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Our review found the effective reproduction number and basic reproduction number of the Omicron variant elicited 3.8 and 2.5 times higher transmissibility than the Delta variant, respectively. The Omicron variant has an average basic and effective reproduction number of 8.2 and 3.6.

Since the first confirmation of African swine fever (ASF) in domestic pig farms in South Korea in September 2019, ASF continues to expand and most notifications have been reported in wild boar populations. In this study, we first performed a spatio-temporal cluster analysis to understand ASF spread in wild boar. Secondly, generalized linear logistic regression (GLLR) model analysis was performed to identify environmental factors contributing to cluster formation. In the meantime, the basic reproduction number (R0) for each cluster was estimated to understand the growth of the epidemic. The cluster analysis resulted in the detection of 17 spatio-temporal clusters. The GLLR model analysis identified factors influencing cluster formation and indicated the possibility of estimating ASF epidemic areas based on environmental conditions. In a scenario only considering direct transmission among wild boar, R0 ranged from 1.01 to 1.5 with an average of 1.10, while, in another scenario including indirect transmission via an infected carcass, R0 ranged from 1.03 to 4.38 with an average of 1.56. We identified factors influencing ASF expansion based on spatio-temporal clusters. The results obtained would be useful for selecting priority areas for ASF control and would greatly assist in identifying efficient vaccination areas in the future.

Digital contact tracing is a relevant tool to control infectious disease outbreaks, including the COVID-19 epidemic. Early work evaluating digital contact tracing omitted important features and heterogeneities of real-world contact patterns influencing contagion dynamics. We fill this gap with a modeling framework informed by empirical high-resolution contact data to analyze the impact of digital contact tracing in the COVID-19 pandemic. We investigate how well contact tracing apps, coupled with the quarantine of identified contacts, can mitigate the spread in real environments. We find that restrictive policies are more effective in containing the epidemic but come at the cost of unnecessary large-scale quarantines. Policy evaluation through their efficiency and cost results in optimized solutions which only consider contacts longer than 15–20 minutes and closer than 2–3 meters to be at risk. Our results show that isolation and tracing can help control re-emerging outbreaks when some conditions are met: (i) a reduction of the reproductive number through masks and physical distance; (ii) a low-delay isolation of infected individuals; (iii) a high compliance. Finally, we observe the inefficacy of a less privacy-preserving tracing involving second order contacts. Our results may inform digital contact tracing efforts currently being implemented across several countries worldwide. Digital contact tracing is increasingly considered as one of the tools to control infectious disease outbreaks, in particular the COVID-19 epidemic. Here, the authors present a modeling framework informed by empirical high-resolution contact data to analyze the impact of digital contact tracing apps.

We construct a recursive Bayesian smoother, termed EpiFilter, for estimating the effective reproduction number, R, from the incidence of an infectious disease in real time and retrospectively. Our approach borrows from Kalman filtering theory, is quick and easy to compute, generalisable, deterministic and unlike many current methods, requires no change-point or window size assumptions. We model R as a flexible, hidden Markov state process and exactly solve forward-backward algorithms, to derive R estimates that incorporate all available incidence information. This unifies and extends two popular methods, EpiEstim, which considers past incidence, and the Wallinga-Teunis method, which looks forward in time. We find that this combination of maximising information and minimising assumptions significantly reduces the bias and variance of R estimates. Moreover, these properties make EpiFilter more statistically robust in periods of low incidence, where several existing methods can become destabilised. As a result, EpiFilter offers improved inference of time-varying transmission patterns that are advantageous for assessing the risk of upcoming waves of infection or the influence of interventions, in real time and at various spatial scales.

The role of school-based contacts in the epidemiology of SARS-CoV-2 is incompletely understood. We use an age-structured transmission model fitted to age-specific seroprevalence and hospital admission data to assess the effects of school-based measures at different time points during the COVID-19 pandemic in the Netherlands. Our analyses suggest that the impact of measures reducing school-based contacts depends on the remaining opportunities to reduce non-school-based contacts. If opportunities to reduce the effective reproduction number ( R e ) with non-school-based measures are exhausted or undesired and R e is still close to 1, the additional benefit of school-based measures may be considerable, particularly among older school children. As two examples, we demonstrate that keeping schools closed after the summer holidays in 2020, in the absence of other measures, would not have prevented the second pandemic wave in autumn 2020 but closing schools in November 2020 could have reduced R e below 1, with unchanged non-school-based contacts. The role of school-based contacts in the epidemiology of SARS-CoV-2 is incompletely understood. Here, the authors use an age-structured transmission model fitted to age-specific seroprevalence and hospital admission data to assess the effects of school-based measures during the COVID-19 pandemic in the Netherlands.

In this paper, a reaction–diffusion system is proposed to model the spatial spreading of West Nile virus in vector mosquitoes and host birds in North America. Transmission dynamics are based on a simplified model involving mosquitoes and birds, and the free boundary is introduced to model and explore the expanding front of the infected region. The spatial-temporal risk index R 0 F ( t ) , which involves regional characteristic and time, is defined for the simplified reaction–diffusion model with the free boundary to compare with other related threshold values, including the usual basic reproduction number R 0 . Sufficient conditions for the virus to vanish or to spread are given. Our results suggest that the virus will be in a scenario of vanishing if R 0 ≤ 1 , and will spread to the whole region if R 0 F ( t 0 ) ≥ 1 for some t 0 ≥ 0 , while if R 0 F ( 0 ) < 1 < R 0 , the spreading or vanishing of the virus depends on the initial number of infected individuals, the area of the infected region, the diffusion rate and other factors. Moreover, some remarks on the basic reproduction numbers and the spreading speeds are presented and compared.

In this paper, we propose a time-periodic reaction–diffusion model which incorporates seasonality, spatial heterogeneity and the extrinsic incubation period (EIP) of the parasite. The basic reproduction number R0 is derived, and it is shown that the disease-free periodic solution is globally attractive if R0<1, while there is an endemic periodic solution and the disease is uniformly persistent if R0>1. Numerical simulations indicate that prolonging the EIP may be helpful in the disease control, while spatial heterogeneity of the disease transmission coefficient may increase the disease burden.

Host heterogeneity can be modeled by using multi-group structures in the population. In this paper we investigate the existence and nonexistence of traveling waves of a two-group SIR epidemic model with time delay and constant recruitment and show that the existence of traveling waves is determined by the basic reproduction number \\[R_{0}.\\] More specifically, we prove that (i) when the basic reproduction number \\[R_{0}>1,\\] there exists a minimal wave speed \\[c^*>0,\\] such that for each \\[c \\ge c^*\\] the system admits a nontrivial traveling wave solution with wave speed c and for \\[c

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