Quantitative Biology

This paper provides a mathematical model to show that the incorrect estimation of r, the fraction of asymptomatic COVID-19 carriers in the general population, can account for much of the world's failure to contain the pandemic in its early phases. The SE(A+O)R model with infectives separated into asymptomatic and ordinary carriers, supplemented by a model of the data generation process, is calibrated to standard datasets for several countries. It is shown that certain fundamental parameters, notably r, are unidentifiable with this data. A number of potential types of policy intervention are analyzed. It is found that the lack of parameter identifiability implies that only some, but not all, potential policy interventions can be correctly predicted. In an example representing Italy in March 2020, a hypothetical optimal policy of isolating confirmed cases that aims to reduce the basic reproduction number of the outbreak to R0 = 0.8 assuming r = 10%, only achieves R0 = 1.4 if it turns out that r = 40%.

In this article, we perform an analysis of COVID-19 on one of the South Saharan countries (hot zone), the Senegal (West Africa). Many questions remain unanswered: why the African continent is not very contaminated compared to other continents. Factors of cross immunity, temperature, population density, youth, etc. are taken into account for an analysis of the contamination factors. Numerical simulations are carried out for a prediction over the coming week.

In this paper, we deal with the study of the impact of nationwide measures COVID-19 anti-pandemic. We drive two processes to analyze COVID-19 data considering measures. We associate level of nationwide measure with value of parameters related to the contact rate of the model. Then a parametric solve, with respect to those parameters of measures, shows different possibilities of the evolution of the pandemic. Two machine learning tools are used to forecast the evolution of the pandemic. Finally, we show comparison between deterministic and two machine learning tools.

COVID-19, a viral respiratory pandemic, has rapidly spread throughout the globe. Large scale and rapid testing of the population is required to contain the disease, but such testing is prohibitive in terms of resources, cost and time. Recently RT-PCR based pooled testing has emerged as a promising way to boost testing efficiency. We introduce a stepped pooled testing strategy, a probability driven approach which significantly reduces the number of tests required to identify infected individuals in a large population. Our comprehensive methodology incorporates the effect of false negative and positive rates to accurately determine not only the efficiency of pooling but also it's accuracy. Under various plausible scenarios, we show that this approach significantly reduces the cost of testing and also reduces the effective false positive rate of tests when compared to a strategy of testing every individual of a population. We also outline an optimization strategy to obtain the pool size that maximizes the efficiency of pooling given the diagnostic protocol parameters and local infection conditions.

Nationwide lockdown for COVID-19 created an urgent demand for public transportation among migrant workers stranded at different parts of India to return to their native places. Arranging transportation could spike the number of COVID-19 infected cases. Hence, this paper investigates the potential surge in confirmed and active cases of COVID-19 infection and assesses the train and bus fleet size required for the repatriating migrant workers. The expected to repatriate migrant worker population was obtained by forecasting the 2011 census data and comparing it with the information reported in the news media. A modified susceptible-exposed-infected-removed (SEIR) model was proposed to estimate the surge in confirmed and active cases of COVID-19 patients in India's selected states with high outflux of migrants. The developed model considered combinations of different levels of the daily arrival rate of migrant workers, total migrant workers in need of transportation, and the origin of the trip dependent symptomatic cases on arrival. Reducing the daily arrival rate of migrant workers for states with very high outflux of migrants (i.e., Uttar Pradesh and Bihar) can help to lower the surge in confirmed and active cases. Nevertheless, it could create a disparity in the number of days needed to transport all repatriating migrant workers to the home states. Hence, travel arrangements for about 100,000 migrant workers per day to Uttar Pradesh and Bihar, about 50,000 per day to Rajasthan and Madhya Pradesh, 20,000 per day to Maharashtra and less than 20,000 per day to other states of India was recommended.

I employ a simple mathematical model of an epidemic process to evaluate how four basic quantities: the reproduction number (R), the numbers of sensitive (S) and infectious individuals(I), and total community size (N) affect strategies to control COVID-19. Numerical simulations show that strict suppression measures at the beginning of an epidemic can create low infectious numbers, which thereafter can be managed by mitigation measures over longer periods to flatten the epidemic curve. The stronger the suppression measure, the faster it achieves the low numbers of infections that are conducive to subsequent management. We discuss the predictions of this analysis and how it fits into longer-term sequences of measures, including using the herd immunity concept to leverage acquired immunity.

Raw moments are used as a way to estimate species abundance distribution. The almost linear pattern of the log transformation of raw moments across scales allow us to extrapolate species abundance distribution for larger areas. However, results may produce errors. Some of these errors are due to computational complexity, fittings of patterns, binning methods, and so on. We provide some methods to reduce some of the errors. The main result is introducing new techniques for evaluating a more accurate species abundance distributions across scales through moments across scales.

As the interactions between people increases, the impending menace of COVID-19 outbreaks materialize, and there is an inclination to apply lockdowns. In this context, it is essential to have easy-to-use indicators for people to use as a reference. The basic reproduction number of confirmed positives, R t , fulfill such a role. This document proposes a data-driven approach to nowcast R t based on previous observations' statistical behavior. As more information arrives, the method naturally becomes more precise about the final count of confirmed positives. Our method's strength is that it is based on the self-reported onset of symptoms, in contrast to other methods that use the daily report's count to infer this quantity. We show that our approach may be the foundation for determining useful epidemy tracking indicators.

We consider the control of the COVID-19 pandemic via incentives, through either stochastic SIS or SIR compartmental models. When the epidemic is ongoing, the population can reduce interactions between individuals in order to decrease the rate of transmission of the disease, and thus limit the epidemic. However, this effort comes at a cost for the population. Therefore, the government can put into place incentive policies to encourage the lockdown of the population. In addition, the government may also implement a testing policy in order to know more precisely the spread of the epidemic within the country, and to isolate infected individuals. We provide numerical examples, as well as an extension to a stochastic SEIR compartmental model to account for the relatively long latency period of the COVID-19 disease. The numerical results confirm the relevance of a tax and testing policy to improve the control of an epidemic. More precisely, if a tax policy is put into place, even in the absence of a specific testing policy, the population is encouraged to significantly reduce its interactions, thus limiting the spread of the disease. If the government also adjusts its testing policy, less effort is required on the population side, so individuals can interact almost as usual, and the epidemic is largely contained by the targeted isolation of positively-tested individuals.

The rapid rise of antibiotic resistance is a serious threat to global public health. Without further incentives, pharmaceutical companies have little interest in developing antibiotics, since the success probability is low and development costs are huge. The situation is exacerbated by the "antibiotics dilemma": Developing narrow-spectrum antibiotics against resistant bacteria is most beneficial for society, but least attractive for companies since their usage is more limited than for broad-spectrum drugs and thus sales are low. Starting from a general mathematical framework for the study of antibiotic-resistance dynamics with an arbitrary number of antibiotics, we identify efficient treatment protocols and introduce a market-based refunding scheme that incentivizes pharmaceutical companies to develop narrow-spectrum antibiotics: Successful companies can claim a refund from a newly established antibiotics fund that partially covers their development costs. The proposed refund involves a fixed and variable part. The latter (i) increases with the use of the new antibiotic for currently resistant strains in comparison with other newly developed antibiotics for this purpose---the resistance premium---and (ii) decreases with the use of this antibiotic for non-resistant bacteria. We outline how such a refunding scheme can solve the antibiotics dilemma and cope with various sources of uncertainty inherent in antibiotic R\&D. Finally, connecting our refunding approach to the recently established antimicrobial resistance (AMR) action fund, we discuss how the antibiotics fund can be financed.