Quantitative Biology

Some of the key questions of interest during the COVID-19 pandemic (and all outbreaks) include: where did the disease start, how is it spreading, who is at risk, and how to control the spread. There are a large number of complex factors driving the spread of pandemics, and, as a result, multiple modeling techniques play an increasingly important role in shaping public policy and decision making. As different countries and regions go through phases of the pandemic, the questions and data availability also changes. Especially of interest is aligning model development and data collection to support response efforts at each stage of the pandemic. The COVID-19 pandemic has been unprecedented in terms of real-time collection and dissemination of a number of diverse datasets, ranging from disease outcomes, to mobility, behaviors, and socio-economic factors. The data sets have been critical from the perspective of disease modeling and analytics to support policymakers in real-time. In this overview article, we survey the data landscape around COVID-19, with a focus on how such datasets have aided modeling and response through different stages so far in the pandemic. We also discuss some of the current challenges and the needs that will arise as we plan our way out of the pandemic.

Discrete-time replicator map is a prototype of evolutionary selection game dynamical models that have been very successful across disciplines in rendering insights into the attainment of the equilibrium outcomes, like the Nash equilibrium and the evolutionarily stable strategy. By construction, only the fixed point solutions of the dynamics can possibly be interpreted as the aforementioned game-theoretic solution concepts. Although more complex outcomes like chaos are omnipresent in the nature, it is not known to which game-theoretic solutions they correspond. Here we construct a game-theoretic solution that is realized as the chaotic outcomes in the selection monotone game dynamic. To this end, we invoke the idea that in a population game having two-player--two-strategy one-shot interactions, it is the product of the fitness and the heterogeneity (the probability of finding two individuals playing different strategies in the infinitely large population) that is optimized over the generations of the evolutionary process.

Coronavirus disease 2019 (COVID-19) is a continuously devastating public health and the world economy. One of the major challenges in controlling the COVID-19 outbreak is its asymptomatic infection and transmission, which are elusive and defenseless in most situations. The pathogenicity and virulence of asymptomatic COVID-19 remain mysterious. Based on the genotyping of 20656 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) genome isolates, we reveal that asymptomatic infection is linked to SARS-CoV-2 11083G>T mutation, i.e., leucine (L) to phenylalanine (F) substitution at the residue 37 (L37F) of nonstructure protein 6 (NSP6). By analyzing the distribution of 11083G>T in various countries, we unveil that 11083G>T may correlate with the hypotoxicity of SARS-CoV-2. Moreover, we show a global decaying tendency of the 11083G>T mutation ratio indicating that 11083G>T hinders SARS-CoV-2 transmission capacity. Sequence alignment found both NSP6 and residue 37 neighborhoods are relatively conservative over a few coronaviral species, indicating their importance in regulating host cell autophagy to undermine innate cellular defense against viral infection. Using machine learning and topological data analysis, we demonstrate that mutation L37F has made NSP6 energetically less stable. The rigidity and flexibility index and several network models suggest that mutation L37F may have compromised the NSP6 function, leading to a relatively weak SARS-CoV subtype. This assessment is a good agreement with our genotyping of SARS-CoV-2 evolution and transmission across various countries and regions over the past few months.

In this paper we afford a quantitative analysis of the sustainability of current world population growth in relation to the parallel deforestation process adopting a statistical point of view. We consider a simplified model based on a stochastic growth process driven by a continuous time random walk, which depicts the technological evolution of human kind, in conjunction with a deterministic generalised logistic model for humans-forest interaction and we evaluate the probability of avoiding the self-destruction of our civilisation. Based on the current resource consumption rates and best estimate of technological rate growth our study shows that we have very low probability, less than 10% in most optimistic estimate, to survive without facing a catastrophic collapse.

Dengue fever impacts populations across the tropics. Dengue is caused by a mosquito transmitted flavivirus and its burden is projected to increase under future climate and development scenarios. The transmission process of dengue virus is strongly moderated by hydro-climatic conditions that impact the vector's life cycle and behavior. Here, we study the impact of rainfall seasonality and moisture availability on the monthly distribution of reported dengue cases in Sri Lanka. Through cluster analysis, we find an association between seasonal peaks of rainfall and dengue incidence with a two-month lag. We show that a hydrologically driven epidemiological model (HYSIR), which takes into account hydrologic memory in addition to the nonlinear dynamics of the transmission process, captures the two-month lag between rainfall and dengue cases seasonal peaks. Our analysis reveals a non-monotonic dependence of dengue cases on moisture, whereby an increase of cases with increasing moisture is followed by a reduction for very high levels of water availability. Improvement in prediction of the seasonal peaks in dengue incidence results from a seasonally varying dependence of transmission rate on water availability.

SARS-CoV-2 started propagating worldwide in January 2020 and has now reached virtually all communities on the planet. This short review provides evidence of this spread and documents modelling efforts undertaken to understand and forecast it, including a short section about the new variants that emerged in late 2020.

Relevance: Laboratory diagnosis of the novel coronavirus (SARS-CoV-2) infection combined with quarantine for contacts of infected individuals affects the spread of SARS-CoV-2 infection and levels of related mortality. Practices for testing for SARS-CoV-2 infection vary geographically in Russia. For example, in the city of St. Petersburg, where mortality rate for COVID-19 is the highest in the Russian Federation on Oct. 25, 2020, every death for COVID-19 corresponds to 15.7 detected cases of COVID-19 in the population, while the corresponding number for the whole of Russia is 58.1, suggesting limited detection of mild/moderate cases of COVID-19 in St. Petersburg. Methods: More active testing for SARS-CoV-2 results in lower case-fatality ratio (i.e. the proportion of detected COVID-19 cases among all cases of SARS-CoV-2 infection in the population). We used data on COVID-19 cases and deaths to examine the correlation between case-fatality ratios and rates of mortality for COVID-19 in different regions of the Russian Federation. Results: The correlation between case-fatality ratios and rates of mortality for COVID-19 in different regions of the Russian Federation on Oct. 25, 2020 is 0.64 (0.50,0.75). For several regions of the Russian Federation, detectability of SARS-CoV-2 infection is relatively low, while rates of mortality for COVID-19 are relatively high. Conclusions: Detectability of the SARS-CoV-2 infection is one of the factors that affects the levels of mortality from COVID-19. To increase detectability, one ought to test all individuals with respiratory symptoms seeking medical care for SARS-CoV-2 infection, and to undertake additional measures to increase the volume of testing for SARS-CoV-2. Such measures, in combination with quarantine for infected cases and their close contacts help to mitigate the spread of the SARS-CoV-2 infection and diminish the related mortality.

Within the context of SEIR models, we consider a lockdown that is both imposed and lifted at an early stage of an epidemic. We show that, in these models, although such a lockdown may delay deaths, it eventually does not avert a significant number of fatalities. Therefore, in these models, the efficacy of a lockdown cannot be gauged by simply comparing figures for the deaths at the end of the lockdown with the projected figure for deaths by the same date without the lockdown. We provide a simple but robust heuristic argument to explain why this conclusion should generalize to more elaborate compartmental models. We qualitatively discuss some important effects of a lockdown, which go beyond the scope of simple models, but could cause it to increase or decrease an epidemic's final toll. Given the significance of these effects in India, and the limitations of currently available data, we conclude that simple epidemiological models cannot be used to reliably quantify the impact of the Indian lockdown on fatalities caused by the COVID-19 pandemic.

In order to analyze the effectiveness of three successive nationwide lockdown enforced in India, we present a data-driven analysis of four key parameters, reducing the transmission rate, restraining the growth rate, flattening the epidemic curve and improving the health care system. These were quantified by the consideration of four different metrics, namely, reproduction rate, growth rate, doubling time and death to recovery ratio. The incidence data of the COVID-19 (during the period of 2nd March 2020 to 31st May 2020) outbreak in India was analyzed for the best fit to the epidemic curve, making use of the exponential growth, the maximum likelihood estimation, sequential Bayesian method and estimation of time-dependent reproduction. The best fit (based on the data considered) was for the time-dependent approach. Accordingly, this approach was used to assess the impact on the effective reproduction rate. The period of pre-lockdown to the end of lockdown 3, saw a 45% reduction in the rate of effective reproduction rate. During the same period the growth rate reduced from 393% during the pre-lockdown to 33% after lockdown 3, accompanied by the average doubling time increasing form 4 - 6 days to 12 - 14 days. Finally, the death-to-recovery ratio dropped from 0.28 (pre-lockdown) to 0.08 after lockdown 3. In conclusion, all the four metrics considered to assess the effectiveness of the lockdown, exhibited significant favourable changes, from the pre-lockdown period to the end of lockdown 3. Analysis of the data in the post-lockdown period with these metrics will provide greater clarity with regards to the extent of the success of the lockdown.

We here propose to model active and cumulative cases data from COVID-19 by a continuous effective model based on a modified diffusion equation under Lifshitz scaling with a dynamic diffusion coefficient. The proposed model is rich enough to capture different aspects of a complex virus diffusion as humanity has been recently facing. The model being continuous it is bound to be solved analytically and/or numerically. So, we investigate two possible models where the diffusion coefficient associated with possible types of contamination are captured by some specific profiles. The active cases curves here derived were able to successfully describe the pandemic behavior of Germany and Spain. Moreover, we also predict some scenarios for the evolution of COVID-19 in Brazil. Furthermore, we depicted the cumulative cases curves of COVID-19, reproducing the spreading of the pandemic between the cities of São Paulo and São José dos Campos, Brazil. The scenarios also unveil how the lockdown measures can flatten the contamination curves. We can find the best profile of the diffusion coefficient that better fit the real data of pandemic.