Infectious Disease Modelling最新文献

{"title":"Evolution into chaos – Implications of the trade-off between transmissibility and immune evasion","authors":"Golsa Sayyar ,&nbsp;Ábel Garab ,&nbsp;Gergely Röst","doi":"10.1016/j.idm.2025.04.003","DOIUrl":"10.1016/j.idm.2025.04.003","url":null,"abstract":"<div><div>Predicting viral evolution presents a significant challenge and is a critical public health priority. In response to this challenge, we develop a novel model for viral evolution that considers a trade-off between immunity evasion and transmissibility. The model selects for a new strain with the highest invasion fitness, taking into account this trade-off. When the dominant strain of the pathogen is highly transmissible, evolution tends to favor immune evasion, whereas for less contagious strains the direction of evolution leads toward increasing transmissibility. Assuming a linear functional form of this trade-off, we can express the long-term evolutionary patterns following the emergence of subsequent strains by a non-linear difference equation. We provide sufficient criteria for when evolution converges, and successive strains exhibit similar transmissibility. We also identify scenarios characterized by a two-periodic pattern in upcoming strains, indicating a situation where a highly transmissible but not immune-evasive strain is replaced by a less transmissible but highly immune-evasive strain, and vice versa, creating a cyclic pattern. Finally, we show that under certain conditions, viral evolution becomes chaotic and thus future transmissibilites become unpredictable in the long run. Visualization via bifurcation diagrams elucidates our analytical findings, revealing complex dynamic behaviors that include the presence of multiple periodic solutions and extend to chaotic regimes. Our analysis provides valuable insights into the complexities of viral evolution in the light of the trade-off between immune evasion and transmissibility.</div></div>","PeriodicalId":36831,"journal":{"name":"Infectious Disease Modelling","volume":"10 3","pages":"Pages 909-923"},"PeriodicalIF":8.8,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143851474","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Invariant set theory for predicting potential failure of antibiotic cycling","authors":"Alejandro Anderson ,&nbsp;Matthew W. Kinahan ,&nbsp;Alejandro H. Gonzalez ,&nbsp;Klas Udekwu ,&nbsp;Esteban A. Hernandez-Vargas","doi":"10.1016/j.idm.2025.04.001","DOIUrl":"10.1016/j.idm.2025.04.001","url":null,"abstract":"<div><div>Collateral sensitivity, where resistance to one drug confers heightened sensitivity to another, offers a promising strategy for combating antimicrobial resistance, yet predicting resultant evolutionary dynamics remains a significant challenge. We propose here a mathematical model that integrates fitness trade-offs and adaptive landscapes to predict the evolution of collateral sensitivity pathways, providing insights into optimizing sequential drug therapies.</div><div>Our approach embeds collateral information into a network of switched systems, allowing us to abstract the effects of sequential antibiotic exposure on antimicrobial resistance. We analyze the system stability at disease-free equilibrium and employ set-control theory to tailor therapeutic windows. Consequently, we propose a computational algorithm to identify effective sequential therapies to counter antibiotic resistance. By leveraging our theory with data on collateral sensivity interactions, we predict scenarios that may prevent bacterial escape for chronic <em>Pseudomonas aeruginosa</em> infections.</div></div>","PeriodicalId":36831,"journal":{"name":"Infectious Disease Modelling","volume":"10 3","pages":"Pages 897-908"},"PeriodicalIF":8.8,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143839190","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stochastic SIRS models on networks: mean and variance of infection","authors":"Tingting Chen ,&nbsp;Guirong Liu ,&nbsp;Zhen Jin","doi":"10.1016/j.idm.2025.03.008","DOIUrl":"10.1016/j.idm.2025.03.008","url":null,"abstract":"<div><div>Due to the heterogeneity of contact structure, it is more reasonable to model on networks for epidemics. Because of the stochastic nature of events and the discrete number of individuals, the spread of epidemics is more appropriately viewed as a Markov chain. Therefore, we establish stochastic SIRS models with vaccination on networks to study the mean and variance of the number of susceptible and infected individuals for large-scale populations. Using van Kampen's system-size expansion, we derive a high-dimensional deterministic system which describes the mean behaviour and a Fokker-Planck equation which characterizes the variance around deterministic trajectories. Utilizing the qualitative analysis technique and Lyapunov function, we demonstrate that the disease-free equilibrium of the deterministic system is globally asymptotically stable if the basic reproduction number <em>R</em>₀ &lt; 1; and the endemic equilibrium is globally asymptotically stable if <em>R</em>₀ &gt; 1. Through the analysis of the Fokker-Planck equation, we obtain the asymptotic expression for the variance of the number of susceptible and infected individuals around the endemic equilibrium, which can be approximated by the elements of principal diagonal of the solution of the corresponding Lyapunov equation. Here, the solution of Lyapunov equation is expressed by vectorization operator of matrices and Kronecker product. Finally, numerical simulations illustrate that vaccination can reduce infections and increase fluctuations of the number of infected individuals and show that individuals with greater degree are more easily infected.</div></div>","PeriodicalId":36831,"journal":{"name":"Infectious Disease Modelling","volume":"10 3","pages":"Pages 875-896"},"PeriodicalIF":8.8,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143844306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Real-time inference of the end of an outbreak: Temporally aggregated disease incidence data and under-reporting","authors":"I. Ogi-Gittins ,&nbsp;J. Polonsky ,&nbsp;M. Keita ,&nbsp;S. Ahuka-Mundeke ,&nbsp;W.S. Hart ,&nbsp;M.J. Plank ,&nbsp;B. Lambert ,&nbsp;E.M. Hill ,&nbsp;R.N. Thompson","doi":"10.1016/j.idm.2025.03.009","DOIUrl":"10.1016/j.idm.2025.03.009","url":null,"abstract":"<div><div>Professor Pierre Magal made important contributions to the field of mathematical biology before his death on February 20, 2024, including research in which epidemiological models were used to study the ends of infectious disease outbreaks. In related work, there has been interest in inferring (in real-time) when outbreaks have ended and control interventions can be relaxed. Here, we analyse data from the 2018 Ebola outbreak in Équateur Province, Democratic Republic of the Congo, during which an Ebola Response Team (ERT) was deployed to implement public health measures. We use a renewal equation transmission model to perform a <em>quasi</em> real-time investigation into when the ERT could be withdrawn safely at the tail end of the outbreak. Specifically, each week following the arrival of the ERT, we calculate the probability of future cases if the ERT is withdrawn. First, we show that similar estimates of the probability of future cases can be obtained from either daily or weekly case reports. This demonstrates that high temporal resolution case reporting may not always be necessary to determine when interventions can be relaxed. Second, we demonstrate how case under-reporting can be accounted for rigorously when estimating the probability of future cases. We find that, the lower the level of case reporting, the longer it is necessary to wait after the apparent final case before interventions can be removed safely (with only a small probability of additional cases). Finally, we show how uncertainty in the extent of case reporting can be included in estimates of the probability of future cases. Our research highlights the importance of accounting for under-reporting in deciding when to remove interventions at the tail ends of infectious disease outbreaks.</div></div>","PeriodicalId":36831,"journal":{"name":"Infectious Disease Modelling","volume":"10 3","pages":"Pages 935-945"},"PeriodicalIF":8.8,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143911693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamics of an epidemic controlled by isolation and quarantine: A probability-based deterministic model","authors":"David V. Kalbaugh","doi":"10.1016/j.idm.2025.03.007","DOIUrl":"10.1016/j.idm.2025.03.007","url":null,"abstract":"<div><div>Assuming a homogeneous population, we employ a deterministic model based on first principles of probability to explore dynamics of an epidemic controlled by isolation alone, quarantine alone, and the two together. We develop explicit closed-form equations for key metrics of control performance: cumulative fraction of population infected over the course of the epidemic (final size), maximum fraction infected at any one time, and epidemic duration. We derive an analytical solution for final size of an epidemic controlled by isolation, when final size is small, and develop empirical relations for the other cases. We frame equations in terms of reproduction numbers, measures of intervention effort and initial conditions. We model both strength and speed of interventions, assume second order gamma distributions for intervention waiting times and employ non-time-invariant equations for quarantine. We also account for quarantine of unexposed, susceptible individuals and for imperfect intervention.</div></div>","PeriodicalId":36831,"journal":{"name":"Infectious Disease Modelling","volume":"10 3","pages":"Pages 813-839"},"PeriodicalIF":8.8,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143820778","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Epidemiological indices with multiple circulating pathogen strains","authors":"Cristiano Trevisin ,&nbsp;Lorenzo Mari ,&nbsp;Marino Gatto ,&nbsp;Vittoria Colizza ,&nbsp;Andrea Rinaldo","doi":"10.1016/j.idm.2025.03.006","DOIUrl":"10.1016/j.idm.2025.03.006","url":null,"abstract":"<div><div>Epidemiological indicators (e.g. reproduction numbers and epidemicity indices) describe long- and short-term behaviour of ongoing epidemics. Their evolving values provide context for designing control measures because maintaining both indices below suitable thresholds warrants waning infection numbers. However, current models for the computation of epidemiological metrics do not consider the stratification of the pathogen into variants endowed with different infectivity and epidemiological severity. This is the case, in particular, with SARS-CoV-2 infections. Failing to account for the variety of epidemiological features of emerging variants prevents epidemiological indices from spotting the possible onset of uncontrolled growth of specific variants, thus significantly limiting the prognostic value of the indicators. Here, we expand an existing framework for the computation of spatially explicit reproduction numbers and epidemicity indices to account for arising variants. By analysing the data of the COVID-19 pandemic in Italy, we show that embedding additional layers of complexity in the mathematical descriptions of unfolding epidemics reveals new angles. In particular, we find epidemiological metrics significantly exceeding their thresholds at the emergence of new variants. Such values foresee a recrudescence in new infections that only becomes evident after emerging new variants have effectively replaced the previous active strains. The demography of the variant composition flags the presence of specific strains growing more rapidly than the total number of infections generated by all variants combined. Variant-aware epidemiological indicators thus allow to engineer better control measures tailored to the shifting patterns of severity and evolving features of infectious disease epidemics.</div></div>","PeriodicalId":36831,"journal":{"name":"Infectious Disease Modelling","volume":"10 3","pages":"Pages 802-812"},"PeriodicalIF":8.8,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143686190","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing the effectiveness of test-trace-isolate interventions using a multi-layered temporal network","authors":"Yunyi Cai ,&nbsp;Weiyi Wang ,&nbsp;Lanlan Yu ,&nbsp;Ruixiao Wang ,&nbsp;Gui-Quan Sun ,&nbsp;Allisandra G. Kummer ,&nbsp;Paulo C. Ventura ,&nbsp;Jiancheng Lv ,&nbsp;Marco Ajelli ,&nbsp;Quan-Hui Liu","doi":"10.1016/j.idm.2025.03.005","DOIUrl":"10.1016/j.idm.2025.03.005","url":null,"abstract":"<div><div>In the early stage of an infectious disease outbreak, public health strategies tend to gravitate towards non-pharmaceutical interventions (NPIs) given the time required to develop targeted treatments and vaccines. One of the most common NPIs is Test-Trace-Isolate (TTI). One of the factors determining the effectiveness of TTI is the ability to identify contacts of infected individuals. In this study, we propose a multi-layer temporal contact network to model transmission dynamics and assess the impact of different TTI implementations, using SARS-CoV-2 as a case study. The model was used to evaluate TTI effectiveness both in containing an outbreak and mitigating the impact of an epidemic. We estimated that a TTI strategy based on home isolation and testing of both primary and secondary contacts can contain outbreaks only when the reproduction number is up to 1.3, at which the epidemic prevention potential is 88.2% (95% CI: 87.9%–88.5%). On the other hand, for higher value of the reproduction number, TTI is estimated to noticeably mitigate disease burden but at high social costs (e.g., over a month in isolation/quarantine per person for reproduction numbers of 1.7 or higher). We estimated that strategies considering quarantine of contacts have a larger epidemic prevention potential than strategies that either avoid tracing contacts or require contacts to be tested before isolation. Combining TTI with other social distancing measures can improve the likelihood of successfully containing an outbreak but the estimated epidemic prevention potential remains lower than 50% for reproduction numbers higher than 2.1. In conclusion, our model-based evaluation highlights the challenges of relying on TTIs to contain an outbreak of a novel pathogen with characteristics similar to SARS-CoV-2, and that the estimated effectiveness of TTI depends on the way contact patterns are modeled, supporting the relevance of obtaining comprehensive data on human social interactions to improve preparedness.</div></div>","PeriodicalId":36831,"journal":{"name":"Infectious Disease Modelling","volume":"10 3","pages":"Pages 775-786"},"PeriodicalIF":8.8,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143654522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A refractory density approach to a multi-scale SEIRS epidemic model","authors":"Anton Chizhov ,&nbsp;Laurent Pujo-Menjouet ,&nbsp;Tilo Schwalger ,&nbsp;Mattia Sensi","doi":"10.1016/j.idm.2025.03.004","DOIUrl":"10.1016/j.idm.2025.03.004","url":null,"abstract":"<div><div>We propose a novel multi-scale modeling framework for infectious disease spreading, borrowing ideas and modeling tools from the so-called Refractory Density (RD) approach. We introduce a microscopic model that describes the probability of infection for a single individual and the evolution of the disease within their body. From the individual-level description, we then present the corresponding population-level model of epidemic spreading on the mesoscopic and macroscopic scale. We conclude with numerical illustrations, taking into account either a white Gaussian noise or an escape noise to showcase the potential of our approach in producing both transient and asymptotic complex dynamics as well as finite-size fluctuations consistently across multiple scales. A comparison with the epidemiology of coronaviruses is also given to corroborate the qualitative relevance of our new approach.</div></div>","PeriodicalId":36831,"journal":{"name":"Infectious Disease Modelling","volume":"10 3","pages":"Pages 787-801"},"PeriodicalIF":8.8,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143686191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The interaction between population age structure and policy interventions on the spread of COVID-19","authors":"Hao Yin ,&nbsp;Zhu Liu ,&nbsp;Daniel M. Kammen","doi":"10.1016/j.idm.2025.03.003","DOIUrl":"10.1016/j.idm.2025.03.003","url":null,"abstract":"<div><div>COVID-19 has triggered an unprecedented public health crisis and a global economic shock. As countries and cities have transitioned away from strict pandemic restrictions, the most effective reopening strategies may vary significantly based on their demographic characteristics and social contact patterns. In this study, we employed an extended age-specific compartment model that incorporates population mobility to investigate the interaction between population age structure and various containment interventions in New York, Los Angeles, Daegu, and Nairobi – four cities with distinct age distributions that served as local epicenters of the epidemic from January 2020 to March 2021. Our results demonstrated that individual social distancing or quarantine strategies alone cannot effectively curb the spread of infection over a one-year period. However, a combined strategy, including school closure, 50 % working from home, 50 % reduction in other mobility, 10 % quarantine rate, and city lockdown interventions, can effectively suppress the infection. Furthermore, our findings revealed that social-distancing policies exhibit strong age-specific effects, and age-targeted interventions can yield significant spillover benefits. Specifically, reducing contact rates among the population under 20 can prevent 14 %, 18 %, 56 %, and 99 % of infections across all age groups in New York, Los Angeles, Daegu, and Nairobi, respectively, surpassing the effectiveness of policies exclusively targeting adults over 60 years old. In particular, to protect the elderly, it is essential to reduce contacts between the younger population and people of all age groups, especially those over 60 years old. While an older population structure may escalate fatality risk, it might also decrease infection risk. Moreover, a higher basic reproduction number amplifies the impact of an older population structure on the fatality risk of the elderly. The considerable variations in susceptibility, severity, and mobility across age groups underscore the need for targeted interventions to effectively control the spread of COVID-19 and mitigate risks in future pandemics.</div></div>","PeriodicalId":36831,"journal":{"name":"Infectious Disease Modelling","volume":"10 3","pages":"Pages 758-774"},"PeriodicalIF":8.8,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143654521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Early prediction of the outbreak risk of dengue fever in Ba Ria-Vung Tau province, Vietnam: An analysis based on Google trends and statistical models","authors":"Dang Anh Tuan ,&nbsp;Pham Vu Nhat Uyen","doi":"10.1016/j.idm.2025.03.001","DOIUrl":"10.1016/j.idm.2025.03.001","url":null,"abstract":"<div><div>Dengue fever (DF), caused by the Dengue virus through the Aedes mosquito vector, is a dangerous infectious disease with the potential to become a global epidemic. Vietnam, particularly Ba Ria-Vung Tau (BRVT) province, is facing a high risk of DF. This study aims to determine the relationship between the search volume for DF on Google Trends and DF cases in BRVT province, thereby constructing a model to predict the early outbreak risk of DF locally. Using Poisson regression (adjusted by quasi-Poisson), considering the lagged effect of Google Trends Index (GTI) search volume on DF cases, and removing the autocorrelation (AC) of DF cases by using appropriate transformations, seven forecast models were surveyed based on the dataset of DF cases and GTI search volume weekly with the phrase \"sốt xuất huyết\" (dengue fever) in BRVT province from January 2019 to August 2023 (243 weeks). The model selected is the one with the lowest dispersion index. The results show that the correlation coefficient (95% confidence interval) and dispersion index of the 7 models including Basis TSR; Basis TSR + AC: Lag(Residuals,1); Basis TSR + AC: Lag(SXH,1); Basis TSR + AC: Lag(log(SXH+1),1); TSR Lag(GTI,2) + AC: Lag(log(SXH+1),2); TSR Lag(GTI,3) + AC: Lag(log(SXH+1),3); TSR Lag(GTI,0) + AC: Lag(log(SXH+1),1) are 0.71 (0.63–0.76) and 74.2; 0.79 (0.73–0.83) and 48.6; 0.89 (0.87–0.92) and 37.3; 0.98 (0.97–0.99) and 7.2; 0.96 (0.95–0.97) and 14.3; 0.93 (0.91–0.94) and 25.7; 0.98 (0.97–0.99) and 6.8, respectively. Therefore, the final model is the most suitable one selected. Testing the accuracy of the selected model using the ROC curve with the Youden criterion, the AUC (threshold 75%) is 0.982, and the AUC (threshold 95%) is 0.984, indicating the very good predictive ability of the model. In summary, the research results show the potential for applying this model in Vietnam, especially in BRVT, to enhance the effectiveness of epidemic prevention measures and protect public health.</div></div>","PeriodicalId":36831,"journal":{"name":"Infectious Disease Modelling","volume":"10 3","pages":"Pages 743-757"},"PeriodicalIF":8.8,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143631905","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}