Abstract: The classical SEIR model, being an autonomous system of differential equations, has important limitations when representing a pandemic situation. Particularly, the geometric unimodal shape of the epidemic curve is not what is generally observed. This work introduces the beta SEIR model, which adds to the classical SEIR model a differential law to model the variation in the transmission rate. It considers two opposite thrives generally found in a population: first, reaction to disease presence that may be linked to mitigation strategies, which tends to decrease transmission, and second, the urge to return to normal conditions that pulls to restore the initial value of the transmission rate. Our results open a wide spectrum of dynamic variabilities in the curve of new infected, which are justified by reaction and restoration thrives that affect disease transmission over time. Some of these dynamics have been observed in the existing COVID-19 disease data. In particular and to further exemplify the potential of the model proposed in this article, we show its capability of capturing the evolution of the number of new confirmed cases of Chile and Italy for several months after epidemic onset, while incorporating a reaction to disease presence with decreasing adherence to mitigation strategies, as well as a seasonal effect on the restoration of the initial transmissibility conditions.

Abstract: Human interactions and perceptions about health risk are essential to understand the evolution over the course of a pandemic. We present a Susceptible-Exposed-Asymptomatic-Infectious-Recovered-Susceptible mathematical model with quarantine and social-distance-dependent transmission rates, to study COVID-19 dynamics. Human activities are split across different location settings: home, work, school, and elsewhere. Individuals move from home to the other locations at rates dependent on their epidemiological conditions and maintain a social distancing behavior, which varies with their location. We perform simulations and analyze how distinct social behaviors and restrictive measures affect the dynamic of the disease within a population. The model proposed in this study revealed that the main focus on the transmission of COVID-19 is attributed to the “home” location setting, which is understood as family gatherings including relatives and close friends. Limiting encounters at work, school and other locations will only be effective if COVID-19 restrictions occur simultaneously at all those locations and/or contact tracing or social distancing measures are effectively and strictly implemented, especially at the home setting.

Abstract: Evidence suggests a strong correlation between the prevalence of HSV-2 (genital herpes) and the perseverance of the HIV epidemic. HSV-2 is an incurable viral infection, characterized by periodic reactivation. We construct a model of the co-infection dynamics between the two diseases by incorporating a time-since-infection variable to track the alternating periods of infectiousness of HSV-2. The model considers only heterosexual relationships and distinguishes three population groups: males, general population females, and female sex workers. We calculate the basic reproduction numbers for each disease that provide threshold conditions, which determine whether a disease dies out or becomes endemic in the absence of the other disease. We also derive the invasion reproduction numbers that determine whether or not a disease can invade into a population in which the other disease is endemic. The calculations of the invasion reproduction numbers suggest a new aspect in their interpretation – the class from which the initial disease carrier arises is important for understanding the invasion dynamics and biological interpretation of the expressions of the reproduction numbers. Sensitivity analysis is conducted to examine the role of model parameters in influencing the model outcomes. The results are discussed in the last section.

Abstract: ince the detection of the first case of COVID-19 in Chile on March 3(rd), 2020, a total of 513,188 cases, including similar to 14,302 deaths have been reported in Chile as of November 2(nd), 2020. Here, we estimate the reproduction number throughout the epidemic in Chile and study the effectiveness of control interventions especially the effectiveness of lockdowns by conducting short-term forecasts based on the early transmission dynamics of COVID-19. Chile's incidence curve displays early sub-exponential growth dynamics with the deceleration of growth parameter, p, estimated at 0.8 (95% CI: 0.7, 0.8) and the reproduction number, R, estimated at 1.8 (95% CI: 1.6, 1.9). Our findings indicate that the control measures at the start of the epidemic significantly slowed down the spread of the virus. However, the relaxation of restrictions and spread of the virus in low-income neighborhoods in May led to a new surge of infections, followed by the reimposition of lockdowns in Greater Santiago and other municipalities. These measures have decelerated the virus spread with R estimated at similar to 0.96 (95% CI: 0.95, 0.98) as of November 2(nd), 2020. The early sub-exponential growth trend (p similar to 0.8) of the COVID-19 epidemic transformed into a linear growth trend (p similar to 0.5) as of July 7(th), 2020, after the reimposition of lockdowns. While the broad scale social distancing interventions have slowed the virus spread, the number of new COVID-19 cases continue to accrue, underscoring the need for persistent social distancing and active case detection and isolation efforts to maintain the epidemic under control.
Author summary
In context of the ongoing COVID-19 pandemic, Chile has been one of the hardest-hit countries in Latin America, struggling to contain the spread of the virus. In this manuscript, we employ renewal equation to estimate the reproduction number (R) for the early ascending phase of the COVID-19 epidemic and by July 7(th), 2020 to guide the magnitude and intensity of interventions required to combat the COVID-19 epidemic. We also estimate the instantaneous reproduction number throughout the epidemic in Chile. Moreover, we generate short-term forecasts based on the epidemic trajectory using phenomenological models, and assess counterfactual scenarios to understand any additional resources required to contain the virus' spread. Our results indicate early sustained transmission of SARS-CoV-2. However, the initial control measures at the start of the epidemic significantly slowed down the spread of the virus. The easing of COVID-19 restrictions in April led to a new wave of infections, followed by the re-imposition of lockdowns in Greater Santiago and several municipalities. Most recent estimates of reproduction number indicate a decline in the virus transmission. While broad-scale social distancing interventions have slowed the virus spread, the number of new COVID-19 cases continue to accrue, underscoring the need for persistent social distancing efforts.

Abstract: A deterministic model for the effects on disease prevalence of the most advanced preerythrocytic vaccine against malaria is proposed and studied. The model includes two vaccinated classes that correspond to initially vaccinated and booster dose vaccinated individuals. These two classes are structured by time-since-initial-vaccination (vaccine-age). This structure is a novelty for vector-host models; it allows us to explore the effects of parameters that describe timed and delayed delivery of a booster dose, and immunity waning on disease prevalence. Incorporating two vaccinated classes can predict more accurately threshold vaccination coverages for disease eradication under multi-dose vaccination programs. We derive a vaccine-age-structured control reproduction number R and establish conditions for the existence and stability of equilibria to the system. The model is bistable when R < 1. In particular, it exhibits a backward (sub-critical) bifurcation, indicating that R = 1 is no longer the threshold value for disease eradication. Thus, to achieve eradication we must identify and implement control measures that will reduce R to a value smaller than unity. Therefore, it is crucial to be cautious when using R to guide public health policy, although it remains a key quantity for decision making. Our results show that if the booster vaccine dose is administered with delay, individuals may not acquire its full protective effect, and that incorporating waning efficacy into the system improves the accuracy of the model outcomes. This study suggests that it is critical to follow vaccination schedules closely, and anticipate the consequences of delays in those schedules.