Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Many models for the spread of infectious diseases in populations have been analyzed mathematically and applied to specific diseases. Threshold theorems involving the basic reproduction number $R_{0}$, the contact number $\sigma$, and the replacement number $R$ are reviewed for the classic SIR epidemic and endemic models. Similar results with new expressions for $R_{0}$ are obtained for MSEIR and SEIR endemic models with either continuous age or age groups. Values of $R_{0}$ and $\sigma$ are estimated for various diseases including measles in Niger and pertussis in the United States. Previous models with age structure, heterogeneity, and spatial structure are surveyed.

https://epubs.siam.org/doi/pdf/10.1137/S0036144500371907

The Mathematics of Infectious Diseases

Summary Background Since December, 2019, Wuhan, China, has experienced an outbreak of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Epidemiological and clinical characteristics of patients with COVID-19 have been reported but risk factors for mortality and a detailed clinical course of illness, including viral shedding, have not been well described. Methods In this retrospective, multicentre cohort study, we included all adult inpatients (≥18 years old) with laboratory-confirmed COVID-19 from Jinyintan Hospital and Wuhan Pulmonary Hospital (Wuhan, China) who had been discharged or had died by Jan 31, 2020. Demographic, clinical, treatment, and laboratory data, including serial samples for viral RNA detection, were extracted from electronic medical records and compared between survivors and non-survivors. We used univariable and multivariable logistic regression methods to explore the risk factors associated with in-hospital death. Findings 191 patients (135 from Jinyintan Hospital and 56 from Wuhan Pulmonary Hospital) were included in this study, of whom 137 were discharged and 54 died in hospital. 91 (48%) patients had a comorbidity, with hypertension being the most common (58 [30%] patients), followed by diabetes (36 [19%] patients) and coronary heart disease (15 [8%] patients). Multivariable regression showed increasing odds of in-hospital death associated with older age (odds ratio 1·10, 95% CI 1·03–1·17, per year increase; p=0·0043), higher Sequential Organ Failure Assessment (SOFA) score (5·65, 2·61–12·23; p Interpretation The potential risk factors of older age, high SOFA score, and d-dimer greater than 1 μg/mL could help clinicians to identify patients with poor prognosis at an early stage. Prolonged viral shedding provides the rationale for a strategy of isolation of infected patients and optimal antiviral interventions in the future. Funding Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences; National Science Grant for Distinguished Young Scholars; National Key Research and Development Program of China; The Beijing Science and Technology Project; and Major Projects of National Science and Technology on New Drug Creation and Development.

Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study

Complex networks arise in a wide range of biological and sociotechnical systems. Epidemic spreading is central to our understanding of dynamical processes in complex networks, and is of interest to physicists, mathematicians, epidemiologists, and computer and social scientists. This review presents the main results and paradigmatic models in infectious disease modeling and generalized social contagion processes.

Epidemic processes in complex networks

https://deim.urv.cat/~alexandre.arenas/publicacions/pdf/review.pdf

Synchronization in complex networks

/pdf/correction-appropriate-models-for-the-management-of-4933gcwygb.pdf

Correction: Appropriate Models for the Management of Infectious Diseases

Understanding the mechanisms that generate oscillations in the incidence of childhood infectious diseases has preoccupied epidemiologists and population ecologists for nearly two centuries. This body of work has generated simple yet powerful explanations for the epidemics of measles and chickenpox, while the dynamics of other infectious diseases, such as whooping cough, have proved more challenging to decipher. A number of authors have, in recent years, proposed that the noisy and somewhat irregular epidemics of whooping cough may arise due to stochasticity and its interaction with nonlinearity in transmission and seasonal variation in contact rates. The reason underlying the susceptibility of whooping cough dynamics to noise and the precise nature of its transient dynamics remain poorly understood. Here we use household data on the incubation period in order to parametrize more realistic distributions of the latent and infectious periods. We demonstrate that previously reported phenomena result from transients following the interaction between the stable annual attractor and unstable multiennial solutions.

/pdf/noise-nonlinearity-and-seasonality-the-epidemics-of-whooping-37ubzewm3u.pdf

Noise, nonlinearity and seasonality: the epidemics of whooping cough revisited.

Recent studies of host-parasitoid metapopulations have shown how uniform dispersal, from a patch to its neighbouring patches, can result in the persistence of an otherwise non-persistent interaction. Here these models are extended to include density-dependent parasitoid aggregation. The fraction of dispersing hosts colonize the neighbouring patches equally, whereas parasitoid dispersal is related to the relative density of healthy hosts in each surrounding patch. Interestingly, this shows that the degree of parasitoid aggregation is associated with the self-organization of spatial structures and, in particular, spiral waves. Regions where spirals are most pronounced correspond to minimal variance in population densities. It is demonstrated, however, that parasitoid searching efficiency is highest (and mean host densities lowest) for levels of aggregation where the spatial dynamics consist of an even mixture of spirals and disordered patterns. Using an algorithmic complexity measure, it is verified that spatial transitions are also reflected in the temporal dynamics. Finally, it is demonstrated that multiple episodes of parasitoid dispersal, within a host generation, can inhibit persistence, particularly for large parasitoid movement rates.

Host―parasitoid metapopulations : the consequences of parasitoid aggregation on spatial dynamics and searching efficiency

Summary 1. The development of transgenic technologies, coupled with sterile insect techniques (SIT), is being explored in relation to new approaches for the biological control of insect pests. Recent studies have shown that there are often fitness costs associated with transgenic insect strains, but the impact of these costs on their potential use in pest control is poorly understood. 2. In this paper, we explore the impact of an insect fitness cost on two control strategies (classical SIT and transgenic late-acting bisex lethality) using a stage-structured mathematical model, which is parameterized for the mosquito Aedes aegypti. Counter to the majority of studies, we use realistic pulsed release strategies and incorporate a fitness cost, which is manifested as a reduction in male mating competitiveness. 3. For both models we show that the level of control of a pest mosquito population is highly sensitive to the rate at which the transgenic or sterile males are released. Population control is more effective when smaller numbers of sterile/transgenic males are released more frequently than larger and less frequent releases. 4. If the wild-type mosquito population exhibits cycles of peaks and troughs in abundance, as is the case for many insect species, then high frequency releases of transgenic males not only reduce mosquito abundance, but they may dampen future pest outbreaks, whereas the use of SIT alone may have an adverse effect, causing an increase in mosquito abundance. Additionally, the timing of sterile/transgenic male release during the mosquito population cycle is critical in reducing pest outbreak levels. 5. In all cases, the reduced fitness of the sterile/transgenic males causes reductions in control, thus requiring more frequent or greater magnitude releases. 6. Synthesis and applications. The sterile insect technique is considered to be a valuable non-chemical tool for pest management. With the potential application of recent genetic developments to enhance the technique, it is becoming increasingly important to consider the wider ecological implications of this biological control strategy. Predicting the most efficient release strategies will be important in combating pest and vector insects as well as for limiting potential broader ecological effects. Although the focus of our models are based on the mosquito, A. aegypti, which can spread yellow fever, dengue fever and Chikungunya disease, our modelling approach and results can be applied more broadly to other species.

https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2664.2010.01880.x

Modelling pulsed releases for sterile insect techniques: fitness costs of sterile and transgenic males and the effects on mosquito dynamics

N, +, = N,(1 + aN,). eqn 1 Here N is the population density in successive generations, t and t+ 1, A is the finite rate of increase of the population, and a and # are constants defining the density-dependent survival. The stability properties of this model hinge solely on A and ft, as shown in Fig. 1 a. Bascompte & Sole (henceforth referred to as 'B&S') applied this model to a grid or array of local populations which they linked with dispersal to four nearest neighbours, with the aim of exploring how such spatial structure affects the population dynamics. Using the Coupled Map Lattice formalism (Kaneko 1993), they express their model as:

Pejman Rohani

Papers

Correction: Appropriate Models for the Management of Infectious Diseases

Noise, nonlinearity and seasonality: the epidemics of whooping cough revisited.

Host―parasitoid metapopulations : the consequences of parasitoid aggregation on spatial dynamics and searching efficiency

Modelling pulsed releases for sterile insect techniques: fitness costs of sterile and transgenic males and the effects on mosquito dynamics

Appropriate formulations for dispersal in spatially structured models: Comments on Bascompte & Sole