Disentangling the role of virus infectiousness and awareness-based human behavior during the early phase of the COVID-19 pandemic in the European Union.

In this work, we manage to disentangle the role of virus infectiousness and awareness-based human behavior in the COVID-19 pandemic. Using Bayesian inference, we quantify the uncertainty of a state-space model whose propagator is based on an unusual SEIR-type model since it incorporates the effective population fraction as a parameter. Within the Markov Chain Monte Carlo (MCMC) algorithm, Unscented Kalman Filter (UKF) may be used to evaluate the likelihood approximately. UKF is a suitable strategy in many cases, but it is not well-suited to deal with non-negativity restrictions on the state variables. To overcome this difficulty, we modify the UKF, conveniently truncating Gaussian distributions, which allows us to deal with such restrictions. We use official infection notification records to analyze the first 22 weeks of infection spread in each of the 27 countries of the European Union (EU). It is known that such records are the primary source of information to assess the early evolution of the pandemic and, at the same time, usually suffer underreporting and backlogs. Our model explicitly accounts for uncertainty in the dynamic model parameters, the dynamic model adequacy, and the infection observation process. We argue that this modeling paradigm allows us to disentangle the role of the contact rate, the effective population fraction, and the infection observation probability across time and space with an imperfect first principles model. Our findings agree with phylogenetic evidence showing little variability in the contact rate, or virus infectiousness, across EU countries during the early phase of the pandemic, highlighting the advantage of incorporating the effective population fraction into pandemic modeling for heterogeneity in both human behavior and reporting. Finally, to evaluate the consistency of our data assimilation method, we performed a forecast that adequately fits the actual data. Statement of significance: Data-driven and model-based epidemiological studies aimed at learning the number of people infected early during a pandemic should explicitly consider the behavior-induced effective population effect. Indeed, the non-isolated, or effective, fraction of the population during the early phase of the pandemic is time-varying, and first-principles modeling with quantified uncertainty is imperative for an adequate analysis across time and space. We argue that, although good inference results may be obtained using the classical SEIR type model, the model posed in this work has allowed us to disentangle the role of virus infectiousness and awareness-based human behavior during the early phase of the COVID-19 pandemic in the European Union from official infection notification records.

Improving Short-Term QPF Using Geostationary Satellite All-Sky Infrared Radiances: Real-Time Ensemble Data Assimilation and Forecast during the PRECIP 2020 and 2021 Experiments

The Prediction of Rainfall Extremes Campaign In the Pacific (PRECIP) aims to improve our understanding of extreme rainfall processes in the East Asian summer monsoon. A convection-permitting ensemble-based data assimilation and forecast system (the PSU WRF-EnKF system) was run in real time in the summers of 2020–21 in advance of the 2022 field campaign, assimilating all-sky infrared (IR) radiances from the geostationary Himawari-8 and GOES-16 satellites, and providing 48-h ensemble forecasts every day for weather briefings and discussions. This is the first time that all-sky IR data assimilation has been performed in a real-time forecast system at a convection-permitting resolution for several seasons. Compared with retrospective forecasts that exclude all-sky IR radiances, rainfall predictions are statistically significantly improved out to at least 4–6 h for the real-time forecasts, which is comparable to the time scale of improvements gained from assimilating observations from the dense ground-based Doppler weather radars. The assimilation of all-sky IR radiances also reduced the forecast errors of large-scale environments and helped to maintain a more reasonable ensemble spread compared with the counterpart experiments that did not assimilate all-sky IR radiances. The results indicate strong potential for improving routine short-term quantitative precipitation forecasts using these high-spatiotemporal-resolution satellite observations in the future.Significance StatementDuring the summers of 2020/21, the PSU WRF-EnKF data assimilation and forecast system was run in real time in advance of the 2022 Prediction of Rainfall Extremes Campaign In the Pacific (PRECIP), assimilating all-sky (clear-sky and cloudy) infrared radiances from geostationary satellites into a numerical weather prediction model and providing ensemble forecasts. This study presents the first-of-its-kind systematic evaluation of the impacts of assimilating all-sky infrared radiances on short-term qualitative precipitation forecasts using multiyear, multiregion, real-time ensemble forecasts. Results suggest that rainfall forecasts are improved out to at least 4–6 h with the assimilation of all-sky infrared radiances, comparable to the influence of assimilating radar observations, with benefits in forecasting large-scale environments and representing atmospheric uncertainties as well.

The YOPP Final Summit: Assessing Past and Forecasting Future Polar Prediction Research

The successes of YOPP from the presentations and keynote presentations included * a better understanding of the impact of key polar measurements (radiosondes and space-based instruments such as microwave radiometers), and recent advancements in the current NWP observing system, achieved through coordinated OSEs in both polar regions (e.g., Sandu et al. 2021);* enhanced understanding of the linkages between Arctic and midlatitude weather (e.g., Day et al. 2019);* advancements in the atmosphere–ocean–sea ice and atmosphere–land–cryosphere coupling in NWP, and in assessing and recognizing the added value of coupling in Earth system models (e.g., Bauer et al. 2016);* deployment of tailored polar observation campaigns to address yet-unresolved polar processes (e.g., Renfrew et al. 2019);* progress in verification and forecasting techniques for sea ice, including a novel headline score (e.g., Goessling and Jung 2018);* advances in process understanding and process-based evaluation with the establishment of the YOPPsiteMIP framework and tools (Svensson 2020);* better understanding of emerging societal and stakeholder needs in the Arctic and Antarctic (e.g., Dawson et al. 2017);and * innovative transdisciplinary methodologies for coproducing salient information services for various user groups (Jeuring and Lamers 2021). The YOPP Final Summit identified a number of areas worthy of prioritized research in the area of environmental prediction and services for the polar regions: * coupled atmosphere, sea ice, and ocean models with an emphasis on advanced parameterizations and enhanced resolution at which critical phenomena start to be resolved (e.g., ocean eddies);* improved definition and representation of stable boundary layer processes, including mixed-phase clouds and aerosols;incorporation of wave–ice–ocean interactions;* radiance assimilation over sea ice, land ice, and ice sheets;understanding of linkages between polar regions and lower latitudes from a prediction perspective;* exploring the limits of predictability of the atmosphere–cryosphere–ocean system;* an examination of the observational representativeness over land, sea ice, and ocean;better representation of the hydrological cycle;and * transdisciplinary work with the social science community around the use of forecasting services and operational decision-making to name but a few. The presentations and discussions at the YOPP Final Summit identified the major legacy elements of YOPP: the YOPPsiteMIP approach to enable easy comparison of collocated multivariate model and observational outputs with the aim of enhancing process understanding, the development of an international and multi-institutional community across many disciplines investigating aspects of polar prediction and services, the YOPP Data Portal3 (https://yopp.met.no/), and the education and training delivered to early-career polar researchers. Next steps Logistical issues, the COVID-19 pandemic, but also new scientific questions (e.g., the value of targeted observations in the Southern Hemisphere), as well as technical issues emerging toward the end of the YOPP Consolidation Phase, resulted in the decision to continue the following three YOPP activities to the end of 2023: (i) YOPP Southern Hemisphere (YOPP-SH);(ii) Model Intercomparison and Improvement Project (MIIP);of which YOPPSiteMIP is a critical element;and (iii) the Societal, Economics and Research Applications (PPP-SERA) Task Team.

Global Atmospheric Composition Needs from Future Ultraviolet–Visible–Near-Infrared (UV–Vis–NIR) NOAA Satellite Instruments

Presentations spanned a range of applications: the public health impacts of poor air quality and environmental justice;greenhouse gas measuring, monitoring, reporting, and verification (GHG MMRV);stratospheric ozone monitoring;and various applications of satellite observations to improve models, including data assimilation in global Earth system models. The combination of methane (CH4), carbon dioxide (CO2), carbon monoxide (CO), and NO2 retrievals can improve confidence in emissions inventories and model performance, and together these data products would be of use in future air quality management tools. The ability to retrieve additional trace gases (e.g., ethane, isoprene, and ammonia) in the thermal IR along with those measured in the UV–Vis–NIR region would be extremely useful for air quality applications, including source apportionment analysis (e.g., for oil/natural gas extraction, biogenic, and agricultural sources). Ground-level ozone is one of six criteria pollutants for which the EPA sets National Ambient Air Quality Standards (NAAQS) to protect against human health and welfare effects.

Real-time updating of dynamic social networks for COVID-19 vaccination strategies.

Vaccination strategy is crucial in fighting the COVID-19 pandemic. Since the supply is still limited in many countries, contact network-based interventions can be most powerful to set an efficient strategy by identifying high-risk individuals or communities. However, due to the high dimension, only partial and noisy network information can be available in practice, especially for dynamic systems where contact networks are highly time-variant. Furthermore, the numerous mutations of SARS-CoV-2 have a significant impact on the infectious probability, requiring real-time network updating algorithms. In this study, we propose a sequential network updating approach based on data assimilation techniques to combine different sources of temporal information. We then prioritise the individuals with high-degree or high-centrality, obtained from assimilated networks, for vaccination. The assimilation-based approach is compared with the standard method (based on partially observed networks) and a random selection strategy in terms of vaccination effectiveness in a SIR model. The numerical comparison is first carried out using real-world face-to-face dynamic networks collected in a high school, followed by sequential multi-layer networks generated relying on the Barabasi-Albert model emulating large-scale social networks with several communities.

Assimilation of aircraft observations over the Indian monsoon region: Investigation of the effects of COVID-19 on a reanalysis

Since March 2020, the COVID-19 pandemic has significantly reduced the availability of global aircraft-based observations (ABOs), which has been restored later in 2021. This study focuses on the impact of ABOs on a regional reanalysis. Indian Monsoon Data Assimilation and Analysis (IMDAA) is a regional reanalysis for a period from 1979 to 2020 (originally up to 2018) over India and surrounding regions produced at the National Centre for Medium Range Weather Forecasting (NCMRWF), India, in collaboration with the UK Met Office. A comparison of the impact of ABOs on other conventional and satellite observations assimilated in the NCMRWF global model and IMDAA during 2019 and 2020 revealed the importance of ABOs, particularly in IMDAA, since it did not assimilate the latest satellite data as the IMDAA system was frozen in October 2016. A data denial experiment that removes all the ABOs from the IMDAA assimilation system for a period from March to November 2019 is designed. The results from the IMDAA reanalysis run, which assimilates ABOs during the same period, are compared with the data denial experiment. Assimilation of ABOs strengthened the upper tropospheric circulation, the Tropical Easterly Jet (TEJ), during the Indian summer monsoon compared to the data denial experiment. Analysis of the features of two cyclones that developed over the North Indian Ocean during the study period revealed that ABO assimilation played a key role in simulating the track and intensity of these cyclones when they were in the ‘severe' category. Since the sample is small, more cyclone cases need to be analysed to consolidate the result. © 2023 Royal Meteorological Society.

Effectiveness analysis of multiple epidemic prevention measures in the context of COVID-19 using the SVIRD model and ensemble Kalman filter.

The ability to accurately forecast the spread of coronavirus disease 2019 (COVID-19) is of great importance to the resumption of societal normality. Existing methods of epidemic forecasting often ignore the comprehensive analysis of multiple epidemic prevention measures. This paper aims to analyze various epidemic prevention measures through a compound framework. Here, a susceptible-vaccinated-infected-recovered-deceased (SVIRD) model is constructed to consider the effects of population mobility among origin and destination, vaccination, and positive retest populations. And we further use real-time observations to correct the model trajectory with the help of data assimilation. Seven prevention measures are used to analyze the short-term trend of active cases. The results of the synthetic scene recommended that four measures-improving the vaccination protection rate (IVPR), reducing the number of contacts per person per day (RNCP), selecting the region with less infected people as origin A (SES-O) and limiting population flow entering from A to B per day (LAIP-OD)-are the most effective in the short-term, with maximum reductions of 75%, 53%, 35% and 31%, respectively, in active cases after 150 days. The results of the real-world experiment with Hong Kong as the origin and Shenzhen as the destination indicate that when the daily vaccination rate increased from 5% to 9.5%, the number of active cases decreased by only 7.35%. The results demonstrate that reducing the number of contacts per person per day after productive life resumes is more effective than increasing vaccination rates.

Near-real-time CO2 fluxes from CarbonTracker Europe for high-resolution atmospheric modeling

We present the CarbonTracker Europe High-Resolution (CTE-HR) system that estimates carbon dioxide (CO2) exchange over Europe at high resolution (0.1 × 0.2∘) and in near real time (about 2 months' latency). It includes a dynamic anthropogenic emission model, which uses easily available statistics on economic activity, energy use, and weather to generate anthropogenic emissions with dynamic time profiles at high spatial and temporal resolution (0.1×0.2∘, hourly). Hourly net ecosystem productivity (NEP) calculated by the Simple Biosphere model Version 4 (SiB4) is driven by meteorology from the European Centre for Medium-Range Weather Forecasts (ECMWF) Reanalysis 5th Generation (ERA5) dataset. This NEP is downscaled to 0.1×0.2∘ using the high-resolution Coordination of Information on the Environment (CORINE) land-cover map and combined with the Global Fire Assimilation System (GFAS) fire emissions to create terrestrial carbon fluxes. Ocean CO2 fluxes are included in our product, based on Jena CarboScope ocean CO2 fluxes, which are downscaled using wind speed and temperature. Jointly, these flux estimates enable modeling of atmospheric CO2 mole fractions over Europe.We assess the skill of the CTE-HR CO2 fluxes (a) to reproduce observed anomalies in biospheric fluxes and atmospheric CO2 mole fractions during the 2018 European drought, (b) to capture the reduction of anthropogenic emissions due to COVID-19 lockdowns, (c) to match mole fraction observations at Integrated Carbon Observation System (ICOS) sites across Europe after atmospheric transport with the Transport Model, version 5 (TM5) and the Stochastic Time-Inverted Lagrangian Transport (STILT), driven by ECMWF-IFS, and (d) to capture the magnitude and variability of measured CO2 fluxes in the city center of Amsterdam (the Netherlands).We show that CTE-HR fluxes reproduce large-scale flux anomalies reported in previous studies for both biospheric fluxes (drought of 2018) and anthropogenic emissions (COVID-19 pandemic in 2020). After applying transport of emitted CO2, the CTE-HR fluxes have lower median root mean square errors (RMSEs) relative to mole fraction observations than fluxes from a non-informed flux estimate, in which biosphere fluxes are scaled to match the global growth rate of CO2 (poor person's inversion). RMSEs are close to those of the reanalysis with the CTE data assimilation system. This is encouraging given that CTE-HR fluxes did not profit from the weekly assimilation of CO2 observations as in CTE.We furthermore compare CO2 concentration observations at the Dutch Lutjewad coastal tower with high-resolution STILT transport to show that the high-resolution fluxes manifest variability due to different emission sectors in summer and winter. Interestingly, in periods where synoptic-scale transport variability dominates CO2 concentration variations, the CTE-HR fluxes perform similarly to low-resolution fluxes (5–10× coarsened). The remaining 10 % of the simulated CO2 mole fraction differs by >2 ppm between the low-resolution and high-resolution flux representation and is clearly associated with coherent structures ("plumes”) originating from emission hotspots such as power plants. We therefore note that the added resolution of our product will matter most for very specific locations and times when used for atmospheric CO2 modeling. Finally, in a densely populated region like the Amsterdam city center, our modeled fluxes underestimate the magnitude of measured eddy covariance fluxes but capture their substantial diurnal variations in summertime and wintertime well.We conclude that our product is a promising tool for modeling the European carbon budget at a high resolution in near real time. The fluxes are freely available from the ICOS Carbon Portal (CC-BY-4.0) to be used for near-real-time monitoring and modeling, for example, as an a priori flux product in a CO2 data assimilation system. The data are available at 10.18160/20Z1-AYJ2 .

Data Assimilation Predictive GAN (DA-PredGAN) Applied to a Spatio-Temporal Compartmental Model in Epidemiology.

We propose a novel use of generative adversarial networks (GANs) (i) to make predictions in time (PredGAN) and (ii) to assimilate measurements (DA-PredGAN). In the latter case, we take advantage of the natural adjoint-like properties of generative models and the ability to simulate forwards and backwards in time. GANs have received much attention recently, after achieving excellent results for their generation of realistic-looking images. We wish to explore how this property translates to new applications in computational modelling and to exploit the adjoint-like properties for efficient data assimilation. We apply these methods to a compartmental model in epidemiology that is able to model space and time variations, and that mimics the spread of COVID-19 in an idealised town. To do this, the GAN is set within a reduced-order model, which uses a low-dimensional space for the spatial distribution of the simulation states. Then the GAN learns the evolution of the low-dimensional states over time. The results show that the proposed methods can accurately predict the evolution of the high-fidelity numerical simulation, and can efficiently assimilate observed data and determine the corresponding model parameters.

Analysis of COVID-19 in Japan with extended SEIR model and ensemble Kalman filter.

We introduce an extended SEIR infectious disease model with data assimilation for the study of the spread of COVID-19. In this framework, undetected asymptomatic and pre-symptomatic cases are taken into account, and the impact of their uncertain proportion is fully investigated. The standard SEIR model does not consider these populations, while their role in the propagation of the disease is acknowledged. An ensemble Kalman filter is implemented to assimilate reliable observations of three compartments in the model. The system tracks the evolution of the effective reproduction number and estimates the unobservable subpopulations. The analysis is carried out for three main prefectures of Japan and for the entire country of Japan. For these four communities, our estimated effective reproduction numbers are more stable than the corresponding ones estimated by a different method (Toyokeizai). We also perform sensitivity tests for different values of some uncertain medical parameters, like the relative infectivity of symptomatic/asymptomatic cases. The regional analysis results suggest the decreasing efficiency of the states of emergency.

An Application of Artificial Neural Network to Evaluate the Influence of Weather Conditions on the Variation of PM2.5-Bound Carbonaceous Compositions and Water-Soluble Ionic Species

Previous studies have determined biomass burning as a major source of air pollutants in the ambient air in Thailand. To analyse the impacts of meteorological parameters on the variation of carbonaceous aerosols and water-soluble ionic species (WSIS), numerous statistical models, including a source apportionment analysis with the assistance of principal component analysis (PCA), hierarchical cluster analysis (HCA), and artificial neural networks (ANNs), were employed in this study. A total of 191 sets of PM2.5 samples were collected from the three monitoring stations in Chiang-Mai, Bangkok, and Phuket from July 2020 to June 2021. Hotspot numbers and other meteorological parameters were obtained using NOAA-20 weather satellites coupled with the Global Land Data Assimilation System. Although PCA revealed that crop residue burning and wildfires are the two main sources of PM2.5, ANNs highlighted the importance of wet deposition as the main depletion mechanism of particulate WSIS and carbonaceous aerosols. Additionally, Mg2+ and Ca2+ were deeply connected with albedo, plausibly owing to their strong hygroscopicity as the CCNs responsible for cloud formation.

Evaluating the impact of stay-at-home and quarantine measures on COVID-19 spread.

BACKGROUND: During the early stage of the COVID-19 pandemic, many countries implemented non-pharmaceutical interventions (NPIs) to control the transmission of SARS-CoV-2, the causative pathogen of COVID-19. Among those NPIs, stay-at-home and quarantine measures were widely adopted and enforced. Understanding the effectiveness of stay-at-home and quarantine measures can inform decision-making and control planning during the ongoing COVID-19 pandemic and for future disease outbreaks. METHODS: In this study, we use mathematical models to evaluate the impact of stay-at-home and quarantine measures on COVID-19 spread in four cities that experienced large-scale outbreaks in the spring of 2020: Wuhan, New York, Milan, and London. We develop a susceptible-exposed-infected-removed (SEIR)-type model with components of self-isolation and quarantine and couple this disease transmission model with a data assimilation method. By calibrating the model to case data, we estimate key epidemiological parameters before lockdown in each city. We further examine the impact of stay-at-home and quarantine rates on COVID-19 spread after lockdown using counterfactual model simulations. RESULTS: Results indicate that self-isolation of susceptible population is necessary to contain the outbreak. At a given rate, self-isolation of susceptible population induced by stay-at-home orders is more effective than quarantine of SARS-CoV-2 contacts in reducing effective reproductive numbers [Formula: see text]. Variation in self-isolation and quarantine rates can also considerably affect the duration of outbreaks, attack rates and peak timing. We generate counterfactual simulations to estimate effectiveness of stay-at-home and quarantine measures. Without these two measures, the cumulative confirmed cases could be much higher than reported numbers within 40 days after lockdown in Wuhan, New York, Milan, and London. CONCLUSIONS: Our findings underscore the essential role of stay-at-home orders and quarantine of SARS-CoV-2 contacts during the early phase of the pandemic.

Merging Real Images with Physics Simulations via Data Assimilation

This work has started from the necessity of improving the accuracy of numerical simulations of COVID-19 transmission. Coughing is one of the most effective ways to transmit SARS-CoV-2, the strain of coronavirus that causes COVID-19. Cough is a spontaneous reflex that helps to protect the lungs and airways from unwanted irritants and pathogens and it involves droplet expulsion at speeds close to 50 miles/h. Unfortunately, it’s also one of the most efficient ways to spread diseases, especially respiratory viruses that need host cells in which to reproduce. Computational Fluid Dynamics (CFD) are a powerful way to simulate droplets expelled by mouth and nose when people are coughing and/or sneezing. As with all numerical models, the models for coughing and sneezing introduce uncertainty through the selection of scales and parameters. Considering these uncertainties is essential for the acceptance of any numerical simulation. Numerical forecasting models often use Data Assimilation (DA) methods for uncertainty quantification in the medium to long-term analysis. DA is the approximation of the true state of some physical system at a given time by combining time-distributed observations with a dynamic model in an optimal way. DA incorporates observational data into a prediction model to improve numerically forecast results. In this paper, we develop a Variational Data Assimilation model to assimilate direct observation of the physical mechanisms of droplet formation at the exit of the mouth during coughing. Specifically, we use high-speed imaging, from prior research work, which directly examines the fluid fragmentation at the exit of the mouths of healthy subjects in a sneezing condition. We show the impact of the proposed approach in terms of accuracy with respect to CFD simulations. © 2022, Springer Nature Switzerland AG.

A Hybrid System For Pandemic Evolution Prediction

The areas of data science and data engineering have experienced strong advances in recent years. This has had a particular impact on areas such as healthcare, where, as a result of the pandemic caused by the COVID-19 virus, technological development has accelerated. This has led to a need to produce solutions that enable the collection, integration and efficient use of information for decision making scenarios. This is evidenced by the proliferation of monitoring, data collection, analysis, and prediction systems aimed at controlling the pandemic. To go beyond current epidemic prediction possibilities, this article proposes a hybrid model that combines the dynamics of epidemiological processes with the predictive capabilities of artificial neural networks. In addition, the system allows for the introduction of additional information through an expert system, thus allowing the incorporation of additional hypotheses on the adoption of containment measures.

Analysis of COVID-19 Spread in Tokyo through an Agent-Based Model with Data Assimilation.

In this paper, we introduce an agent-based model together with a particle filter approach to study the spread of COVID-19. Investigations are mainly performed on the metropolis of Tokyo, but other prefectures of Japan are also briefly surveyed. A novel method for evaluating the effective reproduction number is one of the main outcomes of our approach. Other unknown parameters are also evaluated. Uncertain quantities, such as, for example, the probability that an infected agent develops symptoms, are tested and discussed, and the stability of our computations is examined. Detailed explanations are provided for the model and for the assimilation process.

Bayesian sequential data assimilation for COVID-19 forecasting.

We introduce a Bayesian sequential data assimilation and forecasting method for non-autonomous dynamical systems. We applied this method to the current COVID-19 pandemic. It is assumed that suitable transmission, epidemic and observation models are available and previously validated. The transmission and epidemic models are coded into a dynamical system. The observation model depends on the dynamical system state variables and parameters, and is cast as a likelihood function. The forecast is sequentially updated over a sliding window of epidemic records as new data becomes available. Prior distributions for the state variables at the new forecasting time are assembled using the dynamical system, calibrated for the previous forecast. Epidemic outbreaks are non-autonomous dynamical systems depending on human behavior, viral evolution and climate, among other factors, rendering it impossible to make reliable long-term epidemic forecasts. We show our forecasting method's performance using a SEIR type model and COVID-19 data from several Mexican localities. Moreover, we derive further insights into the COVID-19 pandemic from our model predictions. The rationale of our approach is that sequential data assimilation is an adequate compromise between data fitting and dynamical system prediction.

Spatialized epidemiological forecasting applied to Covid-19 pandemic at departmental scale in France.

In this paper, we present a spatialized extension of a SIR model that accounts for undetected infections and recoveries as well as the load on hospital services. The spatialized compartmental model we introduce is governed by a set of partial differential equations (PDEs) defined on a spatial domain with complex boundary. We propose to solve the set of PDEs defining our model by using a meshless numerical method based on a finite difference scheme in which the spatial operators are approximated by using radial basis functions. Such an approach is reputed as flexible for solving problems on complex domains. Then we calibrate our model on the French department of Isère during the first period of lockdown, using daily reports of hospital occupancy in France. Our methodology allows to simulate the spread of Covid-19 pandemic at a departmental level, and for each compartment. However, the simulation cost prevents from online short-term forecast. Therefore, we propose to rely on reduced order modeling to compute short-term forecasts of infection number. The strategy consists in learning a time-dependent reduced order model with few compartments from a collection of evaluations of our spatialized detailed model, varying initial conditions and parameter values. A set of reduced bases is learnt in an offline phase while the projection on each reduced basis and the selection of the best projection is performed online, allowing short-term forecast of the global number of infected individuals in the department. The original approach proposed in this paper is generic and could be adapted to model and simulate other dynamics described by a model with spatially distributed parameters of the type diffusion-reaction on complex domains. Also, the time-dependent model reduction techniques we introduced could be leveraged to compute control strategies related to such dynamics.

Data-assimilation and state estimation for contact-based spreading processes using the ensemble kalman filter: Application to COVID-19.

The main aim of the present paper is threefold. First, it aims at presenting an extended contact-based model for the description of the spread of contagious diseases in complex networks with consideration of asymptomatic evolutions. Second, it presents a parametrization method of the considered model, including validation with data from the actual spread of COVID-19 in Germany, Mexico and the United States of America. Third, it aims at showcasing the fruitful combination of contact-based network spreading models with a modern state estimation and filtering technique to (i) enable real-time monitoring schemes, and (ii) efficiently deal with dimensionality and stochastic uncertainties. The network model is based on an interpretation of the states of the nodes as (statistical) probability densities samples, where nodes can represent individuals, groups or communities, cities or countries, enabling a wide field of application of the presented approach.

Improving PM2.5 predictions during COVID-19 lockdown by assimilating multi-source observations and adjusting emissions.

The Coronavirus Disease 2019 (COVID-19) outbreak caused a suspension of almost all non-essential human activities, leading to a significant reduction of anthropogenic emissions. However, the emission inventory of the chemistry transport model cannot be updated in time, resulting in large uncertainty in PM2.5 predictions. This study adopted a three-dimensional variational approach to assimilate multi-source PM2.5 data from satellite and ground observations and jointly adjusted emissions to improve PM2.5 predictions of the WRF-Chem model. Experiments were conducted to verify the method over Hubei Province, China, during the COVID-19 epidemic from Jan 21st to Mar 20th, 2020. The results showed that PM2.5 predictions were improved at almost all the validation sites, and the benefit of data assimilation (DA) can last for 48 h. However, the benefits of DA diminished quickly with the increase of the forecast time. By adjusting emissions, the PM2.5 predictions showed a much slower error accumulation along forecast time. At 48Z, the RMSE still has an 8.85 µg/m3 (19.49%) improvement, suggesting the effectiveness of emissions adjustment based on the improved initial conditions via DA.

Analyzing the effects of observation function selection in ensemble Kalman filtering for epidemic models.

The Ensemble Kalman Filter (EnKF) is a popular sequential data assimilation method that has been increasingly used for parameter estimation and forecast prediction in epidemiological studies. The observation function plays a critical role in the EnKF framework, connecting the unknown system variables with the observed data. Key differences in observed data and modeling assumptions have led to the use of different observation functions in the epidemic modeling literature. In this work, we present a novel computational analysis demonstrating the effects of observation function selection when using the EnKF for state and parameter estimation in this setting. In examining the use of four epidemiologically-inspired observation functions of different forms in connection with the classic Susceptible-Infectious-Recovered (SIR) model, we show how incorrect observation modeling assumptions (i.e., fitting incidence data with a prevalence model, or neglecting under-reporting) can lead to inaccurate filtering estimates and forecast predictions. Results demonstrate the importance of choosing an observation function that well interprets the available data on the corresponding EnKF estimates in several filtering scenarios, including state estimation with known parameters, and combined state and parameter estimation with both constant and time-varying parameters. Numerical experiments further illustrate how modifying the observation noise covariance matrix in the filter can help to account for uncertainty in the observation function in certain cases.