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The COVID-19 pandemic disrupted health systems and economies throughout the world during 2020 and was particularly devastating for the United States, which experienced the highest numbers of reported cases and deaths during 2020 1 – 3 . Many of the epidemiological features responsible for observed rates of morbidity and mortality have been reported 4 – 8 ; however, the overall burden and characteristics of COVID-19 in the United States have not been comprehensively quantified. Here we use a data-driven model-inference approach to simulate the pandemic at county-scale in the United States during 2020 and estimate critical, time-varying epidemiological properties underpinning the dynamics of the virus. The pandemic in the United States during 2020 was characterized by national ascertainment rates that increased from 11.3% (95% credible interval (CI): 8.3–15.9%) in March to 24.5% (18.6–32.3%) during December. Population susceptibility at the end of the year was 69.0% (63.6–75.4%), indicating that about one third of the US population had been infected. Community infectious rates, the percentage of people harbouring a contagious infection, increased above 0.8% (0.6–1.0%) before the end of the year, and were as high as 2.4% in some major metropolitan areas. By contrast, the infection fatality rate fell to 0.3% by year’s end. Data-driven modelling including numbers of cases and population movements is used to simulate the COVID-19 pandemic in the United States in 2020, providing insights into the transmission of the disease.

Influenza infects an estimated 9–35 million individuals each year in the United States and is a contributing cause for between 12,000 and 56,000 deaths annually. Seasonal outbreaks of influenza are common in temperate regions of the world, with highest incidence typically occurring in colder and drier months of the year. Real-time forecasts of influenza transmission can inform public health response to outbreaks. We present the results of a multiinstitution collaborative effort to standardize the collection and evaluation of forecasting models for influenza in the United States for the 2010/2011 through 2016/2017 influenza seasons. For these seven seasons, we assembled weekly real-time forecasts of seven targets of public health interest from 22 different models. We compared forecast accuracy of each model relative to a historical baseline seasonal average. Across all regions of the United States, over half of the models showed consistently better performance than the historical baseline when forecasting incidence of influenza-like illness 1 wk, 2 wk, and 3 wk ahead of available data and when forecasting the timing and magnitude of the seasonal peak. In some regions, delays in data reporting were strongly and negatively associated with forecast accuracy. More timely reporting and an improved overall accessibility to novel and traditional data sources are needed to improve forecasting accuracy and its integration with real-time public health decision making.

Recent research has produced a number of methods for forecasting seasonal influenza outbreaks. However, differences among the predicted outcomes of competing forecast methods can limit their use in decision-making. Here, we present a method for reconciling these differences using Bayesian model averaging. We generated retrospective forecasts of peak timing, peak incidence, and total incidence for seasonal influenza outbreaks in 48 states and 95 cities using 21 distinct forecast methods, and combined these individual forecasts to create weighted-average superensemble forecasts. We compared the relative performance of these individual and superensemble forecast methods by geographic location, timing of forecast, and influenza season. We find that, overall, the superensemble forecasts are more accurate than any individual forecast method and less prone to producing a poor forecast. Furthermore, we find that these advantages increase when the superensemble weights are stratified according to the characteristics of the forecast or geographic location. These findings indicate that different competing influenza prediction systems can be combined into a single more accurate forecast product for operational delivery in real time.

Seasonal influenza results in substantial annual morbidity and mortality in the United States and worldwide. Accurate forecasts of key features of influenza epidemics, such as the timing and severity of the peak incidence in a given season, can inform public health response to outbreaks. As part of ongoing efforts to incorporate data and advanced analytical methods into public health decision-making, the United States Centers for Disease Control and Prevention (CDC) has organized seasonal influenza forecasting challenges since the 2013/2014 season. In the 2017/2018 season, 22 teams participated. A subset of four teams created a research consortium called the FluSight Network in early 2017. During the 2017/2018 season they worked together to produce a collaborative multi-model ensemble that combined 21 separate component models into a single model using a machine learning technique called stacking. This approach creates a weighted average of predictive densities where the weight for each component is determined by maximizing overall ensemble accuracy over past seasons. In the 2017/2018 influenza season, one of the largest seasonal outbreaks in the last 15 years, this multi-model ensemble performed better on average than all individual component models and placed second overall in the CDC challenge. It also outperformed the baseline multi-model ensemble created by the CDC that took a simple average of all models submitted to the forecasting challenge. This project shows that collaborative efforts between research teams to develop ensemble forecasting approaches can bring measurable improvements in forecast accuracy and important reductions in the variability of performance from year to year. Efforts such as this, that emphasize real-time testing and evaluation of forecasting models and facilitate the close collaboration between public health officials and modeling researchers, are essential to improving our understanding of how best to use forecasts to improve public health response to seasonal and emerging epidemic threats.

By August 1, 2022, the SARS-CoV-2 virus had caused over 90 million cases of COVID-19 and one million deaths in the United States. Since December 2020, SARS-CoV-2 vaccines have been a key component of US pandemic response; however, the impacts of vaccination are not easily quantified. Here, we use a dynamic county-scale metapopulation model to estimate the number of cases, hospitalizations, and deaths averted due to vaccination during the first six months of vaccine availability. We estimate that COVID-19 vaccination was associated with over 8 million fewer confirmed cases, over 120 thousand fewer deaths, and 700 thousand fewer hospitalizations during the first six months of the campaign.

The 2020 Atlantic hurricane season was extremely active and included, as of early November, six hurricanes that made landfall in the United States during the global coronavirus disease 2019 (COVID‐19) pandemic. Such an event would necessitate a large‐scale evacuation, with implications for the trajectory of the pandemic. Here we model how a hypothetical hurricane evacuation from four counties in southeast Florida would affect COVID‐19 case levels. We find that hurricane evacuation increases the total number of COVID‐19 cases in both origin and destination locations; however, if transmission rates in destination counties can be kept from rising during evacuation, excess evacuation‐induced case numbers can be minimized by directing evacuees to counties experiencing lower COVID‐19 transmission rates. Ultimately, the number of excess COVID‐19 cases produced by the evacuation depends on the ability of destination counties to meet evacuee needs while minimizing virus exposure through public health directives. These results are relevant to disease transmission during evacuations stemming from additional climate‐related hazards such as wildfires and floods. Plain Language Summary In recent years hurricane evacuations in the United States have displaced millions of people from their homes. Amid the ongoing coronavirus disease 2019 (COVID‐19) pandemic, such an evacuation—and the associated increase in human‐to‐human interactions—poses an additional risk of disease transmission. In this study, we use an epidemiological model to simulate a hypothetical hurricane evacuation from southeast Florida. We find that evacuation is likely to increase the total number of COVID‐19 cases. However, directing evacuees to locations experiencing lower COVID‐19 transmission rates and simultaneously minimizing human contact during evacuation could reduce the excess number of infections. Our results indicate that evacuation‐induced COVID‐19 infections can be minimized by optimizing evacuation plans based on real‐time information about disease incidence and transmission. Key Points Hurricane evacuation increases the total number of COVID‐19 cases in both the origin and destination counties of evacuees We can minimize excess COVID‐19 cases by directing evacuees to counties with low COVID‐19 transmission rates Minimizing evacuation‐related COVID‐19 cases will also require keeping virus transmission rates low in evacuees' destination counties

Climate change is expected to affect the distribution of environmental suitability for malaria transmission by altering temperature and rainfall patterns; however, the local and global impacts of climate change on malaria transmission are uncertain. We assessed the effect of climate change on malaria transmission in West Africa. We coupled a detailed mechanistic hydrology and entomology model with climate projections from general circulation models (GCMs) to predict changes in vectorial capacity, an indication of the risk of human malaria infections, resulting from changes in the availability of mosquito breeding sites and temperature-dependent development rates. Because there is strong disagreement in climate predictions from different GCMs, we focused on the GCM projections that produced the best and worst conditions for malaria transmission in each zone of the study area. Simulation-based estimates suggest that in the desert fringes of the Sahara, vectorial capacity would increase under the worst-case scenario, but not enough to sustain transmission. In the transitional zone of the Sahel, climate change is predicted to decrease vectorial capacity. In the wetter regions to the south, our estimates suggest an increase in vectorial capacity under all scenarios. However, because malaria is already highly endemic among human populations in these regions, we expect that changes in malaria incidence would be small. Our findings highlight the importance of rainfall in shaping the impact of climate change on malaria transmission in future climates. Even under the GCM predictions most conducive to malaria transmission, we do not expect to see a significant increase in malaria prevalence in this region.

Background The Covid-19 pandemic has been characterized by the emergence of novel SARS-CoV-2 variants, each with distinct properties influencing transmission dynamics, immune escape, and virulence, which, in turn, influence their impact on local populations. Swift analysis of the properties of newly emerged variants is essential in the initial days and weeks to enhance readiness and facilitate the scaling of clinical and public health system responses. Methods This paper introduces a two-variant metapopulation compartmental model of disease transmission to simulate the dynamics of disease transmission during a period of transition to a newly dominant strain. Leveraging novel S-gene dropout analysis data and genomic sequencing data, combined with confirmed Covid-19 case data, we estimate the epidemiological characteristics of the Omicron variant, which replaced the Delta variant in late 2021 in Philadelphia, PA. We utilized a grid-search method to identify plausible combinations of model parameters, followed by an ensemble adjustment Kalman filter for parameter inference. Results The model successfully estimated key epidemiological parameters; we estimated the ascertainment rate of 0.22 (95% credible interval 0.15–0.29) and transmission rate of 5.0 (95% CI 2.4–6.6) for the Omicron variant. Conclusions The study demonstrates the potential for this model-inference framework to provide real-time insights during the emergence of novel variants, aiding in timely public health responses.

The importance of climate change for malaria transmission has been hotly debated. Research based on ten years of field observations and a model that simulates village-scale transmission for West Africa suggests that we should not be overly concerned. The impact of climate change on malaria transmission has been hotly debated. Recent conclusions have been drawn using relatively simple biological models 1 , 2 and statistical approaches 3 , 4 , 5 , with inconsistent predictions. Consequently, the Intergovernmental Panel on Climate Change Fifth Assessment Report (IPCC AR5) echoes this uncertainty, with no clear guidance for the impacts of climate change on malaria transmission, yet recognizing a strong association between local climate and malaria 6 , 7 . Here, we present results from a decade-long study involving field observations and a sophisticated model simulating village-scale transmission. We drive the malaria model using select climate models that correctly reproduce historical West African climate, and project reduced malaria burden in a western sub-region and insignificant impact in an eastern sub-region. Projected impacts of climate change on malaria transmission in this region are not of serious concern.