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Bayesian estimation of the time-varying reproduction number for pulmonary tuberculosis in Iran:A registry-based study from 2018 to 2022 using new smear-positive cases

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Infectious Disease Modelling 2024年第3期9卷 963-974页

作者： Maryam Rastegar Eisa Nazar Mahshid Nasehi Saeed Sharafi Vahid Fakoor Mohammad Taghi Shakeri Department of Biostatistics School of HealthMashhad University of Medical SciencesMashhadIran Orthopedic Research Center Mazandaran University of Medical SciencesSariIran Centre for Communicable Diseases Control Ministry of Health and Medical EducationTehranIran Department of Statistics Faculty of Mathematical SciencesFerdowsi University of MashhadMashhadIran Social Determinants of Health Research Center Mashhad University of Medical SciencesMashhadIran Department of Epidemiology School of Public HealthIran University of Medical SciencesTehran

Introduction Tuberculosis(TB)is one of the most prevalent infectious diseases in the world,causing major public health problems in developing *** rate of TB incidence in Iran was estimated to be 13 per 100,000 in *** study aimed to estimate the reproduction number and serial interval for pulmonary tuberculosis in *** and methods The present national historical cohort study was conducted from March 2018 to March 2022 based on data from the National Tuberculosis and Leprosy Registration Center of Iran's Ministry of Health and Medical Education(MOHME).The study included 30,762 tuberculosis cases and 16,165 new smear-positive pulmonary tuberculosis patients in *** estimated the reproduction number of pulmonary tuberculosis in a Bayesian framework,which can incorporate uncertainty in estimating *** analyses were accomplished in R *** The mean age at diagnosis of patients was 52.3±21.2 years,and most patients were in the 35–63 age group(37.1%).Among the data,9121(56.4%)cases were males,and 7044(43.6%)were *** patients,7459(46.1%)had a delayed diagnosis between 1 and 3 ***,3039(18.8%)cases were non-Iranians,and 2978(98%)were *** time-varying reproduction number for pulmonary tuberculosis disease was calculated at an average of 1.06±0.05(95%Crl 0.96–1.15).Conclusions In this study,the incidence and the time-varying reproduction number of pulmonary tuberculosis showed the same *** mean of the time-varying reproduction number indicated that each infected person is causing at least one new infection over time,and the chain of transmission is not being disrupted.

关键词： reproduction number Bayesian modeling Tuberculosis Iran

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EpiMix:A novel method to estimate effective reproduction number

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Infectious Disease Modelling 2023年第3期8卷 704-716页

作者： Shihui Jin Borame Lee Dickens Jue Tao Lim Alex R.Cook Saw Swee Hock School of Public Health National University of Singapore and National University Health SystemSingapore Lee Kong Chian School of Medicine Nanyang Technological UniversitySingapore Department of Statistics and Data Science National University of SingaporeSingapore

Transmission potential of a pathogen,often quantified by the time-varying reproduction number R t,provides the current pace of infection for a disease and indicates whether an emerging epidemic is under *** this study,we proposed a novel method,EpiMix,for R t estimation,wherein we incorporated the impacts of exogenous factors and random effects under a Bayesian regression *** Integrated Nested Laplace Approx-imation,EpiMix is able to efficiently generate reliable,deterministic R t *** the simulations and case studies performed,we further demonstrated the method's robust-ness in low-incidence scenarios,together with other merits,including its flexibility in selecting variables and tolerance of varying reporting *** these make EpiMix a potentially useful tool for real-time R t estimation provided that the serial interval distri-bution,time series of case counts and external influencing factors are available.

关键词： Epidemics INLA Regression reproduction number SARS-CoV-2 Transmission dynamics

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Disease momentum: Estimating the reproduction number in the presence of superspreading

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Infectious Disease Modelling 2021年第1期6卷 706-728页

作者： Kory D.Johnson Mathias Beiglböck Manuel Eder Annemarie Grass Joachim Hermisson Gudmund Pammer Jitka Polechova Daniel Toneian Benjamin Wölfl Vienna University of Economics and Business Welthandelsplatz 1Vienna1020Austria University of Vienna Oskar-Morgenstern-Platz 1Vienna1090Austria

A primary quantity of interest in the study of infectious diseases is the average number of new infections that an infected person *** so-called reproduction number has significant implications for the disease *** has been increasing literature suggesting that superspreading,the significant variability in number of new infections caused by individuals,plays an important role in the spread of *** this paper,we consider the effect that such superspreading has on the estimation of the reproduction number and subsequent estimates of future ***,we employ a simple extension to models currently used in the literature to estimate the reproduction number and present a case-study of the progression of COVID-19 in *** models demonstrate that the estimation uncertainty of the reproduction number increases with superspreading and that this improves the performance of prediction *** independent interest is the derivation of a transparent formula that connects the extent of superspreading to the width of credible intervals for the reproduction *** serves as a valuable heuristic for understanding the uncertainty surrounding diseases with superspreading.

关键词： COVID-19 reproduction number Overdispersion Superspreading

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Replicating and projecting the path of COVID-19 with a model-implied reproduction number

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Infectious Disease Modelling 2020年第1期5卷 635-651页

作者： Shelby R.Buckman Reuven Glick Kevin J.Lansing Nicolas Petrosky-Nadeau Lily M.Seitelman Federal Reserve Bank of San Francisco 101 Market StreetSan Francisco CA94105USA

We demonstrate a methodology for replicating and projecting the path of COVID-19 using a simple epidemiology *** fit the model to daily data on the number of infected cases in China,Italy,the United States,and *** four countries can be viewed as representing different stages,from later to earlier,of a COVID-19 epidemic *** solve for a model-implied effective reproduction number R t each day so that the model closely replicates the daily number of currently infected cases in each *** out-of-sample projections,we fit a behavioral function to the in-sample data that allows for the endogenous response of R t to movements in the lagged number of infected *** show that declines in measures of population mobility tend to precede declines in the model-implied reproduction numbers for each *** pattern suggests that mandatory and voluntary stay-at-home behavior and social distancing during the early stages of the epidemic worked to reduce the effective reproduction number and mitigate the spread of COVID-19.

关键词： Coronavirus COVID-19 SEIR Model Epidemics reproduction number

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Estimating effective reproduction number using generation time versus serial interval,with application to COVID-19 in the Greater Toronto Area,Canada

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Infectious Disease Modelling 2020年第1期5卷 889-896页

作者： Jesse Knight Sharmistha Mishra Institute of Medical Science University of TorontoCanada MAP Centre for Urban Health Solutions Unity Health TorontoCanada Division of Infectious Disease Department of MedicineUniversity of TorontoCanada Institute of Health Policy Management and EvaluationDalla Lana School of Public HealthUniversity of TorontoCanada

*** effective reproduction number Re(t)is a critical measure of epidemic ***(t)can be calculated in near real time using an incidence time series and the generation time distribution:the time between infection events in an infector-infectee *** calculating Re(t),the generation time distribution is often approximated by the serial interval distribution:the time between symptom onset in an infector-infectee ***,while generation time must be positive by definition,serial interval can be negative if transmission can occur before symptoms,such as in COVID-19,rendering such an approximation improper in some *** developed a method to infer the generation time distribution from parametric definitions of the serial interval and incubation period *** then compared estimates of Re(t)for COVID-19 in the Greater Toronto Area of Canada using:negative-permitting versus non-negative serial interval distributions,versus the inferred generation time *** estimated the generation time of COVID-19 to be Gamma-distributed with mean 3.99 and standard deviation 2.96 *** to the generation time distribution,non-negative serial interval distribution caused overestimation of Re(t)due to larger mean,while negative-permitting serial interval distribution caused underestimation of Re(t)due to larger *** of the generation time distribution of COVID-19 with non-negative or negative-permitting serial interval distributions when calculating Re(t)may result in over or underestimation of transmission potential,respectively.

关键词： reproduction number Generation time Serial interval Incubation period COVID-19

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Estimation of reproduction numbers of COVID-19 in typical countries and epidemic trends under different prevention and control scenarios

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Frontiers of Medicine 2020年第5期14卷 613-622页

作者： Chen Xu Yinqiao Dong Xiaoyue Yu Huwen Wang Lhakpa Tsamlag Shuxian Zhang Ruijie Chang Zezhou Wang Yuelin Yu Rusi Long Ying Wang Gang Xu Tian Shen Suping Wang Xinxin Zhang Hui Wang Yong Cai School of Public Health Shanghai Jiao Tong University School of MedicineShanghai 200025China Department of Environmental and Occupational Health School of Public HealthChina Medical UniversityShenyang 110122China Department of Cancer Prevention Shanghai Cancer CenterFudan UniversityDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai 200025China Research Laboratory of Clinical Virology National Research Center for Translational Medicine(Shanghai)Ruijin Hospital and Ruijin Hospital North Affiliated to Shanghai Jiao Tong University School of MedicineShanghai 200025China

The coronavirus disease 2019(COVID-19)has become a life-threatening *** epidemic trends in different countries vary considerably due to different policy-making and resources *** calculated basic reproduction number(R0)and the time-varying estimate of the effective reproductive number(Rt)of COVID-19 by using the maximum likelihood method and the sequential Bayesian method,*** and North American countries possessed higher (R0)and unsteady Rt fluctuations,whereas some heavily affected Asian countries showed relatively low (R0)and declining Rt *** numbers of patients in Africa and Latin America are still low,but the potential risk of huge outbreaks cannot be *** scenarios were then simulated,generating distinct outcomes by using SEIR(susceptible,exposed,infectious,and removed)***,evidence-based prompt responses yield lower transmission rate followed by decreasing ***,implementation of effective control policies at a relatively late stage,in spite of huge casualties at early phase,can still achieve containment and ***,wisely taking advantage of the time-window for developing countries in Africa and Latin America to adopt adequate measures can save more people’s *** mathematical modeling provides evidence for international communities to develop sound design of containment and mitigation policies for COVID-19.

关键词： reproduction number SEIR model COVID-19 estimate

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The Complex Dynamics of Hepatitis B Infected Individuals with Optimal Control

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Journal of Systems Science & Complexity 2021年第4期34卷 1301-1323页

作者： DIN Anwarud LI Yongjin SHAH Murad Ali Department of Mathematics Sun Yat-sen UniversityGuangzhou 510275China School of Mathematical Sciences Beiing Normal UniversityBeijing 100875China

This paper proposes various stages of the hepatitis B virus(HBV)besides its transmissibility and nonlinear incidence rate to develop an epidemic *** authors plan the model,and then prove some basic results for the well-posedness in term of boundedness and ***,the authors find the threshold parameter R0,called the basic/effective reproductive number and carry out local sensitive ***,the authors examine stability and hence condition for stability in terms of *** using sensitivity analysis,the authors formulate a control problem in order to eradicate HBV from the population and proved that the control problem actually *** complete characterization of the optimum system was achieved by using the 4th-order Runge-Kutta procedure.

关键词： Hepatitis B epidemic model non-linear incidence normalized sensitivity index numerical simulation optimization theory reproduction number stability analysis

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Dynamical Behavior and Sensitivity Analysis of a Delayed Coronavirus Epidemic Model

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Computers, Materials & Continua 2020年第10期65卷 225-241页

作者： Muhammad Naveed Dumitru Baleanu Muhammad Rafiq Ali Raza Atif Hassan Soori Nauman Ahmed Department of Mathematics Air UniversityIslamabadPakistan Department of Mathematics Cankaya UniversityAnkara06530Turkey Department of Medical Research China Medical University HospitalChina Medical UniversityTaichungTaiwan Institute of Space Sciences Magurele-BucharestRomania Faculty of Engineering University of Central PunjabLahorePakistan Department of Mathematics National College of Business Administration and EconomicsLahorePakistan Department of Mathematics and Statistics The University of LahoreLahorePakistan

Mathematical delay modelling has a significant role in the different disciplines such as behavioural,social,physical,biological engineering,and bio-mathematical *** present work describes mathematical formulation for the transmission mechanism of a novel coronavirus(COVID-19).Due to the unavailability of vaccines for the coronavirus worldwide,delay factors such as social distance,quarantine,travel restrictions,extended holidays,hospitalization,and isolation have contributed to controlling the coronavirus *** have analysed the reproduction number and its sensitivity to ***,R_(covid)>1then this situation will help to eradicate the disease and if,R_(covid)>1 the virus will spread rapidly in the human ***-known theorems such as Routh Hurwitz criteria and Lasalle invariance principle have presented for *** local and global stabilizes for both equilibria of the model have also been ***,we have analysed the effect of delay reason on the reproduction *** the last,some very useful numerical consequences have presented in support of hypothetical analysis.

关键词： Coronavirus(COVID-19) delay mathematical model reproduction number sensitive analysis stability analysis

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The Mathematical Model for Streptococcus suis Infection in Pig-Human Population with Humidity Effect

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Computers, Materials & Continua 2022年第5期71卷 2981-2998页

作者： Inthira Chaiya Kamonchat Trachoo Kamsing Nonlaopon Din Prathumwan Department of Mathematics Faculty of ScienceMahasarakham UniversityMahasarakham44150Thailand Department of Mathematics Faculty of ScienceKhon Kaen UniversityKhon Kaen40002Thailand

In this paper,we developed a mathematical model for Streptococcus suis,which is an epidemic by considering the moisture that affects the *** disease is caused by Streptococcus suis infection found in pigs which can be transmitted to *** patients of Streptococcus suis were generally found in adults males and the elderly who contacted pigs or who ate uncooked *** human cases,the infection can cause a severe illness and *** disease has an impact to the financial losses in the swine *** the development of models for this disease,we have divided the population into 7 related groups which are susceptible pig compartment,infected pig compartment,quarantined pig compartment,recovered pig compartment,susceptible human compartment,infected human compartment,and recovered human *** that,we use this model and a quarantine strategy to analyze the spread of the *** addition,the basic reproduction number R0 is determined by using the next-generation matrix which can analyze the stability of the *** numerical simulations of the proposed model are illustrated to confirm the results from *** results showed that there is an effect from moisture to the disease *** the moisture increases the disease infection also increases.

关键词： Streptococcus suis mathematical model stability analysis infectious disease reproduction number

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A Study on the Transmission Dynamics of the Omicron Variant of COVID-19 Using Nonlinear Mathematical Models

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Computer Modeling in Engineering & Sciences 2024年第6期139卷 2265-2287页

作者： S.Dickson S.Padmasekaran Pushpendra Kumar Kottakkaran Sooppy Nisar Hamidreza Marasi Department of Mathematics Periyar UniversitySalemTamilnadu636011India Faculty of Engineering and Natural Sciences Istanbul Okan UniversityIstanbulTurkey Department of Mathematics College of Science and Humanities in AlkharjPrince Sattam Bin Abdulaziz UniversityAlkharj11942Saudi Arabia Department of Applied Mathematics Faculty of MathematicsStatistics and Computer ScienceUniversity of TabrizTabrizIran

This research examines the transmission dynamics of the Omicron variant of COVID-19 using SEIQIcRVW and SQIRV models,considering the delay in converting susceptible individuals into infected *** significant delays eventually resulted in the pandemic’s *** ensure the safety of the host population,this concept integrates quarantine and the COVID-19 *** investigate the stability of the proposed *** fundamental reproduction number influences stability *** to our findings,asymptomatic cases considerably impact the prevalence of Omicron infection in the *** real data of the Omicron variant from Chennai,Tamil Nadu,India,is used to validate the outputs.

关键词： Omicron local stability reproduction number steady states global stability

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