Quantitative Biology

We provide a probabilistic SIRD model for the COVID-19 pandemic in Italy, where we allow the infection, recovery and death rates to be random. In particular, the underlying random factor is driven by a fractional Brownian motion. Our model is simple and needs only some few parameters to be calibrated.

We propose a time-fractional compartmental model (SEI A I S HRD) comprising of the susceptible, exposed, infected (asymptomatic and symptomatic), hospitalized, recovered and dead population for the Covid-19 pandemic. We study the properties and dynamics of the proposed model. The conditions under which the disease-free and endemic equilibrium points are asymptotically stable are discussed. Furthermore, we study the sensitivity of the parameters and use the data from Tennessee state (as a case study) to discuss identifiability of the parameters of the model. The non-negative parameters in the model are obtained by solving inverse problems with empirical data from California, Florida, Georgia, Maryland, Tennessee, Texas, Washington and Wisconsin. The basic reproduction number is seen to be slightly above the critical value of one suggesting that stricter measures such as the use of face-masks, social distancing, contact tracing, and even longer stay-at-home orders need to be enforced in order to mitigate the spread of the virus. As stay-at-home orders are rescinded in some of these states, we see that the number of cases began to increase almost immediately and may continue to rise until the end of the year 2020 unless stricter measures are taken.

Although extensive behavioral changes often exist between closely related animal species, our understanding of the genetic basis underlying the evolution of behavior has remained limited. Here, we propose a new framework to study behavioral evolution by computational estimation of ancestral behavioral repertoires. We measured the behaviors of individuals from six species of fruit flies using unsupervised techniques and identified suites of stereotyped movements exhibited by each species. We then fit a Generalized Linear Mixed Model to estimate the suites of behaviors exhibited by ancestral species, as well as the intra- and inter-species behavioral covariances. We found that much of intraspecific behavioral variation is explained by differences between individuals in the status of their behavioral hidden states, what might be called their "mood." Lastly, we propose a method to identify groups of behaviors that appear to have evolved together, illustrating how sets of behaviors, rather than individual behaviors, likely evolved. Our approach provides a new framework for identifying co-evolving behaviors and may provide new opportunities to study the genetic basis of behavioral evolution.

We analyze a general theory for coexistence and extinction of ecological communities that are influenced by stochastic temporal environmental fluctuations. The results apply to discrete time (stochastic difference equations), continuous time (stochastic differential equations), compact and non-compact state spaces and degenerate or non-degenerate noise. In addition, we can also include in the dynamics auxiliary variables that model environmental fluctuations, population structure, eco-environmental feedbacks or other internal or external factors. We are able to significantly generalize the recent discrete time results by Benaim and Schreiber (Journal of Mathematical Biology '19) to non-compact state spaces, and we provide stronger persistence and extinction results. The continuous time results by Hening and Nguyen (Annals of Applied Probability '18) are strengthened to include degenerate noise and auxiliary variables. Using the general theory, we work out several examples. In discrete time, we classify the dynamics when there are one or two species, and look at the Ricker model, Log-normally distributed offspring models, lottery models, discrete Lotka-Volterra models as well as models of perennial and annual organisms. For the continuous time setting we explore models with a resource variable, stochastic replicator models, and three dimensional Lotka-Volterra models.

A compartmental epidemic model based on genetic fitting algorithm and a cross-validation method to overcome the overfitting problem are proposed. This generic enhanced SEIR model allows to estimate approximate nowcast and forecast of epidemic evolution including key epidemic parameters and non-measurable asymptomatic infected portion of the susceptible population. The model is used to study COVID-19 outbreak dynamics in Algeria between February 25th and May 24th. The Basic reproduction number is estimated to 3.78 (95% CI 3.033-4.53) and effective reproduction number on May 24th after three months of the outbreak is estimated to 0.651 (95% CI 0.539-0.761). The Infections peak time is predicted to the end of April while active cases peak time is predicted to the end of May 2020. The disease incidence, CFR and IFR are calculated. Information provided by this study could help establish a realistic assessment of the situation in Algeria for the time being, inform predictions about potential future evolution, and guide the design of appropriate public health measures.

This work constructs, analyzes, and simulates a new compartmental SEIR-type model for the dynamics and potential control of the current COVID-19 pandemic. The novelty in this work is two-fold. First, the population is divided according to its compliance with disease control directives (lockdown, shelter-in-place, masks/face coverings, physical distancing, etc.) into those who fully comply and those who follow the directives partially, or are necessarily mobile (such as medical staff). This split, indirectly, reflects on the quality and consistency of these measures. This allows the assessment of the overall effectiveness of the control measures and the impact of their relaxing or tightening on the disease spread. Second, the adequate contact rate, which directly affects the infection rate, is one of the model unknowns, as it keeps track of the changes in the population behavior and the effectiveness of various disease treatment modalities via a differential inclusion. Existence, uniqueness and positivity results are proved using a nonstandard convex analysis-based approach. As a case study, the pandemic outbreak in the Republic of Korea (South Korea) is simulated. The model parameters were found by minimizing the deviation of the model prediction from the reported data over the first 100 days of the pandemic in South Korea.The simulations show that the model captures accurately the pandemic dynamics in the subsequent 75 days, which provides confidence in the model predictions and its future use. In particular, the model predicts that about 40% of the infections were not documented, which implies that asymptomatic infections contribute silently but substantially to the spread of the disease indicating that more widespread asymptomatic testing is necessary.

We discuss the generation of various reproduction ratios or numbers that are very useful to monitor an ongoing epidemic like Covid-19 and examine the effects of intervention measures. A detailed SEIR algorithm is described for their computation, with applications given to the current Covid-19 outbreaks in a number of countries (Argentina, Brazil, France, Italy, Mexico, Spain, UK and USA). The corresponding matlab script, complete and ready to use, is provided for free downloading.

In this article we propose a compartmental model for the dynamics of Coronavirus Disease 2019 (COVID-19). We take into account the presence of asymptomatic infections and the main policies that have been adopted so far to contain the epidemic: isolation (or social distancing) of a portion of the population, quarantine for confirmed cases and testing. We model isolation by separating the population in two groups: one composed by key-workers that keep working during the pandemic and have a usual contact rate, and a second group consisting of people that are enforced/recommended to stay at home. We refer to quarantine as strict isolation, and it is applied to confirmed infected cases. In the proposed model, the proportion of people in isolation, the level of contact reduction and the testing rate are control parameters that can vary in time, representing policies that evolve in different stages. We obtain an explicit expression for the basic reproduction number R 0 in terms of the parameters of the disease and of the control policies. In this way we can quantify the effect that isolation and testing have in the evolution of the epidemic. We present a series of simulations to illustrate different realistic scenarios. From the expression of R 0 and the simulations we conclude that isolation (social distancing) and testing among asymptomatic cases are fundamental actions to control the epidemic, {and the stricter these measures are and the sooner they are implemented,} the more lives can be saved. Additionally, we show that people that remain in isolation significantly reduce their probability of contagion, so risk groups should be recommended to maintain a low contact rate during the course of the epidemic.

We present a compartmental mathematical model with demography for the spread of the COVID-19 disease, considering also asymptomatic infectious individuals. We compute the basic reproductive ratio of the model and study the local and global stability for it. We solve the model numerically based on the case of Italy. We propose a vaccination model and we derive threshold conditions for preventing infection spread in the case of imperfect vaccines.

We consider a model of cultural evolution for a strategy selection in a population of individuals who interact in a game theoretic framework. The evolution combines individual learning of the environment (population strategy profile), reproduction, proportional to the success of the acquired knowledge, and social transmission of the knowledge to the next generation. A mean-field type equation is derived that describes the dynamics of the distribution of cultural traits, in terms of the rate of learning, the reproduction rate and population size. We establish global well-posedness of the initial-boundary value problem for this equation and give several examples that illustrate the process of the cultural evolution for some classical games.