Infectious Disease Modelling最新文献

{"title":"Mathematical assessment of the roles of age heterogeneity and vaccination on the dynamics and control of SARS-CoV-2","authors":"Binod Pant ,&nbsp;Abba B. Gumel","doi":"10.1016/j.idm.2024.04.007","DOIUrl":"https://doi.org/10.1016/j.idm.2024.04.007","url":null,"abstract":"<div><p>The COVID-19 pandemic, caused by SARS-CoV-2, disproportionately affected certain segments of society, particularly the elderly population (which suffered the brunt of the burden of the pandemic in terms of severity of the disease, hospitalization, and death). This study presents a generalized multigroup model, with <em>m</em> heterogeneous sub-populations, to assess the population-level impact of age heterogeneity and vaccination on the transmission dynamics and control of the SARS-CoV-2 pandemic in the United States. Rigorous analysis of the model for the homogeneous case (i.e., the model with <em>m</em> = 1) reveal that its disease-free equilibrium is globally-asymptotically stable for two special cases (with perfect vaccine efficacy or negligible disease-induced mortality) whenever the associated reproduction number is less than one. The model has a unique and globally-asymptotically stable endemic equilibrium, for special a case, when the associated reproduction threshold exceeds one. The homogeneous model was fitted using the observed cumulative mortality data for the United States during three distinct waves (Waves A (October 17, 2020 to April 5, 2021), B (July 9, 2021 to November 7, 2021) and C (January 1, 2022 to May 7, 2022)) chosen to align with time periods when the Alpha, Delta and Omicron were, respectively, the predominant variants in the United States. The calibrated model was used to derive a theoretical expression for achieving vaccine-derived herd immunity (needed to eliminate the disease in the United States). It was shown that, using the one-group homogeneous model, vaccine-derived herd immunity is not attainable during Wave C of the pandemic in the United States, regardless of the coverage level of the fully-vaccinated individuals. Global sensitivity analysis was carried out to determine the parameters of the model that have the most influence on the disease dynamics and burden. These analyses reveal that control and mitigation strategies that may be very effective during one wave may not be so very effective during the other wave or waves. However, strategies that target asymptomatic and pre-symptomatic infectious individuals are shown to be consistently effective across all waves. To study the impact of the disproportionate effect of COVID-19 on the elderly population, we considered the heterogeneous model for the case where the total population is subdivided into the sub-populations of individuals under 65 years of age and those that are 65 and older. The resulting two-group heterogeneous model, which was also fitted using the cumulative mortality data for wave C, was also rigorously analysed. Unlike for the case of the one-group model, it was shown, for the two-group model, that vaccine-derived herd immunity can indeed be achieved during Wave C of the pandemic if at least 61% of the populace is fully vaccinated. Thus, this study shows that adding age heterogeneity into a SARS-CoV-2 vaccination model with homogeneo","PeriodicalId":36831,"journal":{"name":"Infectious Disease Modelling","volume":"9 3","pages":"Pages 828-874"},"PeriodicalIF":8.8,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2468042724000617/pdfft?md5=4173f89027009f57f890dc1c2d8b19df&pid=1-s2.0-S2468042724000617-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140822617","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":"Mathematical modeling for estimating influenza vaccine efficacy: A case study of the Valencian Community, Spain.","authors":"Carlos Andreu-Vilarroig ,&nbsp;Rafael J. Villanueva ,&nbsp;Gilberto González-Parra","doi":"10.1016/j.idm.2024.04.006","DOIUrl":"https://doi.org/10.1016/j.idm.2024.04.006","url":null,"abstract":"<div><p>Vaccine efficacy and its quantification is a crucial concept for the proper design of public health vaccination policies. In this work we proposed a mathematical model to estimate the efficacy of the influenza vaccine in a real-word scenario. In particular, our model is a SEIR-type epidemiological model, which distinguishes vaccinated and unvaccinated populations. Mathematically, its dynamics is governed by a nonlinear system of ordinary differential equations, where the non-linearity arises from the effective contacts between susceptible and infected individuals. Two key aspects of this study is that we use a vaccine distribution over time that is based on real data specific to the elderly people in the Valencian Community and the calibration process takes into account that over one influenza season a specific proportion of the population becomes infected with influenza. To consider the effectiveness of the vaccine, the model incorporates a parameter, the vaccine attenuation factor, which is related with the vaccine efficacy against the influenza virus. With this framework, in order to calibrate the model parameters and to obtain an influenza vaccine efficacy estimation, we considered the 2016–2017 influenza season in the Valencian Community, Spain, using the influenza reported cases of vaccinated and unvaccinated. In order to ensure the model identifiability, we choose to deterministically calibrate the parameters for different scenarios and we find the one with the minimum error in order to determine the vaccine efficacy. The calibration results suggest that the influenza vaccine developed for 2016–2017 influenza season has an efficacy of approximately 76.7%, and that the risk of becoming infected is five times higher for an unvaccinated individual in comparison with a vaccinated one. This estimation partially agrees with some previous studies related to the influenza vaccine. This study presents a new integrated mathematical approach to study the influenza vaccine efficacy and gives further insight into this important public health topic.</p></div>","PeriodicalId":36831,"journal":{"name":"Infectious Disease Modelling","volume":"9 3","pages":"Pages 744-762"},"PeriodicalIF":8.8,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2468042724000605/pdfft?md5=8fc1d6caf8b368db5d3314fc89bd250c&pid=1-s2.0-S2468042724000605-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140639152","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":"An SEIHR model with age group and social contact for analysis of Fuzhou COVID-19 large wave","authors":"Xiaomin Lan ,&nbsp;Guangmin Chen ,&nbsp;Ruiyang Zhou ,&nbsp;Kuicheng Zheng ,&nbsp;Shaojian Cai ,&nbsp;Fengying Wei ,&nbsp;Zhen Jin ,&nbsp;Xuerong Mao","doi":"10.1016/j.idm.2024.04.003","DOIUrl":"https://doi.org/10.1016/j.idm.2024.04.003","url":null,"abstract":"<div><h3>Background</h3><p>The structure of age groups and social contacts of the total population influenced infection scales and hospital-bed requirements, especially influenced severe infections and deaths during the global prevalence of COVID-19. Before the end of the year 2022, Chinese government implemented the national vaccination and had built the herd immunity cross the country, and announced Twenty Measures (November 11) and Ten New Measures (December 7) for further modifications of dynamic zero-COVID polity on the Chinese mainland. With the nation-wide vaccination and modified measures background, Fuzhou COVID-19 large wave (November 19, 2022–February 9, 2023) led by Omicron BA.5.2 variant was recorded and prevailed for three months in Fujian Province.</p></div><div><h3>Methods</h3><p>A multi-age groups susceptible-exposed-infected-hospitalized-recovered (SEIHR) COVID-19 model with social contacts was proposed in this study. The main object was to evaluate the impacts of age groups and social contacts of the total population. The idea of Least Squares method was governed to perform the data fittings of four age groups against the surveillance data from Fujian Provincial Center for Disease Control and Prevention (Fujian CDC). The next generation matrix method was used to compute basic reproduction number for the total population and for the specific age group. The tendencies of effective reproduction number of four age groups were plotted by using the Epiestim R package and the SEIHR model for in-depth discussions. The sensitivity analysis by using sensitivity index and partial rank correlation coefficients values (PRCC values) were operated to reveal the differences of age groups against the main parameters.</p></div><div><h3>Results</h3><p>The main epidemiological features such as basic reproduction number, effective reproduction number and sensitivity analysis were extensively discussed for multi-age groups SEIHR model in this study. Firstly, by using of the next generation matrix method, basic reproduction number <em>R</em>₀ of the total population was estimated as 1.57 using parameter values of four age groups of Fuzhou COVID-19 large wave. Given age group <em>k</em>, the values of <em>R</em>_0<em>k</em> (age group <em>k</em> to age group <em>k</em>), the values of <span><math><msubsup><mrow><mi>R</mi></mrow><mrow><mn>0</mn></mrow><mrow><mi>k</mi></mrow></msubsup></math></span> (an infected of age group <em>k</em> to the total population) and the values of <span><math><msubsup><mrow><mover><mrow><mi>R</mi></mrow><mo>^</mo></mover></mrow><mrow><mn>0</mn></mrow><mrow><mi>k</mi></mrow></msubsup></math></span> (an infected of the total population to age group <em>k</em>) were also estimated, in which the explorations of the impacts of age groups revealed that the relationship <span><math><msubsup><mrow><mi>R</mi></mrow><mrow><mn>0</mn></mrow><mrow><mi>k</mi></mrow></msubsup><mo>&gt;</mo><msub><mrow><mi>R</mi></mrow","PeriodicalId":36831,"journal":{"name":"Infectious Disease Modelling","volume":"9 3","pages":"Pages 728-743"},"PeriodicalIF":8.8,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2468042724000575/pdfft?md5=67edae2dc28cb9d838a6fe0d0a2ad7a2&pid=1-s2.0-S2468042724000575-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140632680","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 compartment and metapopulation model of Rocky Mountain spotted fever in southwestern United States and northern Mexico","authors":"Laura Backus ,&nbsp;Patrick Foley ,&nbsp;Janet Foley","doi":"10.1016/j.idm.2024.04.008","DOIUrl":"https://doi.org/10.1016/j.idm.2024.04.008","url":null,"abstract":"<div><p>Rocky Mountain spotted fever (RMSF) is a fatal tick-borne zoonotic disease that has emerged as an epidemic in western North America since the turn of the 21st century. Along the US south-western border and across northern Mexico, the brown dog tick, <em>Rhipicephalus sanguineus</em>, is responsible for spreading the disease between dogs and humans. The widespread nature of the disease and the ongoing epidemics contrast with historically sporadic patterns of the disease. Because dogs are amplifying hosts for the <em>Rickettsia rickettsii</em> bacteria, transmission dynamics between dogs and ticks are critical for understanding the epidemic. In this paper, we developed a compartment metapopulation model and used it to explore the dynamics and drivers of RMSF in dogs and brown dog ticks in a theoretical region in western North America. We discovered that there is an extended lag—as much as two years—between introduction of the pathogen to a naïve population and epidemic-level transmission, suggesting that infected ticks could disseminate extensively before disease is detected. A single large city-size population of dogs was sufficient to maintain the disease over a decade and serve as a source for disease in surrounding smaller towns. This model is a novel tool that can be used to identify high risk areas and key intervention points for epidemic RMSF spread by brown dog ticks.</p></div>","PeriodicalId":36831,"journal":{"name":"Infectious Disease Modelling","volume":"9 3","pages":"Pages 713-727"},"PeriodicalIF":8.8,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2468042724000629/pdfft?md5=edc37dd0327abb5221f25a23c1b12c3c&pid=1-s2.0-S2468042724000629-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140622438","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":"Integrating immunoinformatics and computational epitope prediction for a vaccine candidate against respiratory syncytial virus","authors":"Truc Ly Nguyen ,&nbsp;Heebal Kim","doi":"10.1016/j.idm.2024.04.005","DOIUrl":"https://doi.org/10.1016/j.idm.2024.04.005","url":null,"abstract":"<div><p>Respiratory syncytial virus (RSV) poses a significant global health threat, especially affecting infants and the elderly. Addressing this, the present study proposes an innovative approach to vaccine design, utilizing immunoinformatics and computational strategies. We analyzed RSV's structural proteins across both subtypes A and B, identifying potential helper T lymphocyte, cytotoxic T lymphocyte, and linear B lymphocyte epitopes. Criteria such as antigenicity, allergenicity, toxicity, and cytokine-inducing potential were rigorously examined. Additionally, we evaluated the conservancy of these epitopes and their population coverage across various RSV strains. The comprehensive analysis identified six major histocompatibility complex class I (MHC-I) binding, five MHC-II binding, and three B-cell epitopes. These were integrated with suitable linkers and adjuvants to form the vaccine. Further, molecular docking and molecular dynamics simulations demonstrated stable interactions between the vaccine candidate and human Toll-like receptors (TLR4 and TLR5), with a notable preference for TLR4. Immune simulation analysis underscored the vaccine's potential to elicit a strong immune response. This study presents a promising RSV vaccine candidate and offers theoretical support, marking a significant advancement in vaccine development efforts. However, the promising in silico findings need to be further validated through additional in vivo studies.</p></div>","PeriodicalId":36831,"journal":{"name":"Infectious Disease Modelling","volume":"9 3","pages":"Pages 763-774"},"PeriodicalIF":8.8,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2468042724000599/pdfft?md5=e66736343bb91b884036f02184de01a1&pid=1-s2.0-S2468042724000599-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140644269","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":"An effectiveness study of vaccination and quarantine combination strategies for containing mpox transmission on simulated college campuses","authors":"Qiangru Huang ,&nbsp;Yanxia Sun ,&nbsp;Mengmeng Jia ,&nbsp;Mingyue Jiang ,&nbsp;Yunshao Xu ,&nbsp;Luzhao Feng ,&nbsp;Weizhong Yang","doi":"10.1016/j.idm.2024.04.004","DOIUrl":"10.1016/j.idm.2024.04.004","url":null,"abstract":"<div><p>The ongoing transmission of mpox in specific countries and regions necessitates urgent action. It is essential to implement targeted containment strategies that concentrate on high-risk populations and critical locations, such as college campuses, to effectively curb the spread of mpox. This study is dedicated to evaluating the performance of various vaccination and quarantine strategies in curbing the spread of mpox and estimating the outbreak risk. To accomplish this, we constructed a stochastic, agent-based, discrete-time susceptible-latent-infectious-recovered (SLIR) model, to examine mpox transmission on a simulated college campus. Our findings reveal that relying solely on PEP is insufficient in containing mpox effectively. To bolster the population immunity and protect the vulnerable, pre-exposure vaccination among high-risk populations prior to an outbreak is imperative. Our study demonstrates that a pre-exposure vaccination rate of 50% in high-risk populations can led to a remarkable 74.2% reduction of infections. This translated to a mere 1.0% cumulative infection incidence in the overall population. In cases where the desired vaccination coverage is not attainable, enhancing case detection and isolation measures can serve as an effective emergency response to contain mpox outbreaks. For pre-exposure vaccination coverage of 20% or lower, a 40% isolation ratio is necessary to keep the cumulative number of infections in check. However, when the coverage exceeds 30%, a reduced isolation ratio of 20% becomes sufficient to manage the outbreak effectively. These insights underscore the importance of strategic pre-exposure vaccination in conjunction with robust surveillance and isolation protocols to safeguard public health and prevent the escalation of mpox outbreaks.</p></div>","PeriodicalId":36831,"journal":{"name":"Infectious Disease Modelling","volume":"9 3","pages":"Pages 805-815"},"PeriodicalIF":8.8,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2468042724000587/pdfft?md5=ed8306a1a23d6ff32c59d0519558c942&pid=1-s2.0-S2468042724000587-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140783054","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":"Examining the effects of voluntary avoidance behaviour and policy-mediated behaviour change on the dynamics of SARS-CoV-2: A mathematical model","authors":"Gabrielle Brankston ,&nbsp;David N. Fisman ,&nbsp;Zvonimir Poljak ,&nbsp;Ashleigh R. Tuite ,&nbsp;Amy L. Greer","doi":"10.1016/j.idm.2024.04.001","DOIUrl":"https://doi.org/10.1016/j.idm.2024.04.001","url":null,"abstract":"<div><h3>Background</h3><p>Throughout the SARS-CoV-2 pandemic, policymakers have had to navigate between recommending voluntary behaviour change and policy-driven behaviour change to mitigate the impact of the virus. While individuals will voluntarily engage in self-protective behaviour when there is an increasing infectious disease risk, the extent to which this occurs and its impact on an epidemic is not known.</p></div><div><h3>Methods</h3><p>This paper describes a deterministic disease transmission model exploring the impact of individual avoidance behaviour and policy-mediated avoidance behaviour on epidemic outcomes during the second wave of SARS-CoV-2 infections in Ontario, Canada (September 1, 2020 to February 28, 2021). The model incorporates an information feedback function based on empirically derived behaviour data describing the degree to which avoidance behaviour changed in response to the number of new daily cases COVID-19.</p></div><div><h3>Results</h3><p>Voluntary avoidance behaviour alone was estimated to reduce the final attack rate by 23.1%, the total number of hospitalizations by 26.2%, and cumulative deaths by 27.5% over 6 months compared to a counterfactual scenario in which there were no interventions or avoidance behaviour. A provincial shutdown order issued on December 26, 2020 was estimated to reduce the final attack rate by 66.7%, the total number of hospitalizations by 66.8%, and the total number of deaths by 67.2% compared to the counterfactual scenario.</p></div><div><h3>Conclusion</h3><p>Given the dynamics of SARS-CoV-2 in a pre-vaccine era, individual avoidance behaviour in the absence of government action would have resulted in a moderate reduction in disease however, it would not have been sufficient to entirely mitigate transmission and the associated risk to the population in Ontario. Government action during the second wave of the COVID-19 pandemic in Ontario reduced infections, protected hospital capacity, and saved lives.</p></div>","PeriodicalId":36831,"journal":{"name":"Infectious Disease Modelling","volume":"9 3","pages":"Pages 701-712"},"PeriodicalIF":8.8,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2468042724000551/pdfft?md5=026d89ae91ac1fded8d99f0750abc43c&pid=1-s2.0-S2468042724000551-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140554698","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":"Ebola virus disease model with a nonlinear incidence rate and density-dependent treatment","authors":"Jacques Ndé Kengne ,&nbsp;Calvin Tadmon","doi":"10.1016/j.idm.2024.03.007","DOIUrl":"https://doi.org/10.1016/j.idm.2024.03.007","url":null,"abstract":"<div><p>This paper studies an Ebola epidemic model with an exponential nonlinear incidence function that considers the efficacy and the behaviour change. The current model also incorporates a new density-dependent treatment that catches the impact of the disease transmission on the treatment. Firstly, we provide a theoretical study of the nonlinear differential equations model obtained. More precisely, we derive the effective reproduction number and, under suitable conditions, prove the stability of equilibria. Afterwards, we show that the model exhibits the phenomenon of backward-bifurcation whenever the bifurcation parameter and the reproduction number are less than one. We find that the bi-stability and backward-bifurcation are not automatically connected in epidemic models. In fact, when a backward-bifurcation occurs, the disease-free equilibrium may be globally stable. Numerically, we use well-known standard tools to fit the model to the data reported for the 2018–2020 Kivu Ebola outbreak, and perform the sensitivity analysis. To control Ebola epidemics, our findings recommend a combination of a rapid behaviour change and the implementation of a proper treatment strategy with a high level of efficacy. Secondly, we propose and analyze a fractional-order Ebola epidemic model, which is an extension of the first model studied. We use the Caputo operator and construct the Grünwald-Letnikov nonstandard finite difference scheme, and show its advantages.</p></div>","PeriodicalId":36831,"journal":{"name":"Infectious Disease Modelling","volume":"9 3","pages":"Pages 775-804"},"PeriodicalIF":8.8,"publicationDate":"2024-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S246804272400054X/pdfft?md5=b2c4b150c4d0d197e920d6133f09d833&pid=1-s2.0-S246804272400054X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140650510","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":"Estimating the effective reproduction number of COVID-19 from population-wide wastewater data: An application in Kagawa, Japan","authors":"Yuta Okada,&nbsp;Hiroshi Nishiura","doi":"10.1016/j.idm.2024.03.006","DOIUrl":"https://doi.org/10.1016/j.idm.2024.03.006","url":null,"abstract":"<div><p>Although epidemiological surveillance of COVID-19 has been gradually downgraded globally, the transmission of COVID-19 continues. It is critical to quantify the transmission dynamics of COVID-19 using multiple datasets including wastewater virus concentration data. Herein, we propose a comprehensive method for estimating the effective reproduction number using wastewater data. The wastewater virus concentration data, which were collected twice a week, were analyzed using daily COVID-19 incidence data obtained from Takamatsu, Japan between January 2022 and September 2022. We estimated the shedding load distribution (SLD) as a function of time since the date of infection, using a model employing the delay distribution, which is assumed to follow a gamma distribution, multiplied by a scaling factor. We also examined models that accounted for the temporal smoothness of viral load measurement data. The model that smoothed temporal patterns of viral load was the best fit model (WAIC = 2795.8), which yielded a mean estimated distribution of SLD of 3.46 days (95% CrI: 3.01–3.95 days). Using this SLD, we reconstructed the daily incidence, which enabled computation of the effective reproduction number. Using the best fit posterior draws of parameters directly, or as a prior distribution for subsequent analyses, we first used a model that assumed temporal smoothness of viral load concentrations in wastewater, as well as infection counts by date of infection. In the subsequent approach, we examined models that also incorporated weekly reported case counts as a proxy for weekly incidence reporting. Both approaches enabled estimations of the epidemic curve as well as the effective reproduction number from twice-weekly wastewater viral load data. Adding weekly case count data reduced the uncertainty of the effective reproduction number. We conclude that wastewater data are still a valuable source of information for inferring the transmission dynamics of COVID-19, and that inferential performance is enhanced when those data are combined with weekly incidence data.</p></div>","PeriodicalId":36831,"journal":{"name":"Infectious Disease Modelling","volume":"9 3","pages":"Pages 645-656"},"PeriodicalIF":8.8,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2468042724000459/pdfft?md5=04a02f108d128864253a352fffd3e820&pid=1-s2.0-S2468042724000459-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140539387","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":"Epidemiological feature analysis of SVEIR model with control strategy and variant evolution","authors":"Kaijing Chen ,&nbsp;Fengying Wei ,&nbsp;Xinyan Zhang ,&nbsp;Hao Jin ,&nbsp;Zuwen Wang ,&nbsp;Yue Zuo ,&nbsp;Kai Fan","doi":"10.1016/j.idm.2024.03.005","DOIUrl":"10.1016/j.idm.2024.03.005","url":null,"abstract":"<div><p>The complex interactions were performed among non-pharmaceutical interventions, vaccinations, and hosts for all epidemics in mainland China during the spread of COVID-19. Specially, the small-scale epidemic in the city described by SVEIR model was less found in the current studies. The SVEIR model with control was established to analyze the dynamical and epidemiological features of two epidemics in Jinzhou City led by Omicron variants before and after Twenty Measures. In this study, the total population (<em>N</em>) of Jinzhou City was divided into five compartments: the susceptible (<em>S</em>), the vaccinated (<em>V</em>), the exposed (<em>E</em>), the infected (<em>I</em>), and the recovered (<em>R</em>). By surveillance data and the SVEIR model, three methods (maximum likelihood method, exponential growth rate method, next generation matrix method) were governed to estimate basic reproduction number, and the results showed that an increasing tendency of basic reproduction number from Omicron BA.5.2 to Omicron BA.2.12.1. Meanwhile, the effective reproduction number for two epidemics were investigated by surveillance data, and the results showed that Jinzhou wave 1 reached the peak on November 1 and was controlled 7 days later, and that Jinzhou wave 2 reached the peak on November 28 and was controlled 5 days later. Moreover, the impacts of non-pharmaceutical interventions (awareness delay, peak delay, control intensity) were discussed extensively, the variations of infection scales for Omicron variant and EG.5 variant were also discussed. Furthermore, the investigations on peaks and infection scales for two epidemics in dynamic zero-COVID policy were operated by the SVEIR model with control. The investigations on public medical requirements of Jinzhou City and Liaoning Province were analyzed by using SVEIR model without control, which provided a possible perspective on variant evolution in the future.</p></div>","PeriodicalId":36831,"journal":{"name":"Infectious Disease Modelling","volume":"9 3","pages":"Pages 689-700"},"PeriodicalIF":8.8,"publicationDate":"2024-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2468042724000381/pdfft?md5=18eb26a6e31d96f380b7658fb6cf672c&pid=1-s2.0-S2468042724000381-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140406732","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}