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Scholarly Works (23 results)

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UC Berkeley Electronic Theses and Dissertations (2022)

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

by

Jennifer Renee Head

Doctor of Philosophy in Epidemiology

University of California, Berkeley

Professor Justin V Remais, Professor Ellen Eisen, Chairs

Emerging 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.

    Cover page: Role of environmental variability, individual behavior, and public health policy in the transmission dynamics of emerging infectious disease
    • Article
    • Peer Reviewed
    UC Berkeley Previously Published Works (2021)
    BACKGROUND: We examined school reopening policies amidst rising transmission of the highly transmissible Delta variant, accounting for vaccination among individuals aged 12 years and older, with the goal of characterizing risk to students and teachers under various within-school non-pharmaceutical interventions (NPIs) combined with specific vaccination coverage levels. METHODS: We developed an individual-based transmission model to simulate transmission of the Delta variant of SARS-CoV-2 among a synthetic population, representative of Bay Area cities. We parameterized the model using community contact rates from vaccinated households ascertained from a household survey of Bay Area families with children conducted between February - April, 2021. INTERVENTIONS AND OUTCOMES: We evaluated the additional infections in students and teachers/staff resulting over a 128-day semester from in-school instruction compared to remote instruction when various NPIs (mask use, cohorts, and weekly testing of students/teachers) were implemented in schools, across various community-wide vaccination coverages (50%, 60%, 70%), and student (≥12 years) and teacher/staff vaccination coverages (50% - 95%). We quantified the added benefit of universal masking over masking among unvaccinated students and teachers, across varying levels of vaccine effectiveness (45%, 65%, 85%), and compared results between Delta and Alpha variant circulation. RESULTS: The Delta variant sharply increases the risk of within-school COVID-transmission when compared to the Alpha variant. In our highest risk scenario (50% community and within-school vaccine coverage, no within-school NPIs, and predominant circulation of the Delta variant), we estimated that an elementary school could see 33-65 additional symptomatic cases of COVID-19 over a four-month semester (depending on the relative susceptibility of children <10 years). In contrast, under the Bay Area reopening plan (universal mask use, community and school vaccination coverage of 70%), we estimated excess symptomatic infection attributable to school reopening among 2.0-9.7% of elementary students (8-36 excess symptomatic cases per school over the semester), 3.0% of middle school students (13 cases per school) and 0.4% of high school students (3 cases per school). Excess rates among teachers attributable to reopening were similar. Achievement of lower risk tolerances, such as <5 excess infections per 1,000 students or teachers, required a cohort approach in elementary and middle school populations. In the absence of NPIs, increasing the vaccination coverage of community members from 50% to 70% or elementary teachers from 70% to 95% reduced the estimated excess rate of infection among elementary school students attributable to school transmission by 24% and 41%, respectively. We estimated that with 70% coverage of the eligible community and school population with a vaccine that is ≤65% effective, universal masking can avert more cases than masking of unvaccinated persons alone. CONCLUSIONS: Amidst circulation of the Delta variant, our findings demonstrated that schools are not inherently low risk, yet can be made so with high community vaccination coverages and universal masking. Vaccination of adult community members and teachers protects unvaccinated elementary and middle school children. Elementary and middle schools that can support additional interventions, such as cohorts and testing, should consider doing so, particularly if additional studies find that younger children are equally as susceptible as adults to the Delta variant of SARS-CoV-2. LIMITATIONS: We did not consider the effect of social distancing in classrooms, or variation in testing frequency, and considerable uncertainty remains in key transmission parameters.
      Creative Commons 'BY-NC-ND' version 4.0 license
      • Article
      • Peer Reviewed
      UC Berkeley Previously Published Works (2022)

      Background

      We examined school reopening policies amidst ongoing transmission of the highly transmissible Delta variant, accounting for vaccination among individuals ≥12 years.

      Methods

      We collected data on social contacts among school-aged children in the California Bay Area and developed an individual-based transmission model to simulate transmission of the Delta variant of SARS-CoV-2 in schools. We evaluated the additional infections in students and teachers/staff resulting over a 128-day semester from in-school instruction compared to remote instruction when various NPIs (mask use, cohorts, and weekly testing of students/teachers) were implemented, across various community-wide vaccination coverages (50%, 60%, 70%), and student (≥12 years) and teacher/staff vaccination coverages (50% - 95%).

      Findings

      At 70% vaccination coverage, universal masking reduced infections by >57% among students. Masking plus 70% vaccination coverage enabled achievement of <50 excess cases per 1,000 students/teachers, but stricter risk tolerances, such as <25 excess infections per 1,000 students/teachers, required a cohort approach in elementary and middle school populations. In the absence of NPIs, increasing the vaccination coverage of community members from 50% to 70% or elementary teachers from 70% to 95% reduced the excess rate of infection among elementary school students attributable to school transmission by 24% and 37%, respectively.

      Interpretations

      Amidst Delta variant circulation, we found that schools are not inherently low risk, yet can be made so with high community vaccination coverages and masking. Vaccination of adults protects unvaccinated children.

      Funding

      National Science Foundation grant no. 2032210; National Institutes of Health grant nos. R01AI125842 and R01AI148336; MIDAS Coordination Center (MIDASSUP2020-4).
        Cover page: Model-based assessment of SARS-CoV-2 Delta variant transmission dynamics within partially vaccinated K-12 school populations
        • Article
        • Peer Reviewed
        UC Berkeley Previously Published Works (2022)

        Objectives

        We assessed the relative difficulty in meeting food needs during the COVID-19 pandemic compared with before; determined the relationship between pandemic-associated difficulties in food access and household, maternal and child food security; and identified resiliency-promoting strategies.

        Design

        A cross-sectional survey of households undertaken in November 2020.

        Setting

        Rural districts of Luang Prabang Province, Lao People's Democratic Republic.

        Participants

        Households (N=1122) with children under 5 years.

        Primary and secondary outcomes measured

        Survey respondents reported the relative ease of access of food and healthcare as well as changes in income and expenditures compared with before March 2020. We determined indicators of food security and source of foods consumed for households, women and children, as well as prevalence of malnutrition in children under 5.

        Results

        Nearly four-fifths (78.5%) found it harder to meet household food needs during the pandemic. The most common reasons were increased food prices (51.2%), loss of income (45.3%) and decreased food availability (36.6%). Adjusting for demographics, households with increased difficulty meeting food needs had lower food consumption scores and child dietary diversity. Over 85% of households lost income during the pandemic. Decreased expenditures was associated with reliance on more extreme coping strategies to meet food needs. The households who experienced no change in meeting food needs produced a greater percentage of their food from homegrown methods (4.22% more, 95% CI 1.28 to 7.15), than households who found it more difficult.

        Conclusions

        Pandemic-associated shocks may have large effects on food insecurity. Action is needed to mitigate consequences of the pandemic on nutrition. Local food production and safety net programmes that offset income losses may help.
          Cover page: Changes in household food security, access to health services and income in northern Lao PDR during the COVID-19 pandemic: a cross-sectional survey
          • Article
          • Peer Reviewed
          UC Berkeley Previously Published Works (2022)
          Dispersal is a key force in the assembly of fungal communities and the air is the dominant route of dispersal for most fungi. Understanding the dynamics of airborne fungi is important for determining their source and for helping to prevent fungal disease. This understanding is important in the San Joaquin Valley of California, which is home to 4.2 million people and where the airborne fungus Coccidioides is responsible for the most important fungal disease of otherwise healthy humans, coccidioidomycosis. The San Joaquin Valley is the most productive agricultural region in the United States, with the principal crops grown therein susceptible to fungal pathogens. Here, we characterize the fungal community in soil and air on undeveloped and agricultural land in the San Joaquin Valley using metabarcoding of the internal transcribed spacer 2 variable region of fungal rDNA. Using 1,002 individual samples, we report one of the most extensive studies of fungi sampled simultaneously from air and soil using modern sequencing techniques. We find that the air mycobiome in the San Joaquin Valley is distinct from the soil mycobiome, and that the assemblages of airborne fungi from sites as far apart as 160 km are far more similar to one another than to the fungal communities in nearby soils. Additionally, we present evidence that airborne fungi in the San Joaquin Valley are subject to dispersal limitation and cyclical intra-annual patterns of community composition. Our findings are broadly applicable to understanding the dispersal of airborne fungi and the taxonomic structure of airborne fungal assemblages.
            Cover page: The air mycobiome is decoupled from the soil mycobiome in the California San Joaquin ValleyCreative Commons 'BY' version 4.0 license
            • Article
            • Peer Reviewed
            UC Berkeley Previously Published Works (2022)

            Background

            The San Francisco Bay Area was the first region in the United States to enact school closures to mitigate SARS-CoV-2 transmission. The effects of closures on contact patterns for schoolchildren and their household members remain poorly understood.

            Methods

            We conducted serial cross-sectional surveys (May 2020, September 2020, February 2021) of Bay Area households with children to estimate age-structured daily contact rates for children and their adult household members. We examined changes in contact rates over the course of the COVID-19 pandemic, including after vaccination of household members, and compared contact patterns by household demographics using generalized estimating equations clustered by household.

            Results

            We captured contact histories for 1,967 households on behalf of 2,674 children, comprising 15,087 non-household contacts over the three waves of data collection. Shortly after the start of shelter-in-place orders in May 2020, daily contact rates were higher among children from Hispanic families (1.52 more contacts per child per day; [95% CI: 1.14-2.04]), households whose parents were unable to work from home (1.82; [1.40-2.40]), and households with income < $150,000 (1.75; [1.33-2.33]), after adjusting for other demographic characteristics and household clustering. Between May and August 2020, non-household contacts of children increased by 145% (ages 5-12) and 172% (ages 13-17), despite few children returning to in-person instruction. Non-household contact rates among children were higher-by 1.75 [1.28-2.40] and 1.42 [0.89-2.24] contacts per child per day in 5-12 and 13-17 age groups, respectively, in households where at least one adult was vaccinated against COVID-19, compared to children's contact rates in unvaccinated households.

            Conclusions

            Child contact rates rebounded despite schools remaining closed, as parents obtained childcare, children engaged in contact in non-school settings, and family members were vaccinated. The waning reductions observed in non-household contact rates of schoolchildren and their family members during a prolonged school closure suggests the strategy may be ineffective for long-term SARS-CoV-2 transmission mitigation. Reductions in age-assortative contacts were not as apparent amongst children from lower income households or households where adults could not work from home. Heterogeneous reductions in contact patterns raise concerning racial, ethnic and income-based inequities associated with long-term school closures as a COVID-19 mitigation strategy.
              Cover page: Longitudinal social contacts among school-aged children during the COVID-19 pandemic: the Bay Area Contacts among Kids (BACK) study
              • Article
              • Peer Reviewed
              UC Berkeley Previously Published Works (2022)
              Emerging evidence supports a link between environmental factors-including air pollution and chemical exposures, climate, and the built environment-and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and coronavirus disease 2019 (COVID-19) susceptibility and severity. Climate, air pollution, and the built environment have long been recognized to influence viral respiratory infections, and studies have established similar associations with COVID-19 outcomes. More limited evidence links chemical exposures to COVID-19. Environmental factors were found to influence COVID-19 through four major interlinking mechanisms: increased risk of preexisting conditions associated with disease severity; immune system impairment; viral survival and transport; and behaviors that increase viral exposure. Both data and methodologic issues complicate the investigation of these relationships, including reliance on coarse COVID-19 surveillance data; gaps in mechanistic studies; and the predominance of ecological designs. We evaluate the strength of evidence for environment-COVID-19 relationships and discuss environmental actions that might simultaneously address the COVID-19 pandemic, environmental determinants of health, and health disparities.
                Cover page: Environmental Factors Influencing COVID-19 Incidence and Severity
                • Article
                • Peer Reviewed
                UC Berkeley Previously Published Works (2021)
                We review the interaction between coronavirus disease (COVID-19) and coccidioidomycosis, a respiratory infection caused by inhalation of Coccidioides fungal spores in dust. We examine risk for co-infection among construction and agricultural workers, incarcerated persons, Black and Latino populations, and persons living in high dust areas. We further identify common risk factors for co-infection, including older age, diabetes, immunosuppression, racial or ethnic minority status, and smoking. Because these diseases cause similar symptoms, the COVID-19 pandemic might exacerbate delays in coccidioidomycosis diagnosis, potentially interfering with prompt administration of antifungal therapies. Finally, we examine the clinical implications of co-infection, including severe COVID-19 and reactivation of latent coccidioidomycosis. Physicians should consider coccidioidomycosis as a possible diagnosis when treating patients with respiratory symptoms. Preventive measures such as wearing face masks might mitigate exposure to dust and severe acute respiratory syndrome coronavirus 2, thereby protecting against both infections.
                  Cover page: Coccidioidomycosis and COVID-19 Co-Infection, United States, 2020 - Volume 27, Number 5—May 2021 - Emerging Infectious Diseases journal - CDC
                  • Article
                  • Peer Reviewed
                  UC Berkeley Previously Published Works (2023)
                  Coccidioidomycosis is a typically respiratory fungal disease that, in the United States, occurs primarily in Arizona and California. In California, most coccidioidomycosis cases occur in the San Joaquin Valley, a primarily agricultural region where the disease poses a risk for outdoor workers. We collected 710 soil samples and 265 settled dust samples from nine sites in the San Joaquin Valley and examined how Coccidioides detection varied by month, site, and the presence and abundance of other fungal species. We detected Coccidioides in 89 of 238 (37.4%) rodent burrow soil samples at five undeveloped sites and were unable to detect Coccidioides in any of 472 surface and subsurface soil samples at four agricultural sites. In what is the largest sampling effort undertaken on agricultural land, our results provide no evidence that agricultural soils in the San Joaquin Valley harbor Coccidioides. We found no clear association between Coccidioides and the greater soil fungal community, but we identified 19 fungal indicator species that were significantly associated with Coccidioides detection in burrows. We also did not find a seasonal pattern in Coccidioides detection in the rodent burrow soils we sampled. These findings suggest both the presence of a spore bank and that coccidioidomycosis incidence may be more strongly associated with Coccidioides dispersal than Coccidioides growth. Finally, we were able to detect Coccidioides in only five of our 265 near-surface settled dust samples, one from agricultural land, where Coccidioides was undetected in soils, and four from undeveloped land, where Coccidioides was common in the rodent burrow soils we sampled. Our ability to detect Coccidioides in few settled dust samples indicates that improved methods are likely needed moving forward, though raises questions regarding aerial dispersal in Coccidioides, whose key transmission event likely occurs over short distances in rodent burrows from soil to naïve rodent lungs.
                    Cover page: Coccidioides undetected in soils from agricultural land and uncorrelated with time or the greater soil fungal community on undeveloped land
                    • Article
                    • Peer Reviewed
                    UC San Francisco Previously Published Works (2020)
                    Aims: In this study, we aimed to estimate cross-sectional associations of fish or shellfish consumption with diabetes and glycemia in three South Asian mega-cities. Methods: We analyzed baseline data from 2010-2011 of a cohort (n = 16,287) representing the population ≥20 years old that was neither pregnant nor on bedrest from Karachi (unweighted n = 4017), Delhi (unweighted n = 5364), and Chennai (unweighted n = 6906). Diabetes was defined as self-reported physician-diagnosed diabetes, fasting plasma glucose ≥126 mg/dL (7.0 mmol/L), or glycated hemoglobin A1c (HbA1c) ≥6.5% (48 mmol/mol). We estimated adjusted and unadjusted odds ratios for diabetes using survey estimation logistic regression for each city, and differences in glucose and HbA1c using survey estimation linear regression for each city. Adjusted models controlled for age, gender, body mass index, waist-height ratio, sedentary lifestyle, educational attainment, tobacco use, an unhealthy diet index score, income, self-reported physician diagnosis of high blood pressure, and self-reported physician diagnosis of high cholesterol. Results: The prevalence of diabetes was 26.7% (95% confidence interval: 24.8, 28.6) in Chennai, 36.7% (32.9, 40.5) in Delhi, and 24.3% (22.0, 26.6) in Karachi. Fish and shellfish were consumed more frequently in Chennai than in the other two cities. In Chennai, the adjusted odds ratio for diabetes, comparing more than weekly vs. less than weekly fish consumption, was 0.81 (0.61, 1.08); in Delhi, it was 1.18 (0.87, 1.58), and, in Karachi, it was 1.30 (0.94, 1.80). In Chennai, the adjusted odds ratio of prevalent diabetes among persons consuming shellfish more than weekly versus less than weekly was 1.08 (95% CI: 0.90, 1.30); in Delhi, it was 1.35 (0.90, 2.01), and, in Karachi, it was 1.68 (0.98, 2.86). Conclusions: Both the direction and the magnitude of association between seafood consumption and glycemia may vary by city. Further investigation into specific locally consumed seafoods and their prospective associations with incident diabetes and related pathophysiology are warranted.
                      Cover page: Potentially Heterogeneous Cross-Sectional Associations of Seafood Consumption with Diabetes and Glycemia in Urban South Asia.
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