In this paper, an extended SEIR model with a vaccination compartment is proposed to simulate the novel coronavirus disease (COVID-19) spread in Saudi Arabia. The model considers seven stages of infection: susceptible (S), exposed (E), infectious (I), quarantined (Q), recovered (R), deaths (D), and vaccinated (V). Initially, a mathematical analysis is carried out to illustrate the non-negativity, boundedness, epidemic equilibrium, existence, and uniqueness of the endemic equilibrium, and the basic reproduction number of the proposed model. Such numerical models can be, however, subject to various sources of uncertainties, due to an imperfect description of the biological processes governing the disease spread, which may strongly limit their forecasting skills. A data assimilation method, mainly, the ensemble Kalman filter (EnKF), is then used to constrain the model outputs and its parameters with available data. We conduct joint state-parameters estimation experiments assimilating daily data into the proposed model using the EnKF in order to enhance the model’s forecasting skills. Starting from the estimated set of model parameters, we then conduct short-term predictions in order to assess the predicability range of the model. We apply the proposed assimilation system on real data sets from Saudi Arabia. The numerical results demonstrate the capability of the proposed model in achieving accurate prediction of the epidemic development up to two-week time scales. Finally, we investigate the effect of vaccination on the spread of the pandemic.

Spatially and temporally varying adaptive inflation algorithms have been developed to combat the loss of variance during the forecast due to various model and sampling errors. The adaptive Bayesian scheme of Anderson uses available observations to update the Gaussian inflation distribution assigned for every state variable. The likelihood function of the inflation is computed using model-minus-data innovation statistics. A number of enhancements for this inflation scheme are proposed. To prevent excessive deflation, an inverse gamma distribution for the prior inflation is considered. A non-Gaussian distribution offers a flexible framework for the inflation variance to evolve during the update. The innovations are assumed random variables, and a correction term is added to the mode of the likelihood distribution such that the observed inflation is slightly larger. This modification improves the stability of the adaptive scheme by limiting the occurrence of negative and physically intolerable inflations. The enhanced scheme is compared to the original one in twin experiments using the Lorenz-63 model, the Lorenz-96 model, and an idealized, high-dimensional atmospheric model. Results show that the proposed enhancements are capable of generating accurate and consistent state estimates. Allowing moderate deflation is shown to be useful.

Predicting major floods during extreme rainfall events remains an important challenge. Rapid changes in flows over short timescales, combined with multiple sources of model error, makes it difficult to accurately simulate intense floods. This study presents a general data assimilation framework that aims to improve flood predictions in channel routing models. Hurricane Florence, which caused catastrophic flooding and damages in the Carolinas in September 2018, is used as a case study. The National Water Model (NWM) configuration of the WRF-Hydro modeling framework is interfaced with the Data Assimilation Research Testbed (DART) to produce ensemble streamflow forecasts and analyses. Instantaneous streamflow observations from 107 United States Geological Survey (USGS) gauges are assimilated for a period of 1 month. The data assimilation (DA) system developed in this paper explores two novel contributions, namely (1) along-the-stream (ATS) covariance localization and (2) spatially and temporally varying adaptive covariance inflation. ATS localization aims to mitigate not only spurious correlations, due to limited ensemble size, but also physically incorrect correlations between unconnected and indirectly connected state variables in the river network. We demonstrate that ATS localization provides improved information propagation during the model update. Adaptive prior inflation is used to tackle errors in the prior, including large model biases which often occur in flooding situations. Analysis errors incurred during the update are addressed using posterior inflation. Results show that ATS localization is a crucial ingredient of our hydrologic DA system, providing at least 40 % more accurate (root mean square error) streamflow estimates than regular, Euclidean distance-based localization. An assessment of hydrographs indicates that adaptive inflation is extremely useful and perhaps indispensable for improving the forecast skill during flooding events with significant model errors. We argue that adaptive prior inflation is able to serve as a vigorous bias correction scheme which varies both spatially and temporally. Major improvements over the model's severely underestimated streamflow estimates are suggested along the Pee Dee River in South Carolina, and many other locations in the domain, where inflation is able to avoid filter divergence and, thereby, assimilate significantly more observations.

Sampling errors and model errors are major drawbacks from which ensemble Kalman filters suffer. Sampling errors arise because of the use of a limited ensemble size while model errors are de... AbstractSampling errors and model errors are major drawbacks from which ensemble Kalman filters suffer. Sampling errors arise because of the use of a limited ensemble size while model errors are de...

Model errors and sampling errors produce inaccurate sample covariances that limit the performance of ensemble Kalman filters. Linearly hybridizing the flow-dependent ensemble-based covariance with time-invariant background covariance matrix gives a better estimate of the true error covariance. Previous studies have shown this, both in theory and in practice. How to choose the weight for each covariance remains an open question especially in the presence of model biases. This study assumes the weighting coefficient to be a random variable and then introduces a Bayesian scheme to estimate it using the available data. The scheme takes into account the discrepancy between the ensemble mean and the observations, the ensemble variance, the static background variance and the uncertainties in the observations. The proposed algorithm is first derived for a spatially-constant weight and then this assumption is relaxed by estimating a unique scalar weight for each state variable. Using twin-experiments with the 40 variable Lorenz96 system, it is shown that the proposed scheme is able to produce quality forecasts even in the presence of severe sampling errors. The adaptive algorithm allows the hybrid filter to switch between an EnKF and a simple EnOI depending on the statistics of the ensemble. In the presence of model errors, the adaptive scheme demonstrates additional improvements compared with standard enhancements alone, such as inflation and localization. Finally, the potential of the spatially-varying variant to accommodate challenging sparse observation networks is demonstrated. The computational efficiency and storage of the proposed scheme, which remain an obstacle, are discussed.

In this paper, a mathematical model was developed to simulate SARS-CoV-2 dynamics in infected patients. The model considers both the innate and adaptive immune responses and consists of healthy cells, infected cells, viral load, cytokines, natural killer cells, cytotoxic T-lymphocytes, B-lymphocytes, plasma cells, and antibody levels. First, a mathematical analysis was performed to discuss the model’s equilibrium points and compute the basic reproduction number. The accuracy of such mathematical models may be affected by many sources of uncertainties due to the incomplete representation of the biological process and poorly known parameters. This may strongly limit their performance and prediction skills. A state-of-the-art data assimilation technique, the ensemble Kalman filter (EnKF), was then used to enhance the model’s behavior by incorporating available data to determine the best possible estimate of the model’s state and parameters. The proposed assimilation system was applied on the real viral load datasets of six COVID-19 patients. The results demonstrate the efficiency of the proposed assimilation system in improving the model predictions by up to $40\%$.