2 introduction and spread in southern Wisconsin. Chapter 1 reviews the current state of the pandemic and takes a deeper look into what is known about SARS-CoV-2 replication, the factors that influence SARS-CoV-2 spread, and the preventative measure that can be implemented to slow the spread of SARS-CoV-2.In chapter 2, I describe our work characterizing the initial introduction and spread of SARS-CoV-2 in Dane and Milwaukee counties. These counties are the two most populous counties in southern Wisconsin, separated by only ~100km. Dane County had the 12th confirmed SARS-CoV-2 in the United States, but this did not lead to de-scendant cryptic spread, posited as the cause of many local outbreaks early in the pandemic. Instead, the Dane County outbreak was seeded by multiple later introductions, followed by limited community spread. In contrast, relatively few introductions in Milwaukee County led to extensive community spread. We characterized the efficacy of Wisconsin's "Safer at Home" order and found that viral spread decreased by at least 40% in both Dane and Milwaukee counties. This suggested that, at least early in the pandemic, patterns of SARS-CoV-2 transmission varied substantially even in nearby communities.In chapter 3, I describe our work tracing patterns of SARS-CoV-2 spread in the context of hospitals and clinics. Despite the use of personal protective equipment (PPE) and other strategies to decrease risk of infection, front-line healthcare workers (HCWs) are at increased risk for infection with SARS-CoV-2 compared to the general population. Using a computational contact tracing tool, informal interviews, and genomic sequencing of HCWs and patient contacts, we evaluate the efficacy of current PPE protocols and other preventative measures put in place at a major academic biomedical institution in the American Upper Midwest. We found that the majority of HCWs evaluated, had viral sequences that could be traced to the outside community, suggesting that PPE protocols and preventative measures in place were effective at suppressing viral spread within the institution evaluated here.In chapter 4, I describe our work characterizing an outbreak of SARS-CoV-2 in two residence halls on the University of Wisconsin-Madison's campus. Universities represent high-risk settings for COVID-19 outbreaks, as they combine congregate living situations with high levels of social activity, and a young population that is unlikely to experience severe disease. The University of Wisconsin-Madison had an outbreak of SARS-CoV-2 during Fall 2020 resulting in which 3,485 students tested positive during August-October 2020. This rapid uptick in cases led the university to quarantine two residence halls to contain further SARS-CoV-2 spread. We combine genomic sequencing from these two residence halls, and with 5% of community sequences from Dane County to reveal limited downstream transmission from the residence hall viruses. Our results suggest that containment strategies including large-scale quarantines in congregate living situations (such as in dorms) and suspension of on-campus activities may be effective when experiencing large-scale outbreaks, when implemented rapidly and effectively. (PsycInfo Database Record (c) 2021 APA, all rights reserved)