Troy Day, David A. Kennedy, Andrew F. Read, Sylvain Gandon
With the unprecedented global vaccination campaign against SARS-CoV-2 attention has now turned to the potential impact of this large-scale intervention on the evolution of the virus. In this perspective we summarize what is currently known about evolution in the context of vaccination from research on other pathogen species, with an eye towards the future evolution of SARS-CoV-2.
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In this paper, we carry out a computational study using the spectral decomposition of the fluctuations of a two-pathogen epidemic model around its deterministic attractor, i.e., steady state or limit cycle, to examine the role of partial vaccination and between-host pathogen interaction on early pathogen replacement during seasonal epidemics of influenza and respiratory syncytial virus.
The June software package is an open-source framework for the detailed simulation of epidemics based on social interactions in a virtual population reflecting age, gender, ethnicity, and socio-economic indicators in England. In this paper, we present a new version of the framework specifically adapted for Germany, which allows the simulation of the entire German population using publicly available information on households, schools, universities, workplaces, and mobility data for Germany. Moreover, JuneGermany incorporates testing and vaccination strategies within the population as well as the…
We investigate methods to vaccinate contact networks -- i.e. removing nodes in such a way that disease spreading is hindered as much as possible -- with respect to their cost-efficiency. Any real implementation of such protocols would come with costs related both to the vaccination itself, and gathering of information about the network. Disregarding this, we argue, would lead to erroneous evaluation of vaccination protocols. We use the susceptible-infected-recovered model -- the generic model for diseases making patients immune upon recovery -- as our disease-spreading scenario, and analyze ou…
We consider the $SEIRS$ epidemiology model with such features of the COVID-19 outbreak as: abundance of unidentified infected individuals, limited time of immunity and a possibility of vaccination. Within a compartmental realization of this model, we found the disease-free and the endemic stationary states. They exist in their respective restricted regions of the le via linear stability analysis. The expression for the basic reproductive number is obtained as well. The positions and heights of a first peak for the fractions of infected individuals are obtained numerically and are fitted to sim…
Social \textit{vs.} individual age-dependent costs of imperfect vaccination
本文研究不完美疫苗在年龄结构人群中的社会与个体成本，通过耦合病原体动态与理性智能体的模型，刻画了产生积极社会影响的参数区域并求得Nash均衡，最后探讨了促进自愿接种的集体策略。
Synthetic Wastewater Epidemiology Data Generation using Patterns-of-Life Simulation
该研究将生活模式模拟框架扩展为人类移动与行为模型，生成合成废水流行病学数据集，可支持多种公共卫生相关的受控实验，且框架可推广至具备OpenStreetMap信息的其他地区。
A Minimal Framework for Optimizing Vaccination Protocols Targeting Highly Mutable Pathogens
针对高突变病原体免疫难题，提出基于亲和力成熟最小化模型，利用平均场路径积分与算子近似确定时间依赖性疫苗的最优选择力，以最大化广谱中和抗体的产生。
The Impact of Neglecting Vaccine Unwillingness in Epidemiology Models
本研究探讨了在流行病学模型中忽视疫苗拒绝现象对模型结果的影响，并分析了如何通过调整疫苗接种率常数来减少误差。
When the body gets infected by a pathogen or receives a vaccine dose, the immune system develops pathogen-specific immunity. Induced immunity decays in time and years after recovery/vaccination the host might become susceptible again. Exposure to the pathogen in the environment boosts the immune system thus prolonging the duration of the protection. Such an interplay of within host and population level dynamics poses significant challenges in rigorous mathematical modeling of immuno-epidemiology. The aim of this paper is twofold. First, we provide an overview of existing models for waning of d…
Where Do We Poop? City-Wide Simulation of Defecation Behavior for Wastewater-Based Epidemiology
研究基于现有生活模式模型，引入地理空间模拟框架，结合传染病模型，考虑人口流动、厕所使用等因素，模拟废水病原体负荷时空动态，以佐治亚州富尔顿县为例进行研究，展示其对废水监测等方面的支持作用。
Complex networks describe a wide range of systems in nature and society. Frequently cited examples include Internet, WWW, a network of chemicals linked by chemical reactions, social relationship networks, citation networks, etc. The research of complex networks has attracted many scientists' attention. Physicists have shown that these networks exhibit some surprising characters, such as high clustering coefficient, small diameter, and the absence of the thresholds of percolation. Scientists in mathematical epidemiology discovered that the threshold of infectious disease disappears on contact n…
Modelling SARS-CoV-2 epidemics via compartmental and cellular automaton SEIRS model with temporal immunity and vaccination
本文研究了具有时间免疫力和疫苗接种的 SEIRS 模型，分析了流行病动态控制方法，并探讨了社会距离对疫情发展的影响。
The bacterium Group A Streptococcus (Streptococcus pyogenes, GAS) is a human-specific pathogen and a major cause of global morbidity and mortality. Despite decades of research our knowledge of GAS infection and immunity is incomplete, hampering vaccine design and other efforts to reduce disease prevalence. Epidemiological studies indicate positive associations between the prevalence of GAS-related disease, the diversity of circulating strains and the degree of poverty in host populations. However, the infection and immune mechanisms underlying these associations are not clear. In this work, we…
Mass-vaccination campaigns are an important strategy in the global fight against poliomyelitis and measles. The large-scale logistics required for these mass immunisation campaigns magnifies the need for research into the effectiveness and optimal deployment of pulse vaccination. In order to better understand this control strategy, we propose a mathematical model accounting for the disease dynamics in connected regions, incorporating seasonality, environmental reservoirs and independent periodic pulse vaccination schedules in each region. The effective reproduction number, $R_e$, is defined an…
Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees
本文提出在生存分析框架下开发算法，利用系统发育树与流行病学数据的一一对应关系枚举传播树，从而更高效地估计传染性风险比和基线风险，为分子传染病流行病学提供严谨灵活的统计基础。
Despite the availability of effective vaccines, the persistence of SARS-CoV-2 suggests that co-circulation with other pathogens and resulting multi-epidemics may become increasingly frequent. To better forecast and control the risk of such multi-epidemics, it is essential to elucidate the potential interactions of SARS-CoV-2 with other pathogens; these interactions, however, remain poorly defined. Here, we aimed to review the current body of evidence about SARS-CoV-2 interactions. To study pathogen interactions in a systematic way, we first developed a general framework to capture their major …
The COVID-19 pandemic has given rise to numerous articles from different scientific fields (epidemiology, virology, immunology, airflow physics...) without any effort to link these different insights. In this review, we aim to establish relationships between epidemiological data and the characteristics of the virus strain responsible for the epidemic wave concerned. We have carried out this study on the Wuhan, Alpha, Delta and Omicron strains allowing us to illustrate the evolution of the relationships we have highlighted according to these different viral strains. We addressed the following q…
COVID-19 in low-tolerance border quarantine systems: impact of the Delta variant of SARS-CoV-2
本研究建模评估边境检疫系统中疫苗接种对Delta变异株传播的影响，发现疫苗效力从70%升至90%可将疫情暴发时间延长两个数量级，需结合大规模接种以防疫情。
Global stability and uniform persistence in an epidemic model with saturating fomite-mediated transmission
本文研究了具有饱和媒介传播的SVEIR传染病模型的全局动态，通过分析控制基本再生数R_c和经典阈值条件R_c<1，探讨了疫苗接种和媒介传播对疾病消亡与持久性的影响。
Public Goods Games in Disease Evolution and Spread
本文以癌症演化与传染病传播为案例，回顾并比较公共品博弈在疾病建模中的应用，指出流行病学中的合作行为研究可借鉴至癌症决策，并展示其广泛适用性。
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