Role of environmental variability, individual behavior, and public health policy in the transmission dynamics of emerging infectious disease

Role of environmental variability, individual behavior, and public health policy in the transmission dynamics of emerging infectious diseasebyJennifer Renee HeadDoctor of Philosophy in EpidemiologyUniversity of California, BerkeleyProfessor Justin V Remais, Professor Ellen Eisen, ChairsEmerging infectious diseases (EIDs) are infectious diseases that have newly appeared in the population, or have existed but are rapidly increasing in incidence, severity or geographic range. Emergence and re-emergence are attributed to a variety of interacting factors, including global climate change and shifting social behaviors. EIDs represent unique challenges to public health due to the unpredictable nature of epidemics, and lack of prior estimates about which public health policies best mitigate disease transmission. In this dissertation, I examine elements of EID transmission using three diseases: coccidioidomycosis, COVID-19, and hand, foot and mouth disease (HFMD). First, using distributed-lag non-linear modeling and an ensemble modeling approach, I examine how climate variability and drought have contributed to the rise of coccidioidomycosis, an emerging fungal infection, in California, and how underlying regional factors contribute to disproportionate increases in certain geographies. I find that drought temporarily displaces cases, reducing cases during drought, and amplifying cases after, and that the relative increase is highest in areas not typically considered endemic for coccidioidomycosis. The majority of EIDs are zoonotic in nature, with rodents as common reservoir species; yet it remains highly debated whether rodents serve as zoonotic reservoirs for Coccidioides. In Chapter 2, I describe results of an experimental field study to ascertain the role that rodents and burrows have on Coccidioides presence in the soil, finding that both rodents and burrows independently are associated with higher probability of detection of Coccidioides DNA. Overall, the presence of rodents is associated with >15 times higher odds of Coccidioides detection, with nearly 75% of the association mediated via burrows. Beyond coccidioidomycosis, the emergence of SARS-CoV-2 demonstrates the continued threat of emerging infectious diseases with pandemic potential, as well as the challenges in anticipating epidemic dynamics and inferring natural history parameters. Amidst uncertain epidemic predictions, transmission modeling has been a critical decision-making tool for identifying effective public health policy. In Chapter 3, I develop and apply an agent based transmission model to understand the retrospective impact of school closures on COVID-19 outcomes, and project how various within-school policies and individual behaviors will affect transmission within schools. I document evidence of reduced social contact patterns following school closures, and estimate that spring 2020 closures of elementary schools averted 2,167 cases in the Bay Area. I also document benefits of minimizing contacts to within classroom cohorts, classroom, masking and immunization of both children and adults. Finally, interactions between pathogens may affect emergence and re-emergence of other pathogens. Serotype-specific vaccination has, in some cases, led to the emergence of non-vaccine serotypes. In Chapter 4, I estimate the early impact of vaccination of the EV71 vaccine on EV71-associated HFMD in Sichuan Province, China, and explore whether we detect significant rises in non-vaccine serotypes that may be indicative of early serotype emergence using an interrupted time series approach and a change point model. I find that introduction of the EV71 vaccine is associated with a decline of EV71-associated HFMD by 60%, but do not find evidence for substantial serotype replacement. Overall, the social, demographic, and environmental factors that influence disease emergence are expected to increase over the coming decades. Public health will need strong surveillance platforms and disease modeling tools to contend with these emerging public health threats. This dissertation demonstrates a variety of approaches towards contending with such challenges