publications

2025

1. Interplay between climate, childhood mixing, and population-level susceptibility explains a sudden shift in RSV seasonality in Japan

   Sang Woo Park, Inga Holmdahl, Emily Howerton, Wenchang Yang, Rachel E. Baker, Gabriel A. Vecchi, Sarah Cobey, C. Jessica E. Metcalf, and Bryan T. Grenfell

   Mar 2025

   Pages: 2025.03.02.25323095

   Abs DOI

   Titrating the relative importance of endogenous and exogenous drivers for dynamical transitions in host-pathogen systems remains an important research frontier towards predicting future outbreaks and making public health decisions. In Japan, respiratory syncytial virus (RSV), a major childhood respiratory pathogen, displayed a sudden, dramatic shift in outbreak seasonality (from winter to fall) in 2016. This shift was not observed in any other countries. We use mathematical models to identify processes that could lead to this outcome. In line with previous analyses, we identify a robust quadratic relationship between mean specific humidity and transmission, with minimum transmission occurring at intermediate humidity. This drives semiannual patterns of seasonal transmission rates that peak in summer and winter. Under this transmission regime, a subtle increase in population-level susceptibility can cause a sudden shift in seasonality, where the degree of shift is primarily determined by the interval between the two peaks of seasonal transmission rate. We hypothesize that an increase in children attending childcare facilities may have contributed to the increase in susceptibility through increased contact rates with susceptible hosts. Our analysis underscores the power of studying infectious disease dynamics to titrate the roles of underlying drivers of dynamical transitions in ecology.

2. Complex multiannual cycles of Mycoplasma pneumoniae: persistence and the role of stochasticity

   Bjarke Frost Nielsen, Sang Woo Park, Emily Howerton, Olivia Frost Lorentzen, Mogens H. Jensen, and Bryan T. Grenfell

   Apr 2025

   Abs DOI

   The epidemiological dynamics of Mycoplasma pneumoniae are characterized by complex and poorly understood multiannual cycles, posing challenges for forecasting. Using Bayesian methods to fit a seasonally forced transmission model to long-term surveillance data from Denmark (1958-1995, 2010-2025), we investigate the mechanisms driving recurrent outbreaks of M. pneumoniae. The period of the multiannual cycles (predominantly approx. 5 years in Denmark) are explained as a consequence of the interaction of two time-scales in the system, one intrinsic and one extrinsic (seasonal). While it provides an excellent fit to shorter time series (a few decades), we find that the deterministic model eventually settles into an annual cycle, failing to reproduce the observed 4-5-year periodicity long-term. Upon further analysis, the system is found to exhibit transient chaos and thus high sensitivity to stochasticity. We show that environmental (but not purely demographic) stochasticity can sustain the multi-year cycles via stochastic resonance. The disruptive effects of COVID-19 non-pharmaceutical interventions (NPIs) on M. pneumoniae circulation constitute a natural experiment on the effects of large perturbations. Consequently, the effects of NPIs are included in the model and medium-term predictions are explored. Our findings highlight the intrinsic sensitivity of M. pneumoniae dynamics to perturbations and interventions, underscoring the limitations of deterministic epidemic models for long-term prediction. More generally, our results textitasize the potential role of stochasticity as a driver of complex cycles across endemic and recurring pathogens.

2024

1. The US COVID-19 and Influenza Scenario Modeling Hubs: Delivering long-term projections to guide policy

   Sara L. Loo, Emily Howerton, Lucie Contamin, Claire P. Smith, Rebecca K. Borchering, Luke C. Mullany, Samantha Bents, Erica Carcelen, Sung-mok Jung, and 11 more authors

   Epidemics, Mar 2024

   Abs DOI

   Between December 2020 and April 2023, the COVID-19 Scenario Modeling Hub (SMH) generated operational multi-month projections of COVID-19 burden in the US to guide pandemic planning and decision-making in the context of high uncertainty. This effort was born out of an attempt to coordinate, synthesize and effectively use the unprecedented amount of predictive modeling that emerged throughout the COVID-19 pandemic. Here we describe the history of this massive collective research effort, the process of convening and maintaining an open modeling hub active over multiple years, and attempt to provide a blueprint for future efforts. We detail the process of generating 17 rounds of scenarios and projections at different stages of the COVID-19 pandemic, and disseminating results to the public health community and lay public. We also highlight how SMH was expanded to generate influenza projections during the 2022–23 season. We identify key impacts of SMH results on public health and draw lessons to improve future collaborative modeling efforts, research on scenario projections, and the interface between models and policy.

2. People and Data: solving planetary challenges together

   Chiara Vanalli, Emily Howerton, Fuhan Yang, Thu Nguyen-Anh Tran, and Weiming Hu

   Frontiers in Environmental Science, Mar 2024

   Abs DOI

   The advancement of computing and information collection technologies has created vast amounts of data describing the world surrounding us. Yet, our planet continues to face unprecedented challenges, including climate change and biodiversity loss. How do we effectively use this information in an open and collaborative way to tackle these planetary-scale issues? We propose a stronger synergistic integration between people and data as we work toward a healthy planet: crowd empowerment in the collection and analysis of data as well as in the identification and implementation of actionable solutions. We use our unique experience as a diverse winning team of the EY Better Working World 2022 global data challenge to illustrate the great potential and current limitations of such an approach. With the objective of fighting biodiversity loss, we were asked to develop a predictive frog multi-species distribution model using occurrence data, gathered from the FrogID app, and environmental conditions. Despite the great potential of global data challenges focused on planetary health, they comprise about 6% of all challenges in the last 5 years. Moreover, though open in principle, in practice, pre-existing disparities limit the inclusion of a diverse crowd. To address existing gaps, we propose practical guidelines to realize the “People and Data” vision: fostering collaboration, seeking funding, enhancing diversity, and ensuring long-term sustainability. In this way, we can tackle the great challenges our world is facing.

3. Ensemble2: Scenarios ensembling for communication and performance analysis

   Clara Bay, Guillaume St-Onge, Jessica T. Davis, Matteo Chinazzi, Emily Howerton, Justin Lessler, Michael C. Runge, Katriona Shea, Shaun Truelove, and 2 more authors

   Epidemics, Mar 2024

   Abs DOI

   Throughout the COVID-19 pandemic, scenario modeling played a crucial role in shaping the decision-making process of public health policies. Unlike forecasts, scenario projections rely on specific assumptions about the future that consider different plausible states-of-the-world that may or may not be realized and that depend on policy interventions, unpredictable changes in the epidemic outlook, etc. As a consequence, long-term scenario projections require different evaluation criteria than the ones used for traditional short-term epidemic forecasts. Here, we propose a novel ensemble procedure for assessing pandemic scenario projections using the results of the Scenario Modeling Hub (SMH) for COVID-19 in the United States (US). By defining a “scenario ensemble” for each model and the ensemble of models, termed “Ensemble2”, we provide a synthesis of potential epidemic outcomes, which we use to assess projections’ performance, bypassing the identification of the most plausible scenario. We find that overall the Ensemble2 models are well-calibrated and provide better performance than the scenario ensemble of individual models. The ensemble procedure accounts for the full range of plausible outcomes and highlights the importance of scenario design and effective communication. The scenario ensembling approach can be extended to any scenario design strategy, with potential refinements including weighting scenarios and allowing the ensembling process to evolve over time.

4. Misapplied management makes matters worse: Spatially explicit control leverages biotic interactions to slow invasion

   Emily Howerton, Tracy Langkilde, and Katriona Shea

   Ecological Applications, Mar 2024

   Abs DOI

   A wide range of approaches has been used to manage the spread of invasive species, yet invaders continue to be a challenge to control. In some cases, management actions have no effect or may even inadvertently benefit the targeted invader. Here, we use the mid-20th century management of the Red Imported Fire Ant, Solenopsis invicta, in the US as a motivating case study to explore the conditions under which such wasted management effort may occur. Introduced in approximately 1940, the fire ant spread widely through the southeast US and became a problematic pest. Historically, fire ants were managed with broad-spectrum pesticides; unfortunately, these efforts were largely unsuccessful. One hypothesis suggests that, by also killing native ants, mass pesticide application reduced competitive burdens thereby enabling fire ants to invade more quickly than they would in the absence of management. We use a mechanistic competition model to demonstrate the landscape-level effects of such management. We explicitly model the extent and location of pesticide applications, showing that the same pesticide application can have a positive, neutral, or negative effect on the progress of an invasion, depending on where it is applied on the landscape with respect to the invasion front. When designing management, the target species is often considered alone; however, this work suggests that leveraging existing biotic interactions, specifically competition with native species, can increase the efficacy of management. Our model not only highlights the potential unintended consequences of ignoring biotic interactions, but also provides a framework for developing spatially explicit management strategies that take advantage of these biotic interactions to work smarter, not harder.

5. Potential impact of annual vaccination with reformulated COVID-19 vaccines: Lessons from the US COVID-19 scenario modeling hub

   Sung-mok Jung, Sara L. Loo, Emily Howerton, Lucie Contamin, Claire P. Smith, Erica C. Carcelén, Katie Yan, Samantha J. Bents, John Levander, and 50 more authors

   PLOS Medicine, Apr 2024

   Abs DOI

   Background Coronavirus Disease 2019 (COVID-19) continues to cause significant hospitalizations and deaths in the United States. Its continued burden and the impact of annually reformulated vaccines remain unclear. Here, we present projections of COVID-19 hospitalizations and deaths in the United States for the next 2 years under 2 plausible assumptions about immune escape (20% per year and 50% per year) and 3 possible CDC recommendations for the use of annually reformulated vaccines (no recommendation, vaccination for those aged 65 years and over, vaccination for all eligible age groups based on FDA approval). Methods and findings The COVID-19 Scenario Modeling Hub solicited projections of COVID-19 hospitalization and deaths between April 15, 2023 and April 15, 2025 under 6 scenarios representing the intersection of considered levels of immune escape and vaccination. Annually reformulated vaccines are assumed to be 65% effective against symptomatic infection with strains circulating on June 15 of each year and to become available on September 1. Age- and state-specific coverage in recommended groups was assumed to match that seen for the first (fall 2021) COVID-19 booster. State and national projections from 8 modeling teams were ensembled to produce projections for each scenario and expected reductions in disease outcomes due to vaccination over the projection period. From April 15, 2023 to April 15, 2025, COVID-19 is projected to cause annual epidemics peaking November to January. In the most pessimistic scenario (high immune escape, no vaccination recommendation), we project 2.1 million (90% projection interval (PI) [1,438,000, 4,270,000]) hospitalizations and 209,000 (90% PI [139,000, 461,000]) deaths, exceeding pre-pandemic mortality of influenza and pneumonia. In high immune escape scenarios, vaccination of those aged 65+ results in 230,000 (95% confidence interval (CI) [104,000, 355,000]) fewer hospitalizations and 33,000 (95% CI [12,000, 54,000]) fewer deaths, while vaccination of all eligible individuals results in 431,000 (95% CI: 264,000–598,000) fewer hospitalizations and 49,000 (95% CI [29,000, 69,000]) fewer deaths. Conclusions COVID-19 is projected to be a significant public health threat over the coming 2 years. Broad vaccination has the potential to substantially reduce the burden of this disease, saving tens of thousands of lives each year.

6. When do we need multiple infectious disease models? Agreement between projection rank and magnitude in a multi-model setting

   La Keisha Wade-Malone, Emily Howerton, William J. M. Probert, Michael C. Runge, Cécile Viboud, and Katriona Shea

   Epidemics, Jun 2024

   Abs DOI

   Mathematical models are useful for public health planning and response to infectious disease threats. However, different models can provide differing results, which can hamper decision making if not synthesized appropriately. To address this challenge, multi-model hubs convene independent modeling groups to generate ensembles, known to provide more accurate predictions of future outcomes. Yet, these hubs are resource intensive, and how many models are sufficient in a hub is not known. Here, we compare the benefit of predictions from multiple models in different contexts: (1) decision settings that depend on predictions of quantitative outcomes (e.g., hospital capacity planning), where assessments of the benefits of multi-model ensembles have largely focused; and (2) decisions settings that require the ranking of alternative epidemic scenarios (e.g., comparing outcomes under multiple possible interventions and biological uncertainties). We develop a mathematical framework to mimic a multi-model prediction setting, and use this framework to quantify how frequently predictions from different models agree. We further explore multi-model agreement using real-world, empirical data from 14 rounds of U.S. COVID-19 Scenario Modeling Hub projections. Our results suggest that the value of multiple models could be different in different decision contexts, and if only a few models are available, focusing on the rank of alternative epidemic scenarios could be more robust than focusing on quantitative outcomes. Although additional exploration of the sufficient number of models for different contexts is still needed, our results indicate that it may be possible to identify decision contexts where it is robust to rely on fewer models, a finding that can inform the use of modeling resources during future public health crises.

7. Scenario Design for Infectious Disease Projections: Integrating Concepts from Decision Analysis and Experimental Design

   Michael C Runge, Katriona Shea, Emily Howerton, Katie Yan, Harry Hochheiser, Erik Rosenstrom, William J. M Probert, Rebecca Borchering, Madhav V Marathe, and 5 more authors

   Epidemics, May 2024

   Abs DOI

   Across many fields, scenario modeling has become an important tool for exploring long-term projections and how they might depend on potential interventions and critical uncertainties, with relevance to both decision makers and scientists. In the past decade, and especially during the COVID-19 pandemic, the field of epidemiology has seen substantial growth in the use of scenario projections. Multiple scenarios are often projected at the same time, allowing important comparisons that can guide the choice of intervention, the prioritization of research topics, or public communication. The design of the scenarios is central to their ability to inform important questions. In this paper, we draw on the fields of decision analysis and statistical design of experiments to propose a framework for scenario design in epidemiology, with relevance also to other fields. We identify six different fundamental purposes for scenario designs (decision making, sensitivity analysis, situational awareness, horizon scanning, forecasting, and value of information) and discuss how those purposes guide the structure of scenarios. We discuss other aspects of the content and process of scenario design, broadly for all settings and specifically for multi-model ensemble projections. As an illustrative case study, we examine the first 17 rounds of scenarios from the U.S. COVID-19 Scenario Modeling Hub, then reflect on future advancements that could improve the design of scenarios in epidemiological settings.

8. Predicting the impact of non-pharmaceutical interventions against COVID-19 on Mycoplasma pneumoniae in the United States

   Sang Woo Park, Brooklyn Noble, Emily Howerton, Bjarke F. Nielsen, Sarah Lentz, Lilliam Ambroggio, Samuel Dominguez, Kevin Messacar, and Bryan T. Grenfell

   Epidemics, Nov 2024

   Abs DOI

   The introduction of non-pharmaceutical interventions (NPIs) against COVID-19 disrupted circulation of many respiratory pathogens and eventually caused large, delayed outbreaks, owing to the build up of the susceptible pool during the intervention period. In contrast to other common respiratory pathogens that re-emerged soon after the NPIs were lifted, longer delays (\textgreater 3 years) in the outbreaks of Mycoplasma pneumoniae (Mp), a bacterium commonly responsible for respiratory infections and pneumonia, have been reported in Europe and Asia. As Mp cases are continuing to increase in the US, predicting the size of an imminent outbreak is timely for public health agencies and decision makers. Here, we use simple mathematical models to provide robust predictions about a large Mp outbreak ongoing in the US. Our model further illustrates that NPIs and waning immunity are important factors in driving long delays in epidemic resurgence.

2023

1. Multiple models for outbreak decision support in the face of uncertainty

   Katriona Shea, Rebecca K. Borchering, William J. M. Probert, Emily Howerton, Tiffany L. Bogich, Shou-Li Li, Willem G. Panhuis, Cecile Viboud, Ricardo Aguás, and 69 more authors

   Proceedings of the National Academy of Sciences, May 2023

   Abs DOI

   Policymakers must make management decisions despite incomplete knowledge and conflicting model projections. Little guidance exists for the rapid, representative, and unbiased collection of policy-relevant scientific input from independent modeling teams. Integrating approaches from decision analysis, expert judgment, and model aggregation, we convened multiple modeling teams to evaluate COVID-19 reopening strategies for a mid-sized United States county early in the pandemic. Projections from seventeen distinct models were inconsistent in magnitude but highly consistent in ranking interventions. The 6-mo-ahead aggregate projections were well in line with observed outbreaks in mid-sized US counties. The aggregate results showed that up to half the population could be infected with full workplace reopening, while workplace restrictions reduced median cumulative infections by 82%. Rankings of interventions were consistent across public health objectives, but there was a strong trade-off between public health outcomes and duration of workplace closures, and no win-win intermediate reopening strategies were identified. Between-model variation was high; the aggregate results thus provide valuable risk quantification for decision making. This approach can be applied to the evaluation of management interventions in any setting where models are used to inform decision making. This case study demonstrated the utility of our approach and was one of several multimodel efforts that laid the groundwork for the COVID-19 Scenario Modeling Hub, which has provided multiple rounds of real-time scenario projections for situational awareness and decision making to the Centers for Disease Control and Prevention since December 2020.

2. Context-dependent representation of within- and between-model uncertainty: aggregating probabilistic predictions in infectious disease epidemiology

   Emily Howerton, Michael C. Runge, Tiffany L. Bogich, Rebecca K. Borchering, Hidetoshi Inamine, Justin Lessler, Luke C. Mullany, William J. M. Probert, Claire P. Smith, and 3 more authors

   Journal of The Royal Society Interface, Jan 2023

   Abs DOI

   Probabilistic predictions support public health planning and decision making, especially in infectious disease emergencies. Aggregating outputs from multiple models yields more robust predictions of outcomes and associated uncertainty. While the selection of an aggregation method can be guided by retrospective performance evaluations, this is not always possible. For example, if predictions are conditional on assumptions about how the future will unfold (e.g. possible interventions), these assumptions may never materialize, precluding any direct comparison between predictions and observations. Here, we summarize literature on aggregating probabilistic predictions, illustrate various methods for infectious disease predictions via simulation, and present a strategy for choosing an aggregation method when empirical validation cannot be used. We focus on the linear opinion pool (LOP) and Vincent average, common methods that make different assumptions about between-prediction uncertainty. We contend that assumptions of the aggregation method should align with a hypothesis about how uncertainty is expressed within and between predictions from different sources. The LOP assumes that between-prediction uncertainty is meaningful and should be retained, while the Vincent average assumes that between-prediction uncertainty is akin to sampling error and should not be preserved. We provide an R package for implementation. Given the rising importance of multi-model infectious disease hubs, our work provides useful guidance on aggregation and a deeper understanding of the benefits and risks of different approaches.

3. Optimal spatial evaluation of a pro rata vaccine distribution rule for COVID-19

   François M. Castonguay, Julie C. Blackwood, Emily Howerton, Katriona Shea, Charles Sims, and James N. Sanchirico

   Scientific Reports, Feb 2023

   Abs DOI

   The COVID-19 Vaccines Global Access (COVAX) is a World Health Organization (WHO) initiative that aims for an equitable access of COVID-19 vaccines. Despite potential heterogeneous infection levels across a country, countries receiving allotments of vaccines may follow WHO’s allocation guidelines and distribute vaccines based on a jurisdictions’ relative population size. Utilizing economic—epidemiological modeling, we benchmark the performance of this pro rata allocation rule by comparing it to an optimal one that minimizes the economic damages and expenditures over time, including a penalty representing the social costs of deviating from the pro rata strategy. The pro rata rule performs better when the duration of naturally- and vaccine-acquired immunity is short, when there is population mixing, when the supply of vaccine is high, and when there is minimal heterogeneity in demographics. Despite behavioral and epidemiological uncertainty diminishing the performance of the optimal allocation, it generally outperforms the pro rata vaccine distribution rule.

4. Impact of SARS-CoV-2 vaccination of children ages 5–11 years on COVID-19 disease burden and resilience to new variants in the United States, November 2021–March 2022: A multi-model study

   Rebecca K. Borchering, Luke C. Mullany, Emily Howerton, Matteo Chinazzi, Claire P. Smith, Michelle Qin, Nicholas G. Reich, Lucie Contamin, John Levander, and 53 more authors

   The Lancet Regional Health – Americas, Jan 2023

   Abs DOI

   Background SARS-CoV-2 vaccination of persons aged 12 years and older has reduced disease burden in the United States. The COVID-19 Scenario Modeling Hub convened multiple modeling teams in September 2021 to project the impact of expanding vaccine administration to children 5-11 years old on anticipated COVID-19 burden and resilience against variant strains. Methods Nine modeling teams contributed state- and national-level projections for weekly counts of cases, hospitalizations, and deaths in the United States for the period September 12, 2021 to March 12, 2022. Four scenarios covered all combinations of: 1) presence vs. absence of vaccination of children ages 5-11 years starting on November 1, 2021; and 2) continued dominance of the Delta variant vs. emergence of a hypothetical more transmissible variant on November 15, 2021. Individual team projections were combined using linear pooling. The effect of childhood vaccination on overall and age-specific outcomes was estimated by meta-analysis approaches. Findings Absent a new variant, COVID-19 cases, hospitalizations, and deaths among all ages were projected to decrease nationally through mid-March 2022. Under a set of specific assumptions, models projected that vaccination of children 5-11 years old was associated with reductions in all-age cumulative cases (7.2%, mean incidence ratio [IR] 0.928, 95% confidence interval [CI] 0.880-0.977), hospitalizations (8.7%, mean IR 0.913, 95% CI 0.834-0.992), and deaths (9.2%, mean IR 0.908, 95% CI 0.797-1.020) compared with scenarios where children were not vaccinated. This projected effect of vaccinating children 5-11 years old increased in the presence of a more transmissible variant, assuming no change in vaccine effectiveness by variant. Larger relative reductions in cumulative cases, hospitalizations, and deaths were observed for children than for the entire U.S. population. Substantial state-level variation was projected in epidemic trajectories, vaccine benefits, and variant impacts. Conclusions Results from this multi-model aggregation study suggest that, under a specific set of scenario assumptions, expanding vaccination to children 5-11 years old would provide measurable direct benefits to this age group and indirect benefits to the all-age U.S. population, including resilience to more transmissible variants.

5. Evaluation of the US COVID-19 Scenario Modeling Hub for informing pandemic response under uncertainty

   Emily Howerton, Lucie Contamin, Luke C. Mullany, Michelle Qin, Nicholas G. Reich, Samantha Bents, Rebecca K. Borchering, Sung-mok Jung, Sara L. Loo, and 74 more authors

   Nature Communications, Nov 2023

   Abs DOI

   Our ability to forecast epidemics far into the future is constrained by the many complexities of disease systems. Realistic longer-term projections may, however, be possible under well-defined scenarios that specify the future state of critical epidemic drivers. Since December 2020, the U.S. COVID-19 Scenario Modeling Hub (SMH) has convened multiple modeling teams to make months ahead projections of SARS-CoV-2 burden, totaling nearly 1.8 million national and state-level projections. Here, we find SMH performance varied widely as a function of both scenario validity and model calibration. We show scenarios remained close to reality for 22 weeks on average before the arrival of unanticipated SARS-CoV-2 variants invalidated key assumptions. An ensemble of participating models that preserved variation between models (using the linear opinion pool method) was consistently more reliable than any single model in periods of valid scenario assumptions, while projection interval coverage was near target levels. SMH projections were used to guide pandemic response, illustrating the value of collaborative hubs for longer-term scenario projections.

6. The effect of governance structures on optimal control of two-patch epidemic models

   Emily Howerton, Kyle Dahlin, Christina J. Edholm, Lindsey Fox, Margaret Reynolds, Brandon Hollingsworth, George Lytle, Melody Walker, Julie Blackwood, and 1 more author

   Journal of Mathematical Biology, Oct 2023

   Abs DOI

   Infectious diseases continue to pose a significant threat to the health of humans globally. While the spread of pathogens transcends geographical boundaries, the management of infectious diseases typically occurs within distinct spatial units, determined by geopolitical boundaries. The allocation of management resources within and across regions (the “governance structure”) can affect epidemiological outcomes considerably, and policy-makers are often confronted with a choice between applying control measures uniformly or differentially across regions. Here, we investigate the extent to which uniform and non-uniform governance structures affect the costs of an infectious disease outbreak in two-patch systems using an optimal control framework. A uniform policy implements control measures with the same time varying rate functions across both patches, while these measures are allowed to differ between the patches in a non-uniform policy. We compare results from two systems of differential equations representing transmission of cholera and Ebola, respectively, to understand the interplay between transmission mode, governance structure and the optimal control of outbreaks. In our case studies, the governance structure has a meaningful impact on the allocation of resources and burden of cases, although the difference in total costs is minimal. Understanding how governance structure affects both the optimal control functions and epidemiological outcomes is crucial for the effective management of infectious diseases going forward.

7. Benefits of near-universal vaccination and treatment access to manage COVID-19 burden in the United States

   Fuhan Yang, Thu Nguyen-Anh Tran, Emily Howerton, Maciej F. Boni, and Joseph L. Servadio

   BMC Medicine, Aug 2023

   Abs DOI

   As we continue the fourth year of the COVID-19 epidemic, SARS-CoV-2 infections still cause high morbidity and mortality in the United States. During 2020–2022, COVID-19 was one of the leading causes of death in the United States and by far the leading cause among infectious diseases. Vaccination uptake remains low despite this being an effective burden reducing intervention. The development of COVID-19 therapeutics provides hope for mitigating severe clinical outcomes. This modeling study examines combined strategies of vaccination and treatment to reduce the burden of COVID-19 epidemics over the next decade.

2022

1. Projected resurgence of COVID-19 in the United States in July-December 2021 resulting from the increased transmissibility of the Delta variant and faltering vaccination

   Shaun Truelove, Claire P Smith, Michelle Qin, Luke C Mullany, Rebecca K Borchering, Justin Lessler, Katriona Shea, Emily Howerton, Lucie Contamin, and 51 more authors

   eLife, Jun 2022

   Abs DOI

   In Spring 2021, the highly transmissible SARS-CoV-2 Delta variant began to cause increases in cases, hospitalizations, and deaths in parts of the United States. At the time, with slowed vaccination uptake, this novel variant was expected to increase the risk of pandemic resurgence in the US in summer and fall 2021. As part of the COVID-10 Scenario Modeling Hub, an ensemble of nine mechanistic models produced six-month scenario projections for July-December 2021 for the United States. These projections estimated substantial resurgences of COVID-19 across the US resulting from the more transmissible Delta variant, projected to occur across most of the US, coinciding with school and business reopening. The scenarios revealed that reaching higher vaccine coverage in July—December 2021 reduced the size and duration of the projected resurgence substantially, with the expected impacts was largely concentrated in a subset of states with lower vaccination coverage. Despite accurate projection of COVID-19 surges occurring and timing, the magnitude was substantially underestimated 2021 by the models compared with the of the reported cases, hospitalizations, and deaths occurring during July-December, highlighting the continued challenges to predict the evolving COVID-19 pandemic. Vaccination uptake remains critical to limiting transmission and disease, particularly in states with lower vaccination coverage. Higher vaccination goals at the onset of the surge of the new variant were estimated to avert over 1.5 million cases and 21,000 deaths, though may have had even greater impacts, considering the underestimated resurgence magnitude from the model.

2021

1. Synergistic interventions to control COVID-19: Mass testing and isolation mitigates reliance on distancing

   Emily Howerton, Matthew J. Ferrari, Ottar N. Bjørnstad, Tiffany L. Bogich, Rebecca K. Borchering, Chris P. Jewell, James D. Nichols, William J. M. Probert, Michael C. Runge, and 3 more authors

   PLOS Computational Biology, Oct 2021

   Abs DOI

   Stay-at-home orders and shutdowns of non-essential businesses are powerful, but socially costly, tools to control the pandemic spread of SARS-CoV-2. Mass testing strategies, which rely on widely administered frequent and rapid diagnostics to identify and isolate infected individuals, could be a potentially less disruptive management strategy, particularly where vaccine access is limited. In this paper, we assess the extent to which mass testing and isolation strategies can reduce reliance on socially costly non-pharmaceutical interventions, such as distancing and shutdowns. We develop a multi-compartmental model of SARS-CoV-2 transmission incorporating both preventative non-pharmaceutical interventions (NPIs) and testing and isolation to evaluate their combined effect on public health outcomes. Our model is designed to be a policy-guiding tool that captures important realities of the testing system, including constraints on test administration and non-random testing allocation. We show how strategic changes in the characteristics of the testing system, including test administration, test delays, and test sensitivity, can reduce reliance on preventative NPIs without compromising public health outcomes in the future. The lowest NPI levels are possible only when many tests are administered and test delays are short, given limited immunity in the population. Reducing reliance on NPIs is highly dependent on the ability of a testing program to identify and isolate unreported, asymptomatic infections. Changes in NPIs, including the intensity of lockdowns and stay at home orders, should be coordinated with increases in testing to ensure epidemic control; otherwise small additional lifting of these NPIs can lead to dramatic increases in infections, hospitalizations and deaths. Importantly, our results can be used to guide ramp-up of testing capacity in outbreak settings, allow for the flexible design of combined interventions based on social context, and inform future cost-benefit analyses to identify efficient pandemic management strategies.

2. Strategic testing approaches for targeted disease monitoring can be used to inform pandemic decision-making

   James D. Nichols, Tiffany L. Bogich, Emily Howerton, Ottar N. Bjørnstad, Rebecca K. Borchering, Matthew J. Ferrari, Murali Haran, Christopher P. Jewell, Kim Pepin, and 6 more authors

   PLOS Biology, Jun 2021

   Abs DOI

   More than 1.6 million Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) tests were administered daily in the United States at the peak of the epidemic, with a significant focus on individual treatment. Here, we show that objective-driven, strategic sampling designs and analyses can maximize information gain at the population level, which is necessary to increase situational awareness and predict, prepare for, and respond to a pandemic, while also continuing to inform individual treatment. By focusing on specific objectives such as individual treatment or disease prediction and control (e.g., via the collection of population-level statistics to inform lockdown measures or vaccine rollout) and drawing from the literature on capture–recapture methods to deal with nonrandom sampling and testing errors, we illustrate how public health objectives can be achieved even with limited test availability when testing programs are designed a priori to meet those objectives.

3. Modeling of Future COVID-19 Cases, Hospitalizations, and Deaths, by Vaccination Rates and Nonpharmaceutical Intervention Scenarios — United States, April–September 2021

   Rebecca K Borchering, Cécile Viboud, Emily Howerton, Claire P Smith, Shaun Truelove, Michael C Runge, Nicholas G Reich, Lucie Contamin, John Levander, and 48 more authors

   Morbidity and Mortality Weekly Report, Jun 2021

   DOI

2018

1. A flight-based metric for evaluating NFL punters

   R. Drew Pasteur, Emily Howerton, Preston Pozderac, Stuart Young, and Jonathan Moore

   Journal of Sports Analytics, Jan 2018

   Abs DOI

   Common evaluation metrics for NFL punters are outdated, failing to account for field position and touchbacks. Using detailed information on each punt of the 2013 season, a nonlinear model is developed, using these factors alongside hang time, coverag