Computing R0 of dynamic models by a definition-based method

Guo, Xiaoyu; Guo, Yichao; Zhao, Zeyu; Yang, Shiting; Su, Yanhua; Zhao, Bin; Chen, Tianmu

doi:10.1016/j.idm.2022.05.004

Cited by 6 publications

(13 citation statements)

References 47 publications

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“…Therefore, we used R t to assess the transmissibility of mumps. Due to the optimization of the compartments and parameters involved in this research model compared to the previous model, the next-generation matrix method (NGM) was used in this study to calculate R t ( 28 ). The calculation procedure is detailed in Additional file 1 .…”

Section: Model Constructionmentioning

confidence: 99%

Age-specific transmission dynamic of mumps: A long-term large-scale modeling study in Jilin Province, China

Yang

Wang

Zhao³

et al. 2022

Front. Public Health

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ObjectivesDespite the adoption of a new childhood immunization program in China, the incidence of mumps remains high. This study aimed to describe the epidemiological characteristics of mumps in Jilin Province from 2005 to 2019 and to assess the transmissibility of mumps virus among the whole population and different subgroups by regions and age groups.MethodsThe Non-age-specific and age-specific Susceptible–Exposed–Pre-symptomatic–Infectious–Asymptomatic–Recovered (SEPIAR) models were fitted to actual mumps incidence data. The time-varying reproduction number (Rt) was used to evaluate and compare the transmissibility.ResultsFrom 2005 to 2019, a total of 57,424 cases of mumps were reported in Jilin Province. The incidence of mumps was the highest in people aged 5 to 9 years (77.37 per 100,000). The two SEPIAR models fitted the reported data well (P < 0.01). The median transmissibility (Rt) calculated by the two SEPIAR models were 1.096 (range: 1.911 × 10−5–2.192) and 1.074 (range: 0.033–2.114) respectively. The age-specific SEPIAR model was more representative of the actual epidemic of mumps in Jilin Province from 2005–2019.ConclusionsFor mumps control, it is recommended that mumps-containing vaccines (MuCV) coverage be increased nationwide in the 5–9 years age group, either by a mumps vaccine alone or by a combination of vaccines such as measles-mumps-rubella (MMR) vaccine. The coverage of vaccines in Jilin Province should be continuously expanded to establish solid immunity in the population. China needs to redefine the optimal time interval for MuCV immunization.

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Section: Model Constructionmentioning

confidence: 99%

Age-specific transmission dynamic of mumps: A long-term large-scale modeling study in Jilin Province, China

Yang

Wang

Zhao³

et al. 2022

Front. Public Health

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“…We then derivate the expression for the interactive

of SEPIAR model through a definition-based method ( Appendix ) ( Guo et al, 2022 ). The expression is as follows:

…”

Section: Methodsmentioning

confidence: 99%

Simulating potential outbreaks of Delta and Omicron variants based on contact-tracing data: A modelling study in Fujian Province, China

Guo¹,

Ye²,

Zhao³

et al. 2023

Infectious Disease Modelling

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“…This method is an indirect way to calculate the reproduction numbers that use a transmission dynamics model, denoted as effective reproduction number R eff . This refers to the expected number of second-generation cases that can be infected by the first-generation cases with certain effective interventions implemented ( 1 , 11 ).…”

Section: Methodsmentioning

confidence: 99%

“…The formula for calculating the effective reproduction number R eff is as follows: Refer to Supplementary material for detailed calculations ( 11 ).…”

Section: Methodsmentioning

confidence: 99%

“…At the beginning of 2020, researchers calculated R 0 of COVID-19 in Wuhan, China with the definition method, to demonstrate the transmissibility of this emerging infectious disease (EID) for the first time ( 9 ). Recently, there have been some studies published about obtaining R eff and R t by applying the next-generation matrix and serial interval ( SI ) ( 4 , 10 , 11 ). Simultaneously, there are studies about R eff of COVID-19 by establishing transmission dynamics models, such as SEIAR models ( 1 , 12 , 13 ).…”

Section: Introductionmentioning

confidence: 99%

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A comparative study on the three calculation methods for reproduction numbers of COVID-19

Abudunaibi

Liu

Guo³

et al. 2023

Front. Med.

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ObjectiveThis study uses four COVID-19 outbreaks as examples to calculate and compare merits and demerits, as well as applicational scenarios, of three methods for calculating reproduction numbers.MethodThe epidemiological characteristics of the COVID-19 outbreaks are described. Through the definition method, the next-generation matrix-based method, and the epidemic curve and serial interval (SI)-based method, corresponding reproduction numbers were obtained and compared.ResultsReproduction numbers (Reff), obtained by the definition method of the four regions, are 1.20, 1.14, 1.66, and 1.12. Through the next generation matrix method, in region H Reff = 4.30, 0.44; region P Reff = 6.5, 1.39, 0; region X Reff = 6.82, 1.39, 0; and region Z Reff = 2.99, 0.65. Time-varying reproduction numbers (Rt), which are attained by SI of onset dates, are decreasing with time. Region H reached its highest Rt = 2.8 on July 29 and decreased to Rt < 1 after August 4; region P reached its highest Rt = 5.8 on September 9 and dropped to Rt < 1 by September 14; region X had a fluctuation in the Rt and Rt < 1 after September 22; Rt in region Z reached a maximum of 1.8 on September 15 and decreased continuously to Rt < 1 on September 19.ConclusionThe reproduction number obtained by the definition method is optimal in the early stage of epidemics with a small number of cases that have clear transmission chains to predict the trend of epidemics accurately. The effective reproduction number Reff, calculated by the next generation matrix, could assess the scale of the epidemic and be used to evaluate the effectiveness of prevention and control measures used in epidemics with a large number of cases. Time-varying reproduction number Rt, obtained via epidemic curve and SI, can give a clear picture of the change in transmissibility over time, but the conditions of use are more rigorous, requiring a greater sample size and clear transmission chains to perform the calculation. The rational use of the three methods for reproduction numbers plays a role in the further study of the transmissibility of COVID-19.

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Computing R0 of dynamic models by a definition-based method

Cited by 6 publications

References 47 publications

Age-specific transmission dynamic of mumps: A long-term large-scale modeling study in Jilin Province, China

Age-specific transmission dynamic of mumps: A long-term large-scale modeling study in Jilin Province, China

Simulating potential outbreaks of Delta and Omicron variants based on contact-tracing data: A modelling study in Fujian Province, China

A comparative study on the three calculation methods for reproduction numbers of COVID-19

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