Mallory Harris

All Publications

• Social divisions and risk perception drive divergent epidemics and large later waves EVOLUTIONARY HUMAN SCIENCES Harris, M. J., Cardenas, K. J., Mordecai, E. A. 2023; 5

  View details for DOI 10.1017/ehs.2023.2

  View details for Web of Science ID 000943031500001

• Evaluation of an open forecasting challenge to assess skill of West Nile virus neuroinvasive disease prediction. Parasites & vectors Holcomb, K. M., Mathis, S., Staples, J. E., Fischer, M., Barker, C. M., Beard, C. B., Nett, R. J., Keyel, A. C., Marcantonio, M., Childs, M. L., Gorris, M. E., Rochlin, I., Hamins-Puértolas, M., Ray, E. L., Uelmen, J. A., DeFelice, N., Freedman, A. S., Hollingsworth, B. D., Das, P., Osthus, D., Humphreys, J. M., Nova, N., Mordecai, E. A., Cohnstaedt, L. W., Kirk, D., Kramer, L. D., Harris, M. J., Kain, M. P., Reed, E. M., Johansson, M. A. 2023; 16 (1): 11

  Abstract

  West Nile virus (WNV) is the leading cause of mosquito-borne illness in the continental USA. WNV occurrence has high spatiotemporal variation, and current approaches to targeted control of the virus are limited, making forecasting a public health priority. However, little research has been done to compare strengths and weaknesses of WNV disease forecasting approaches on the national scale. We used forecasts submitted to the 2020 WNV Forecasting Challenge, an open challenge organized by the Centers for Disease Control and Prevention, to assess the status of WNV neuroinvasive disease (WNND) prediction and identify avenues for improvement.We performed a multi-model comparative assessment of probabilistic forecasts submitted by 15 teams for annual WNND cases in US counties for 2020 and assessed forecast accuracy, calibration, and discriminatory power. In the evaluation, we included forecasts produced by comparison models of varying complexity as benchmarks of forecast performance. We also used regression analysis to identify modeling approaches and contextual factors that were associated with forecast skill.Simple models based on historical WNND cases generally scored better than more complex models and combined higher discriminatory power with better calibration of uncertainty. Forecast skill improved across updated forecast submissions submitted during the 2020 season. Among models using additional data, inclusion of climate or human demographic data was associated with higher skill, while inclusion of mosquito or land use data was associated with lower skill. We also identified population size, extreme minimum winter temperature, and interannual variation in WNND cases as county-level characteristics associated with variation in forecast skill.Historical WNND cases were strong predictors of future cases with minimal increase in skill achieved by models that included other factors. Although opportunities might exist to specifically improve predictions for areas with large populations and low or high winter temperatures, areas with high case-count variability are intrinsically more difficult to predict. Also, the prediction of outbreaks, which are outliers relative to typical case numbers, remains difficult. Further improvements to prediction could be obtained with improved calibration of forecast uncertainty and access to real-time data streams (e.g. current weather and preliminary human cases).

  View details for DOI 10.1186/s13071-022-05630-y

  View details for PubMedID 36635782

• How will mosquitoes adapt to climate warming? eLife Couper, L. I., Farner, J. E., Caldwell, J. M., Childs, M. L., Harris, M. J., Kirk, D. G., Nova, N., Shocket, M., Skinner, E. B., Uricchio, L. H., Exposito-Alonso, M., Mordecai, E. A. 2021; 10

  Abstract

  The potential for adaptive evolution to enable species persistence under a changing climate is one of the most important questions for understanding impacts of future climate change. Climate adaptation may be particularly likely for short-lived ectotherms, including many pest, pathogen, and vector species. For these taxa, estimating climate adaptive potential is critical for accurate predictive modeling and public health preparedness. Here, we demonstrate how a simple theoretical framework used in conservation biology-evolutionary rescue models-can be used to investigate the potential for climate adaptation in these taxa, using mosquito thermal adaptation as a focal case. Synthesizing current evidence, we find that short mosquito generation times, high population growth rates, and strong temperature-imposed selection favor thermal adaptation. However, knowledge gaps about the extent of phenotypic and genotypic variation in thermal tolerance within mosquito populations, the environmental sensitivity of selection, and the role of phenotypic plasticity constrain our ability to make more precise estimates. We describe how common garden and selection experiments can be used to fill these data gaps. Lastly, we investigate the consequences of mosquito climate adaptation on disease transmission using Aedes aegypti-transmitted dengue virus in Northern Brazil as a case study. The approach outlined here can be applied to any disease vector or pest species and type of environmental change.

  View details for DOI 10.7554/eLife.69630

  View details for PubMedID 34402424

• The interplay of policy, behavior, and socioeconomic conditions in early COVID-19 epidemiology in Georgia. medRxiv : the preprint server for health sciences Harris, M. J., Tessier-Lavigne, E., Mordecai, E. A. 2021

  Abstract

  To investigate the impact of local public health orders, behavior, and population factors on early epidemic dynamics, we investigated variation among counties in the U.S. state of Georgia. We conducted regressions to identify predictors of (1) local public health orders, (2) mobility as a proxy for behavior, and (3) epidemiological outcomes (i.e., cases and deaths). We used an event study to determine whether social distancing and shelter-in-place orders caused a change in mobility. Counties at greater risk for large early outbreaks (i.e., larger populations and earlier first cases) were more likely to introduce local public health orders. Social distancing orders gradually reduced mobility by 19% ten days after their introduction, and lower mobility was associated with fewer cases and deaths. Air pollution and population size were predictors of cases and deaths, while larger elderly or Black population were predictors of lower mobility and greater cases, suggesting self-protective behavior in vulnerable populations. Early epidemiological outcomes reflected responses to policy orders and existing health and socioeconomic disparities related to disease vulnerability and ability to socially distance. Teasing apart the impact of behavior changes and population factors is difficult because the epidemic is embedded in a complex social system with multiple potential feedbacks.

  View details for DOI 10.1101/2021.03.24.21254256

  View details for PubMedID 33791739

  View details for PubMedCentralID PMC8010771

• The impact of long-term non-pharmaceutical interventions on COVID-19 epidemic dynamics and control: the value and limitations of early models. Proceedings. Biological sciences Childs, M. L., Kain, M. P., Harris, M. J., Kirk, D., Couper, L., Nova, N., Delwel, I., Ritchie, J., Becker, A. D., Mordecai, E. A. 2021; 288 (1957): 20210811

  Abstract

  Mathematical models of epidemics are important tools for predicting epidemic dynamics and evaluating interventions. Yet, because early models are built on limited information, it is unclear how long they will accurately capture epidemic dynamics. Using a stochastic SEIR model of COVID-19 fitted to reported deaths, we estimated transmission parameters at different time points during the first wave of the epidemic (March-June, 2020) in Santa Clara County, California. Although our estimated basic reproduction number ([Formula: see text]) remained stable from early April to late June (with an overall median of 3.76), our estimated effective reproduction number ([Formula: see text]) varied from 0.18 to 1.02 in April before stabilizing at 0.64 on 27 May. Between 22 April and 27 May, our model accurately predicted dynamics through June; however, the model did not predict rising summer cases after shelter-in-place orders were relaxed in June, which, in early July, was reflected in cases but not yet in deaths. While models are critical for informing intervention policy early in an epidemic, their performance will be limited as epidemic dynamics evolve. This paper is one of the first to evaluate the accuracy of an early epidemiological compartment model over time to understand the value and limitations of models during unfolding epidemics.

  View details for DOI 10.1098/rspb.2021.0811

  View details for PubMedID 34428971

• Environmental Drivers of Vector-Borne Diseases POPULATION BIOLOGY OF VECTOR-BORNE DISEASES Shocket, M. S., Anderson, C. B., Caldwell, J. M., Childs, M. L., Couper, L. I., Han, S., Harris, M. J., Howard, M. E., Kain, M. P., MacDonald, A. J., Nova, N., Mordecai, E. A., Drake, J. M., Bonsall, M. B., Strand, M. R. 2021: 85-118

  View details for DOI 10.1093/oso/9780198853244.003.0006

  View details for Web of Science ID 000679904700006

• Real-time, interactive website for US-county-level COVID-19 event risk assessment. Nature human behaviour Chande, A., Lee, S., Harris, M., Nguyen, Q., Beckett, S. J., Hilley, T., Andris, C., Weitz, J. S. 2020

  Abstract

  Large events and gatherings, particularly those taking place indoors, have been linked to multitransmission events that have accelerated the pandemic spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To provide real-time, geolocalized risk information, we developed an interactive online dashboard that estimates the risk that at least one individual with SARS-CoV-2 is present in gatherings of different sizes in the United States. The website combines documented case reports at the county level with ascertainment bias information obtained via population-wide serological surveys to estimate real-time circulating, per-capita infection rates. These rates are updated daily as a means to visualize the risk associated with gatherings, including county maps and state-level plots. The website provides data-driven information to help individuals and policy makers make prudent decisions (for example, increasing mask-wearing compliance and avoiding larger gatherings) that could help control the spread of SARS-CoV-2, particularly in hard-hit regions.

  View details for DOI 10.1038/s41562-020-01000-9

  View details for PubMedID 33168955

• The impact of long-term non-pharmaceutical interventions on COVID-19 epidemic dynamics and control. medRxiv : the preprint server for health sciences Childs, M. L., Kain, M. P., Kirk, D., Harris, M., Couper, L., Nova, N., Delwel, I., Ritchie, J., Mordecai, E. A. 2020

  Abstract

  Non-pharmaceutical interventions to combat COVID-19 transmission have worked to slow the spread of the epidemic but can have high socio-economic costs. It is critical we understand the efficacy of non-pharmaceutical interventions to choose a safe exit strategy. Many current models are not suitable for assessing exit strategies because they do not account for epidemic resurgence when social distancing ends prematurely (e.g., statistical curve fits) nor permit scenario exploration in specific locations. We developed an SEIR-type mechanistic epidemiological model of COVID-19 dynamics to explore temporally variable non-pharmaceutical interventions. We provide an interactive tool and code to estimate the transmission parameter, β, and the effective reproduction number, R eff . We fit the model to Santa Clara County, California, where an early epidemic start date and early shelter-in-place orders could provide a model for other regions. As of April 22, 2020, we estimate an R eff of 0.982 (95% CI: 0.849 - 1.107) in Santa Clara County. After June 1 (the end-date for Santa Clara County shelter-in-place as of April 27), we estimate a shift to partial social distancing, combined with rigorous testing and isolation of symptomatic individuals, is a viable alternative to indefinitely maintaining shelter-in-place. We also estimate that if Santa Clara County had waited one week longer before issuing shelter-in-place orders, 95 additional people would have died by April 22 (95% CI: 7 - 283). Given early life-saving shelter-in-place orders in Santa Clara County, longer-term moderate social distancing and testing and isolation of symptomatic individuals have the potential to contain the size and toll of the COVID-19 pandemic in Santa Clara County, and may be effective in other locations.

  View details for DOI 10.1101/2020.05.03.20089078

  View details for PubMedID 32511583

  View details for PubMedCentralID PMC7276010

• Early warning signals of malaria resurgence in Kericho, Kenya. Biology letters Harris, M. J., Hay, S. I., Drake, J. M. 2020; 16 (3): 20190713

  Abstract

  Campaigns to eliminate infectious diseases could be greatly aided by methods for providing early warning signals of resurgence. Theory predicts that as a disease transmission system undergoes a transition from stability at the disease-free equilibrium to sustained transmission, it will exhibit characteristic behaviours known as critical slowing down, referring to the speed at which fluctuations in the number of cases are dampened, for instance the extinction of a local transmission chain after infection from an imported case. These phenomena include increases in several summary statistics, including lag-1 autocorrelation, variance and the first difference of variance. Here, we report the first empirical test of this prediction during the resurgence of malaria in Kericho, Kenya. For 10 summary statistics, we measured the approach to criticality in a rolling window to quantify the size of effect and directions. Nine of the statistics increased as predicted and variance, the first difference of variance, autocovariance, lag-1 autocorrelation and decay time returned early warning signals of critical slowing down based on permutation tests. These results show that time series of disease incidence collected through ordinary surveillance activities may exhibit characteristic signatures prior to an outbreak, a phenomenon that may be quite general among infectious disease systems.

  View details for DOI 10.1098/rsbl.2019.0713

  View details for PubMedID 32183637

• Climate drives spatial variation in Zika epidemics in Latin America. Proceedings. Biological sciences Harris, M. n., Caldwell, J. M., Mordecai, E. A. 2019; 286 (1909): 20191578

  Abstract

  Between 2015 and 2017, Zika virus spread rapidly through populations in the Americas with no prior exposure to the disease. Although climate is a known determinant of many Aedes-transmitted diseases, it is currently unclear whether climate was a major driver of the Zika epidemic and how climate might have differentially impacted outbreak intensity across locations within Latin America. Here, we estimated force of infection for Zika over time and across provinces in Latin America using a time-varying susceptible-infectious-recovered model. Climate factors explained less than 5% of the variation in weekly transmission intensity in a spatio-temporal model of force of infection by province over time, suggesting that week to week transmission within provinces may be too stochastic to predict. By contrast, climate and population factors were highly predictive of spatial variation in the presence and intensity of Zika transmission among provinces, with pseudo-R2 values between 0.33 and 0.60. Temperature, temperature range, rainfall and population size were the most important predictors of where Zika transmission occurred, while rainfall, relative humidity and a nonlinear effect of temperature were the best predictors of Zika intensity and burden. Surprisingly, force of infection was greatest in locations with temperatures near 24°C, much lower than previous estimates from mechanistic models, potentially suggesting that existing vector control programmes and/or prior exposure to other mosquito-borne diseases may have limited transmission in locations most suitable for Aedes aegypti, the main vector of Zika, dengue and chikungunya viruses in Latin America.

  View details for DOI 10.1098/rspb.2019.1578

  View details for PubMedID 31455188