Quantitative Biology

This technical report addresses a pressing issue in the trajectory of the coronavirus outbreak; namely, the rate at which effective immunity is lost following the first wave of the pandemic. This is a crucial epidemiological parameter that speaks to both the consequences of relaxing lockdown and the propensity for a second wave of infections. Using a dynamic causal model of reported cases and deaths from multiple countries, we evaluated the evidence models of progressively longer periods of immunity. The results speak to an effective population immunity of about three months that, under the model, defers any second wave for approximately six months in most countries. This may have implications for the window of opportunity for tracking and tracing, as well as for developing vaccination programmes, and other therapeutic interventions.

There are several reports in India that indicate hospitals and quarantined centers are COVID-19 hotspots. In the absence of efficient contact tracing tools, Govt. and the policymakers may not be paying attention to the risk of hospital-based transmission. To explore more on this important route and its possible impact on lockdown effect, we developed a mechanistic model with hospital-based transmission. Using daily notified COVID-19 cases from six states (Maharashtra, Delhi, Madhya Pradesh, Rajasthan, Gujarat, and Uttar Pradesh) and overall India, we estimated several important parameters of the model. Moreover, we provided an estimation of the basic ( R 0 ), the community ( R C ), and the hospital ( R H ) reproduction numbers for those seven locations. To obtain a reliable forecast of future COVID-19 cases, a BMA post-processing technique is used to ensemble the mechanistic model with a hybrid statistical model. Using the ensemble model, we forecast COVID-19 notified cases (daily and cumulative) from May 3, 2020, till May 20, 2020, under five different lockdown scenarios in the mentioned locations. Our analysis of the mechanistic model suggests that most of the new COVID-19 cases are currently undetected in the mentioned seven locations. Furthermore, a global sensitivity analysis of four epidemiologically measurable \& controllable parameters on R 0 and as well on the lockdown effect, indicate that if appropriate preventive measures are not taken immediately, a much larger COVID-19 outbreak may trigger from hospitals and quarantined centers. In most of the locations, our ensemble model forecast indicates a substantial percentage of increase in the COVID-19 notified cases in the coming weeks in India. Based on our results, we proposed a containment policy that may reduce the threat of a larger COVID-19 outbreak in the coming days.

We propose a mathematical model to analyze the effects of anti-infection behavior on the equilibrium states of an infectious disease. The anti-infection behavior is incorporated into a classical epidemiological SIR model, by considering the behavior adoption rate across the population as an additional variable. We consider also the effects on the adoption rate produced by the disease evolution, using a dynamic payoff function and an additional differential equation. The equilibrium states of the proposed model have remarkable characteristics: possible coexistence of two locally stable endemic equilibria, the coexistence of locally stable endemic and disease-free equilibria, and even the possibility of a stable continuum of endemic equilibrium points. We show how some of the results obtained may be used to support strategic planning leading to effective control of the disease in the long-term.

Recreational fishing is a highly socio-ecological process. Although recreational fisheries are self-regulating and resilient, changing anthropogenic pressure drives these fisheries to overharvest and collapse. Here, we evaluate the effect of demographic and environmental stochasticity for a social-ecological two-species fish model. In the presence of noise, we find that an increase in harvesting rate drives a critical transition from high-yield/low-price fisheries to low-yield/high-price fisheries. To calculate stochastic trajectories for demographic noise, we derive the master equation corresponding to the model and perform Monte-Carlo simulation. Moreover, the analysis of probabilistic potential and mean first-passage time reveals the resilience of alternative steady states. We also describe the efficacy of a few generic indicators in forecasting sudden transitions. Furthermore, we show that incorporating social norms on the model allows moderate fish density to maintain despite higher harvesting rates. Overall, our study highlights the occurrence of critical transitions in a stochastic social-ecological model and suggests ways to mitigate them.

We study the reported data from the COVID-19 pandemic outbreak in January - May 2020 in 119 countries. We observe that the time series of active cases in individual countries (the difference of the total number of confirmed infections and the sum of the total number of reported deaths and recovered cases) display a strong agreement with polynomial growth and at a later epidemic stage also with a combined polynomial growth with exponential decay. Our results are also formulated in terms of compartment type mathematical models of epidemics. Within these models the universal scaling characterizing the observed regime in an advanced epidemic stage can be interpreted as an algebraic decay of the relative reproduction number R 0 as T M /t , where T M is a constant and t is the duration of the epidemic outbreak. We show how our findings can be applied to improve predictions of the reported pandemic data and estimate some epidemic parameters. Note that although the model shows a good agreement with the reported data we do not make any claims about the real size of the pandemics as the relation of the observed reported data to the total number of infected in the population is still unknown.

As per the records of theWorld Health Organization, the first formally reported incidence of Zika virus occurred in Brazil in May 2015. The disease then rapidly spread to other countries in Americas and East Asia, affecting more than 1,000,000 people. Zika virus is primarily transmitted through bites of infected mosquitoes of the species Aedes (Aedes aegypti and Aedes albopictus). The abundance of mosquitoes and, as a result, the prevalence of Zika virus infections are common in areas which have high precipitation, high temperature, and high population density.Nonlinear spatio-temporal dependency of such data and lack of historical public health records make prediction of the virus spread particularly challenging. In this article, we enhance Zika forecasting by introducing the concepts of topological data analysis and, specifically, persistent homology of atmospheric variables, into the virus spread modeling. The topological summaries allow for capturing higher order dependencies among atmospheric variables that otherwise might be unassessable via conventional spatio-temporal modeling approaches based on geographical proximity assessed via Euclidean distance. We introduce a new concept of cumulative Betti numbers and then integrate the cumulative Betti numbers as topological descriptors into three predictive machine learning models: random forest, generalized boosted regression, and deep neural network. Furthermore, to better quantify for various sources of uncertainties, we combine the resulting individual model forecasts into an ensemble of the Zika spread predictions using Bayesian model averaging. The proposed methodology is illustrated in application to forecasting of the Zika space-time spread in Brazil in the year 2018.

We shall apply a generalized SEIR model to study the outbreak of COVID-19 in Brazil. In particular, we would like to explain the projections of the increase in the level of infection over a long period of time, overlapping large local outbreaks in the most populous states in the country. A time-dependent dynamic SEIR model inspired in a model previously used during the outbreak in China was used to analyses the time trajectories of infected, recovered, and deaths. The model has parameters that vary with time and are fitted considering a nonlinear least-squares method. The simulations starting from April 8, 2020, concluded that the time for a peak in Brazil will be in July 21, 2020 with total cumulative infected cases around 982K people; in addition, an estimated total death case will reach to 192K in the end. Besides that, Brazil will reach a peak in terms of daily new infected cases and death cases around the middle of July with 50K cases of infected and almost 6.0K daily deaths.

We interpret attitudes towards science and pseudosciences as cultural traits that diffuse in society through communication efforts exerted by agents. We present a tractable model that allows us to study the interaction among the diffusion of an epidemic, vaccination choices, and the dynamics of cultural traits. We apply it to study the impact of homophily between pro-vaxxers and anti-vaxxers on the total number of cases (the cumulative infection). We show that, during the outbreak of a disease, homophily has the direct effect of decreasing the speed of recovery. Hence, it may increase the number of cases and make the disease endemic. The dynamics of the shares of the two cultural traits in the population is crucial in determining the sign of the total effect on the cumulative infection: more homophily is beneficial if agents are not too flexible in changing their cultural trait, is detrimental otherwise.

Contact-tracing is an essential tool in order to mitigate the impact of pandemic such as the COVID-19. In order to achieve efficient and scalable contact-tracing in real time, digital devices can play an important role. While a lot of attention has been paid to analyzing the privacy and ethical risks of the associated mobile applications, so far much less research has been devoted to optimizing their performance and assessing their impact on the mitigation of the epidemic. We develop Bayesian inference methods to estimate the risk that an individual is infected. This inference is based on the list of his recent contacts and their own risk levels, as well as personal information such as results of tests or presence of syndromes. We propose to use probabilistic risk estimation in order to optimize testing and quarantining strategies for the control of an epidemic. Our results show that in some range of epidemic spreading (typically when the manual tracing of all contacts of infected people becomes practically impossible, but before the fraction of infected people reaches the scale where a lock-down becomes unavoidable), this inference of individuals at risk could be an efficient way to mitigate the epidemic. Our approaches translate into fully distributed algorithms that only require communication between individuals who have recently been in contact. Such communication may be encrypted and anonymized and thus compatible with privacy preserving standards. We conclude that probabilistic risk estimation is capable to enhance performance of digital contact tracing and should be considered in the currently developed mobile applications.

Bovine tuberculosis, a disease that affects cattle and badgers in Ireland, was studied via stochastic epidemic modeling using incidence data from the Four Area Project (Griffin et al., 2005). The Four Area Project was a large scale field trial conducted in four diverse farming regions of Ireland over a five-year period (1997-2002) to evaluate the impact of badger culling on bovine tuberculosis incidence in cattle herds. Based on the comparison of several models, the model with no between-herd transmission and badger-to-herd transmission proportional to the total number of infected badgers culled was best supported by the data. Detailed model validation was conducted via model prediction, identifiability checks and sensitivity analysis. The results suggest that badger-to-cattle transmission is of more importance than between-herd transmission and that if there was no badger-to-herd transmission, levels of bovine tuberculosis in cattle herds in Ireland could decrease considerably.