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

Core pertussis transmission groups in England and Wales: A tale of two eras.

Understanding the determinants of polio transmission and its large-scale epidemiology remains a public health priority. Despite a 99% reduction in annual wild poliovirus (WPV) cases since 1988, tackling the last 1% has proven difficult. We identified key covariates of geographical variation in polio transmission patterns by relating country-specific annual disease incidence to demographic, socio-economic and environmental factors. We assessed the relative contributions of these variables to the performance of computer-generated models for predicting polio transmission. We also examined the effect of spatial coupling on the polio extinction frequency in islands relative to larger land masses. Access to sanitation, population density, forest cover and routine vaccination coverage were the strongest predictors of polio incidence, however their relative effect sizes were inconsistent geographically. The effect of climate variables on polio incidence was negligible, indicating that a climate effect is not identifiable at the annual scale, suggesting a role for climate in shaping the transmission seasonality rather than intensity. We found polio fadeout frequency to depend on both population size and demography, which should therefore be considered in policies aimed at extinction. Our comparative epidemiological approach highlights the heterogeneity among polio transmission determinants. Recognition of this variation is important for the maintenance of population immunity in a post-polio era.

/pdf/comparative-epidemiology-of-poliovirus-transmission-3rq61xe3ln.pdf

Comparative epidemiology of poliovirus transmission.

Despite advances in sanitation and immunization, vaccine-preventable diseases remain a significant cause of morbidity and mortality worldwide. In high-income countries such as the United States, coverage rates for vaccination against childhood infections remains high. However, the phenomenon of vaccine hesitancy makes maintenance of herd immunity difficult, impeding global disease eradication efforts. Reaching the ‘last mile’ will require early detection of vaccine hesitancy (driven by philosophical or religious choices), identifying pockets of susceptibility due to underimmunization (driven by vaccine unavailability, costs ineligibility), determining the factors associated with the behavior and developing targeted strategies to ameliorate the concerns. Towards this goal, we harness high-resolution medical claims data to geographically localize vaccine refusal and underimmunization (collectively, ‘underutilization’) in the United States and identify the socio-economic determinants of the behaviors. Our study represents the first large-scale effort for vaccination behavior surveillance and has the potential to aid in the development of targeted public health strategies for optimizing vaccine uptake.

https://www.biorxiv.org/content/biorxiv/early/2017/03/03/113043.full.pdf

Assessing the distribution and determinants of vaccine underutilization in the United States

There is evidence of inconsistency in sequelae of exclusive enteral nutrition (EEN) as induction therapy in paediatric patients with Crohn's disease (CD).

Meta‐analysis: efficacy of exclusive enteral nutrition as induction therapy on disease activity index, inflammation and growth factors in paediatric Crohn’s disease

Pejman Rohani

Papers

Core pertussis transmission groups in England and Wales: A tale of two eras.

Comparative epidemiology of poliovirus transmission.

Assessing the distribution and determinants of vaccine underutilization in the United States

Meta‐analysis: efficacy of exclusive enteral nutrition as induction therapy on disease activity index, inflammation and growth factors in paediatric Crohn’s disease

Chaos in a cup of flour.