Caveats on COVID-19 herd immunity threshold: the Spain case

After a year of living with the COVID-19 pandemic and its associated consequences, hope looms on the horizon thanks to vaccines. The question is what percentage of the population needs to be immune to reach herd immunity, that is to avoid future outbreaks. The answer depends on the basic reproductive number, R0, a key epidemiological parameter measuring the transmission capacity of a disease. In addition to the virus itself, R0 also depends on the characteristics of the population and their environment. Additionally, the estimate of R0 depends on the methodology used, the accuracy of data and the generation time distribution. This study aims to reflect on the difficulties surrounding R0 estimation, and provides Spain with a threshold for herd immunity, for which we considered the different combinations of all the factors that affect the R0 of the Spanish population. Estimates of R0 range from 1.39 to 3.10 for the ancestral SARS-CoV-2 variant, with the largest differences produced by the method chosen to estimate R0. With these values, the herd immunity threshold (HIT) ranges from 28.1 to 67.7%, which would have made 70% a realistic upper bound for Spain. However, the imposition of the delta variant (B.1.617.2 lineage) in late summer 2021 may have expanded the range of R0 to 4.02–8.96 and pushed the upper bound of the HIT to 90%.

Dynamics of the Rumor-Spreading Model with Control Mechanism in Complex Network

The spread of rumors has a great impact on social order, people’s psychology, and life. In recent years, the application of rumor-spreading models in complex networks has received extensive attention. Taking the management and control of rumors by relevant departments in real life into account, the SIDRQ rumor-spreading model that combines forgetting mechanism, immune mechanism, and suspicion mechanism and guides on a uniform network is established in this paper. Then, the basic reproductive number of the system and the unique existence of the solution are discussed, and the stability of the system is analyzed using the basic reproductive number, Lyapunov function, and Lienard and Chipart theorem; furthermore, the basic reproductive number may not be able to deduce the stability of the system and a counterexample is given. Finally, the influence of different parameters on the spread of rumors is studied, and the validity of the theoretical results is verified.

Modeling the COVID-19 Epidemic With Multi-Population and Control Strategies in the United States

As of January 19, 2021, the cumulative number of people infected with coronavirus disease-2019 (COVID-19) in the United States has reached 24,433,486, and the number is still rising. The outbreak of the COVID-19 epidemic has not only affected the development of the global economy but also seriously threatened the lives and health of human beings around the world. According to the transmission characteristics of COVID-19 in the population, this study established a theoretical differential equation mathematical model, estimated model parameters through epidemiological data, obtained accurate mathematical models, and adopted global sensitivity analysis methods to screen sensitive parameters that significantly affect the development of the epidemic. Based on the established precise mathematical model, we calculate the basic reproductive number of the epidemic, evaluate the transmission capacity of the COVID-19 epidemic, and predict the development trend of the epidemic. By analyzing the sensitivity of parameters and finding sensitive parameters, we can provide effective control strategies for epidemic prevention and control. After appropriate modifications, the model can also be used for mathematical modeling of epidemics in other countries or other infectious diseases.

Understanding drivers of phylogenetic clustering and terminal branch lengths distribution in epidemics of Mycobacterium tuberculosis

Detecting factors associated with transmission is important to understand disease epidemics, and to design effective public health measures. Clustering and terminal branch lengths (TBL) analyses are commonly applied to genomic data sets of Mycobacterium tuberculosis (MTB) to identify sub-populations with increased transmission. Here, I used a simulation-based approach to investigate what epidemiological processes influence the results of clustering and TBL analyses, and whether difference in transmission can be detected with these methods. I simulated MTB epidemics with different dynamics (latency, infectious period, transmission rate, basic reproductive number R0, sampling proportion, and molecular clock), and found that all these factors, except the length of the infectious period and R0, affect the results of clustering and TBL distributions. I show that standard interpretations of this type of analyses ignore two main caveats: 1) clustering results and TBL depend on many factors that have nothing to do with transmission, 2) clustering results and TBL do not tell anything about whether the epidemic is stable, growing, or shrinking. An important consequence is that the optimal SNP threshold for clustering depends on the epidemiological conditions, and that sub-populations with different epidemiological characteristics should not be analyzed with the same threshold. Finally, these results suggest that different clustering rates and TBL distributions, that are found consistently between different MTB lineages, are probably due to intrinsic bacterial factors, and do not indicate necessarily differences in transmission or evolutionary success.

Transmission dynamic and backward bifurcation of Middle Eastern respiratory syndrome coronavirus

Middle East respiratory syndrome coronavirus (MERS-CoV) remains an emerging disease threat with regular human cases on the Arabian Peninsula driven by recurring camels to human transmission events. In this paper, we present a new deterministic model for the transmission dynamics of (MERS-CoV). In order to do this, we develop a model formulation and analyze the stability of the proposed model. The stability conditions are obtained in term of R0, we find those conditions for which the model become stable. We discuss basic reproductive number R0 along with sensitivity analysis to show the impact of every epidemic parameter. We show that the proposed model exhibits the phenomena of backward bifurcation. Finally, we show the numerical simulation of our proposed model for supporting our analytical work. The aim of this work is to show via mathematical model the transmission of MERS-CoV between humans and camels, which are suspected to be the primary source of infection.

The Transmission Dynamics of Hepatitis B Virus via the Fractional-Order Epidemiological Model

We investigate and analyze the dynamics of hepatitis B with various infection phases and multiple routes of transmission. We formulate the model and then fractionalize it using the concept of fractional calculus. For the purpose of fractionalizing, we use the Caputo–Fabrizio operator. Once we develop the model under consideration, existence and uniqueness analysis will be discussed. We use fixed point theory for the existence and uniqueness analysis. We also prove that the model under consideration possesses a bounded and positive solution. We then find the basic reproductive number to perform the steady-state analysis and to show that the fractional-order epidemiological model is locally and globally asymptotically stable under certain conditions. For the local and global analysis, we use linearization, mean value theorem, and fractional Barbalat’s lemma, respectively. Finally, we perform some numerical findings to support the analytical work with the help of graphical representations.

What is the impact of acquired immunity on the transmission of schistosomiasis and the efficacy of current and planned mass drug administration programmes?

Schistosomiasis causes severe morbidity in many countries with endemic infection with the schistosome digenean parasites in Africa and Asia. To control and eliminate the disease resulting from infection, regular mass drug administration (MDA) is used, with a focus on school-aged children (SAC; 5–14 years of age). In some high transmission settings, the World Health Organization (WHO) also recommends the inclusion of at-risk adults in MDA treatment programmes. The question of whether ecology (age-dependant exposure) or immunity (resistance to reinfection), or some combination of both, determines the form of observed convex age-intensity profile is still unresolved, but there is a growing body of evidence that the human hosts acquire some partial level of immunity after a long period of repeated exposure to infection. In the majority of past research modelling schistosome transmission and the impact of MDA programmes, the effect of acquired immunity has not been taken into account. Past work has been based on the assumption that age-related contact rates generate convex horizontal age-intensity profiles. In this paper, we use an individual based stochastic model of transmission and MDA impact to explore the effect of acquired immunity in defined MDA programmes. Compared with scenarios with no immunity, we find that acquired immunity makes the MDA programme less effective with a slower decrease in the prevalence of infection. Therefore, the time to achieve morbidity control and elimination as a public health problem is longer than predicted by models with just age-related exposure and no build-up of immunity. The level of impact depends on the baseline prevalence prior to treatment (the magnitude of the basic reproductive number R0) and the treatment frequency, among other factors. We find that immunity has a larger impact within moderate to high transmission settings such that it is very unlikely to achieve morbidity and transmission control employing current MDA programmes.

The Impact of Vaccination on Covid-19 Disease Transmission Patterns in a Human Population: A Theoretical Analysis

We construct a Mathematical model that describes the effect of vaccination on the dynamics of the transmission of COVID-19 disease in a human population. The model is a system of ordinary differential equations that describes the evolution of humans in a range of Covid-19 states due to emergence of an index case in a disease free region. The analysis of the model shows that effective vaccination can lead to disease eradication, where in the disease free state is locally asymptomatically stable if the basic reproductive number, and unstable when The numerical simulations suggests the use of other social measures alongside vaccination in order to avert the possibility of the disease becoming endemic.

Stability, Bifurcation, and a Pair of Conserved Quantities in a Simple Epidemic System with Reinfection for the Spread of Diseases Caused by Coronaviruses

In this paper, we study a modified SIRI model without vital dynamics, based on a system of nonlinear ordinary differential equations, for epidemics that exhibit partial immunity after infection, reinfection, and disease-induced death. This model can be applied to study epidemics caused by SARS-CoV, MERS-CoV, and SARS-CoV-2 coronaviruses, since there is the possibility that, in diseases caused by these pathogens, individuals recovered from the infection have a decrease in their immunity and can be reinfected. On the other hand, it is known that, in populations infected by these coronaviruses, individuals with comorbidities or older people have significant mortality rates or deaths induced by the disease. By means of qualitative methods, we prove that such system has an endemic equilibrium and an infinite line of nonhyperbolic disease-free equilibria, we determine the local and global stability of these equilibria, and we also show that it has no periodic orbits. Furthermore, we calculate the basic reproductive number R 0 and find that the system exhibits a forward bifurcation: disease-free equilibria are stable when R 0 < 1 / σ and unstable when R 0 > 1 / σ , while the endemic equilibrium consist of an asymptotically stable upper branch that appears from R 0 > 1 / σ , σ being the rate that quantifies reinfection. We also show that this system has two conserved quantities. Additionally, we show some of the most representative numerical solutions of this system.

Epidemic size, trend and spatiotemporal mapping of SARS-CoV-2 using geographical information system in Alborz Province, Iran

Background The first confirmed cases of COVID-19 in Iran were reported in Qom city. Subsequently, the neighboring provinces and gradually all 31 provinces of Iran were involved. This study aimed to investigate the case fatility rate, basic reproductive number in different period of epidemic, projection of daily and cumulative incidence cases and also spatiotemporal mapping of SARS-CoV-2 in Alborz province, Iran. Methods A confirmed case of COVID-19 infection was defined as a case with a positive result of viral nucleic acid testing in respiratory specimens. Serial interval (SI) was fitted by gamma distribution and considered the likelihood-based R0 using a branching process with Poisson likelihood. Seven days average of cases, deaths, doubling times and CFRs used to draw smooth charts. kernel density tool in Arc GIS (Esri) software has been employed to compute hot spot area of the study site. Results The maximum-likelihood value of R0 was 2.88 (95%, CI: 2.57–3.23) in the early 14 days of epidemic. The case fatility rate for Alborz province (Iran) on March 10, was 8.33% (95%, CI:6.3–11), and by April 20, it had an increasing trend and reached 12.9% (95%,CI:11.5–14.4). The doubling time has been increasing from about two days and then reached about 97 days on April 20, 2020, which shows the slowdown in the spread rate of the disease. Also, from March 26 to April 2, 2020 the whole Geographical area of Karj city was almost affected by SARS-CoV-2. Conclusions The R0 of COVID-19 in Alborz province was substantially high at the beginning of the epidemic, but with preventive measures and public education and GIS based monitoring of the cases,it has been reduced to 1.19 within two months. This reduction highpoints the attainment of preventive measures in place, however we must be ready for any second epidemic waves during the next months.