Vaccination compartmental epidemiological models for the delta and omicron SARS-CoV-2 variants.

We explore the inclusion of vaccination in compartmental epidemiological models concerning the delta and omicron variants of the SARS-CoV-2 virus that caused the COVID-19 pandemic. We expand on our earlier compartmental-model work by incorporating vaccinated populations. We present two classes of models that differ depending on the immunological properties of the variant. The first one is for the delta variant, where we do not follow the dynamics of the vaccinated individuals since infections of vaccinated individuals were rare. The second one for the far more contagious omicron variant incorporates the evolution of the infections within the vaccinated cohort. We explore comparisons with available data involving two possible classes of counts, fatalities and hospitalizations. We present our results for two regions, Andalusia and Switzerland (including the Principality of Liechtenstein), where the necessary data are available. In the majority of the considered cases, the models are found to yield good agreement with the data and have a reasonable predictive capability beyond their training window, rendering them potentially useful tools for the interpretation of the COVID-19 and further pandemic waves, and for the design of intervention strategies during these waves.

The Role of Mobility in the Dynamics of the COVID-19 Epidemic in Andalusia.

Metapopulation models have been a popular tool for the study of epidemic spread over a network of highly populated nodes (cities, provinces, countries) and have been extensively used in the context of the ongoing COVID-19 pandemic. In the present work, we revisit such a model, bearing a particular case example in mind, namely that of the region of Andalusia in Spain during the period of the summer-fall of 2020 (i.e., between the first and second pandemic waves). Our aim is to consider the possibility of incorporation of mobility across the province nodes focusing on mobile-phone time-dependent data, but also discussing the comparison for our case example with a gravity model, as well as with the dynamics in the absence of mobility. Our main finding is that mobility is key toward a quantitative understanding of the emergence of the second wave of the pandemic and that the most accurate way to capture it involves dynamic (rather than static) inclusion of time-dependent mobility matrices based on cell-phone data. Alternatives bearing no mobility are unable to capture the trends revealed by the data in the context of the metapopulation model considered herein.

Backcasting COVID-19: a physics-informed estimate for early case incidence.

It is widely accepted that the number of reported cases during the first stages of the COVID-19 pandemic severely underestimates the number of actual cases. We leverage delay embedding theorems of Whitney and Takens and use Gaussian process regression to estimate the number of cases during the first 2020 wave based on the second wave of the epidemic in several European countries, South Korea and Brazil. We assume that the second wave was more accurately monitored, even though we acknowledge that behavioural changes occurred during the pandemic and region- (or country-) specific monitoring protocols evolved. We then construct a manifold diffeomorphic to that of the implied original dynamical system, using fatalities or hospitalizations only. Finally, we restrict the diffeomorphism to the reported cases coordinate of the dynamical system. Our main finding is that in the European countries studied, the actual cases are under-reported by as much as 50%. On the other hand, in South Korea-which had a proactive mitigation approach-a far smaller discrepancy between the actual and reported cases is predicted, with an approximately 18% predicted underestimation. We believe that our backcasting framework is applicable to other epidemic outbreaks where (due to limited or poor quality data) there is uncertainty around the actual cases.

Reaction-diffusion spatial modeling of COVID-19: Greece and Andalusia as case examples.

We examine the spatial modeling of the outbreak of COVID-19 in two regions: the autonomous community of Andalusia in Spain and the mainland of Greece. We start with a zero-dimensional (0D; ordinary-differential-equation-level) compartmental epidemiological model consisting of Susceptible, Exposed, Asymptomatic, (symptomatically) Infected, Hospitalized, Recovered, and deceased populations (SEAIHR model). We emphasize the importance of the viral latent period (reflected in the exposed population) and the key role of an asymptomatic population. We optimize model parameters for both regions by comparing predictions to the cumulative number of infected and total number of deaths, the reported data we found to be most reliable, via minimizing the ℓ^{2} norm of the difference between predictions and observed data. We consider the sensitivity of model predictions on reasonable variations of model parameters and initial conditions, and we address issues of parameter identifiability. We model both the prequarantine and postquarantine evolution of the epidemic by a time-dependent change of the viral transmission rates that arises in response to containment measures. Subsequently, a spatially distributed version of the 0D model in the form of reaction-diffusion equations is developed. We consider that, after an initial localized seeding of the infection, its spread is governed by the diffusion (and 0D model "reactions") of the asymptomatic and symptomatically infected populations, which decrease with the imposed restrictive measures. We inserted the maps of the two regions, and we imported population-density data into the finite-element software package COMSOL Multiphysics®, which was subsequently used to numerically solve the model partial differential equations. Upon discussing how to adapt the 0D model to this spatial setting, we show that these models bear significant potential towards capturing both the well-mixed, zero-dimensional description and the spatial expansion of the pandemic in the two regions. Veins of potential refinement of the model assumptions towards future work are also explored.

Lockdown measures and their impact on single- and two-age-structured epidemic model for the COVID-19 outbreak in Mexico.

The role of lockdown measures in mitigating COVID-19 in Mexico is investigated using a comprehensive nonlinear ODE model. The model includes both asymptomatic and presymptomatic populations with the latter leading to sickness (with recovery, hospitalization and death as possible outcomes). We consider situations involving the application of social-distancing and other intervention measures in the time series of interest. We find optimal parametric fits to the time series of deaths (only), as well as to the time series of deaths and cumulative infections. We discuss the merits and disadvantages of each approach, we interpret the parameters of the model and assess the realistic nature of the parameters resulting from the optimization procedure. Importantly, we explore a model involving two sub-populations (younger and older than a specific age), to more accurately reflect the observed impact as concerns symptoms and behavior in different age groups. For definiteness and to separate people that are (typically) in the active workforce, our partition of population is with respect to members younger vs. older than the age of 65. The basic reproduction number of the model is computed for both the single- and the two-population variant. Finally, we consider what would be the impact of partial lockdown (involving only the older population) and full lockdown (involving the entire population) on the number of deaths and cumulative infections.

Stochastic transport of particles in straining flows.

Important features associated with the segregration of particles in turbulent flow are investigated by considering the statistical distribution (phase-space number density) of particles subject to the combined effects of straining flow and stochastic forcing. A Fokker-Planck model is used to obtain results for the phase-space distributions of particles that are entrained into straining flow fields. The analysis shows that, in marked contrast to the zero strain case, nonsingular steady-state distributions are generated, and also confirms that the diffusional effect resulting from stochastic forcing is sufficient to offset the otherwise singular distributions that would result from the indefinite accumulation of particles along stagnation lines. The influence of particle inertia (Stokes number) on the form of the resulting distributions is considered and several significant results are observed. The influence of strain rate on the attenuation of particle kinetic stresses is quantified and explained. The development of large third-order velocity moments is observed for Stokes numbers above a critical value. The mechanism underlying this phenomenon is seen to be a generic feature of particle transport in flows where vortex structures induce local counterflows of particles. The system therefore provides an ideal test for closure models for third-order moments of particle velocities, and here the standard Chapman-Enskog approximation is assessed.

Translational invariance in nucleation theories: theoretical formulation.

The consequences of spontaneously broken translational invariance on the nucleation-rate statistical prefactor in theories of first-order phase transitions are analyzed. A hybrid, semiphenomenological approach based on field-theoretic analyses of condensation and modern density-functional theories of nucleation is adopted to provide a unified prescription for the incorporation of translational-invariance corrections to nucleation-rate predictions. A connection between these theories is obtained starting from a quantum-mechanical Hamiltonian and using methods developed in the context of studies on Bose-Einstein condensation. An extremum principle is used to derive an integro-differential equation for the spatially nonuniform mean-field order-parameter profile; the appropriate order parameter becomes the square root of the fluid density. The importance of the attractive intermolecular potential is emphasized, whereas the repulsive two-body potential is approximated by considering hard-sphere collisions. The functional form of the degenerate translational eigenmodes in three dimensions is related to the mean-field order parameter, and their contribution to the nucleation-rate prefactor is evaluated. The solution of the Euler-Lagrange variational equation is discussed in terms of either a proposed variational trial function or the complete numerical solution of the associated boundary-value integro-differential problem. Alternatively, if the attractive potential is not explicitly known, an approach that allows its formal determination from its moments is presented.

Scale invariance and intermittency in a creep-slip model of earthquake faults.

The dynamics of a generalization of the one-dimensional, spatially discretized Burridge-Knopoff model (slider-block model) is investigated numerically. Plastic deformation of the fault interface is considered in addition to rigid sliding (creep-slip model). The event-size distribution exhibits scale invariance (beta=1.5), as does the power spectral density of the intermittent time series of the spatially averaged sliding rate (sigma=1.3). A diffusive cellular automaton model that reproduces the algebraic correlations in the event-size distribution in the presence of dissipation is proposed.

Turbulent Resuspension of Small Nondeformable Particles.

An energy-balance resuspension model is modified and applied to the resuspension of a monolayer of nondeformable spherical particles. The particle-surface adhesive force is calculated from a microscopic model based on the Lennard-Jones intermolecular potential. Pairwise additivity of intermolecular interactions is assumed and elastic flattening of the particles is neglected. From the resulting particle-surface interaction potential the natural frequency of vibration of a particle on a surface and the depth of the potential well are calculated. The particle resuspension rate is calculated using the results of a previously developed energy-balance model, where the influence of fluid flow on the bound particle motion is recognized. The effect of surface roughness is included by introducing an effective particle radius that results in log-normally distributed adhesive forces. The predictions of the model are compared with experimental results for the resuspension of Al2O3 particles from stainless steel surfaces. Copyright 1998 Academic Press.