Estimation of the Time-dependent Reproduction Number of Influenza A(H1N1)pdm2009 in South Korea

Abstract Background: The reproduction number is one of the most crucial parameters in determining disease dynamics, providing a summary measure of the transmission potential. However, estimating this value is particularly challenging owing to the characteristics of epidemic data, including non-reproducibility and incompleteness.Methods: In this study, we propose mathematical models with different population structures; each of these models can produce data on the number of cases of the influenza A(H1N1)pdm09 epidemic in South Korea. These structured models incorporating the heterogeneity of age and region are used to estimate the time-dependent effective reproduction numbers. Subsequently, the age- and region-specific reproduction numbers are also computed to analyze the differences illustrated in the incidence data.Results: The basic SIR fails to provide a reasonable estimation of the reproduction numbers. The estimated values demonstrate a large variation and remains outside of the feasible range for the influenza, regardless of the time period for data. Real-time estimation using age- and region-structured models demonstrated that the effective reproduction number rose sharply during mid-October when the ㅜumber of patients increased dramatically. The reproduction number fell below unity at the end of October and stayed lower than unity indicating that the epidemic starts decreasing, which is consistent with the incidence data.Conclusions: Numerical results reveal that the introduction of heterogeneity into the population to represent the general characteristics of dynamics is essential for the robust estimation of parameters.

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Estimation of the Reproduction Number of Influenza A(H1N1)pdm2009 in South Korea Using Heterogeneous Models

10.21203/rs.3.rs-20387/v3 ◽

2020 ◽

Author(s):

Yunjeong Lee ◽

Dong Han Lee ◽

Hee-Dae Kwon ◽

Changsoo Kim ◽

jeehyun lee

Keyword(s):

South Korea ◽

Influenza A ◽

Reproduction Number ◽

Time Estimation ◽

Estimation Of Parameters ◽

Transmission Potential ◽

Incidence Data ◽

Reproduction Numbers ◽

Number Of Patients ◽

Influenza A H1n1

Abstract Background: The reproduction number is one of the most crucial parameters in determining disease dynamics, providing a summary measure of the transmission potential. However, estimating this value is particularly challenging owing to the characteristics of epidemic data, including non-reproducibility and incompleteness.Methods: In this study, we propose mathematical models with different population structures; each of these models can produce data on the number of cases of the influenza A(H1N1)pdm09 epidemic in South Korea. These structured models incorporating the heterogeneity of age and region are used to estimate the reproduction numbers at various terminal times. Subsequently, the age- and region-specific reproduction numbers are also computed to analyze the differences illustrated in the incidence data. Results: The basic SIR fails to provide a reasonable estimation of the reproduction numbers. The estimated values demonstrate a large variation and remains outside of the feasible range for the influenza, regardless of the time period for data. Real-time estimation using age- and region-structured models demonstrated that the effective reproduction number rose sharply during mid-October when the number of patients increased dramatically. The reproduction number fell below unity at the end of October and stayed lower than unity indicating that the epidemic starts decreasing, which is consistent with the incidence data. Conclusions: Numerical results reveal that the introduction of heterogeneity into the population to represent the general characteristics of dynamics is essential for the robust estimation of parameters.

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Estimation of the reproduction number of influenza A(H1N1)pdm09 in South Korea using heterogeneous models

BMC Infectious Diseases ◽

10.1186/s12879-021-06121-8 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Yunjeong Lee ◽

Dong Han Lee ◽

Hee-Dae Kwon ◽

Changsoo Kim ◽

Jeehyun Lee

Keyword(s):

South Korea ◽

Robust Estimation ◽

Influenza A ◽

Reproduction Number ◽

Infectious Period ◽

Estimation Of Parameters ◽

Structured Model ◽

Transmission Potential ◽

Reproduction Numbers ◽

Influenza A H1n1

Abstract Background The reproduction number is one of the most crucial parameters in determining disease dynamics, providing a summary measure of the transmission potential. However, estimating this value is particularly challenging owing to the characteristics of epidemic data, including non-reproducibility and incompleteness. Methods In this study, we propose mathematical models with different population structures; each of these models can produce data on the number of cases of the influenza A(H1N1)pdm09 epidemic in South Korea. These structured models incorporating the heterogeneity of age and region are used to estimate the reproduction numbers at various terminal times. Subsequently, the age- and region-specific reproduction numbers are also computed to analyze the differences illustrated in the incidence data. Results Incorporation of the age-structure or region-structure allows for robust estimation of parameters, while the basic SIR model provides estimated values beyond the reasonable range with severe fluctuation. The estimated duration of infectious period using age-structured model is around 3.8 and the reproduction number was estimated to be 1.6. The estimated duration of infectious period using region-structured model is around 2.1 and the reproduction number was estimated to be 1.4. The estimated age- and region-specific reproduction numbers are consistent with cumulative incidence for corresponding groups. Conclusions Numerical results reveal that the introduction of heterogeneity into the population to represent the general characteristics of dynamics is essential for the robust estimation of parameters.

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Basic and effective reproduction numbers of COVID-19 cases in South Korea excluding Sincheonji cases

10.1101/2020.03.19.20039347 ◽

2020 ◽

Cited By ~ 7

Author(s):

Jeongeun Hwang ◽

Hyunjung Park ◽

Jiwon Jung ◽

Sung-Han Kim ◽

Namkug Kim

Keyword(s):

South Korea ◽

Basic Reproduction Number ◽

Infection Prevention ◽

Reproduction Number ◽

Hand Washing ◽

Time Dependent ◽

Government Policies ◽

Black Swan ◽

Reproduction Numbers ◽

Near Future

AbstractIn February and March 2020, COVID-19 epidemic in South Korea met a large black swan effect by a Sincheonji cult mass infection in Daegu-Gyeongbuk area. The black swan made it difficult to evaluate that the current policies for infection prevention including social distancing, closing schools, hand washing, and wearing masks good enough or not. Therefore, in this study, we evaluated basic reproduction number (R0) and time-dependent reproduction number (Rt) of confirmed cases based on various kinds of populations, including total, Daegu-Geyoengbuk, except-Daegu-Gyeongbuk, Sincheonji, and except-Sincheonji. In total, it seems the infection is going to be under control, but this is never true because in the except-Sincheonji and except-Daegu-Geyongbuk cases, R0 is still above 1.0, and Rt is drifting around 1.0. This study could be used to determine government policies in the near future.

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Estimating reproduction numbers for adults and children from case data

Journal of The Royal Society Interface ◽

10.1098/rsif.2010.0679 ◽

2011 ◽

Vol 8 (62) ◽

pp. 1248-1259 ◽

Cited By ~ 19

Author(s):

K. Glass ◽

G. N. Mercer ◽

H. Nishiura ◽

E. S. McBryde ◽

N. G. Becker

Keyword(s):

Pandemic Influenza ◽

Influenza A ◽

Reproduction Number ◽

Age Groups ◽

Reproduction Numbers ◽

Influenza A H1n1 ◽

Pandemic Influenza H1n1 ◽

Adults And Children ◽

Reporting Rates ◽

The Impact

We present a method for estimating reproduction numbers for adults and children from daily onset data, using pandemic influenza A(H1N1) data as a case study. We investigate the impact of different underlying transmission assumptions on our estimates, and identify that asymmetric reproduction matrices are often appropriate. Under-reporting of cases can bias estimates of the reproduction numbers if reporting rates are not equal across the two age groups. However, we demonstrate that the estimate of the higher reproduction number is robust to disproportionate data-thinning. Applying the method to 2009 pandemic influenza H1N1 data from Japan, we demonstrate that the reproduction number for children was considerably higher than that of adults, and that our estimates are insensitive to our choice of reproduction matrix.

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Transmission potential of the new influenza A(H1N1) virus and its age-specificity in Japan

Eurosurveillance ◽

10.2807/ese.14.22.19227-en ◽

2009 ◽

Vol 14 (22) ◽

Cited By ~ 110

Author(s):

H Nishiura ◽

C Castillo-Chavez ◽

M Safan ◽

G Chowell

Keyword(s):

Influenza A ◽

Reproduction Number ◽

H1n1 Virus ◽

Health Interventions ◽

School Closures ◽

Transmission Potential ◽

Influenza A H1n1 ◽

Overseas Travel ◽

History Of ◽

H1n1 Virus Infection

On 16 May 2009, Japan confirmed its first three cases of new influenza A(H1N1) virus infection without a history of overseas travel, and by 1 June, 361 cases, owing to indigenous secondary transmission, have been confirmed. Of these, 287 cases (79.5%) were teenagers (i.e. between 10 and 19 years of age). The reproduction number is estimated at 2.3 (95% confidence interval: 2.0, 2.6). The average number of secondary transmissions involving minors (those under 20 years of age) traced back to infected minors is estimated at 2.8. That is, minors can sustain transmission even in the absence of adults. Estimates of the effective reproduction number Rt moved below 1 by 17 May. Active surveillance and public health interventions, including school closures most likely have contributed to keeping Rt below one.

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Epidemiological and transmissibility analysis of influenza A(H1N1)v in a southern hemisphere setting: Peru

Eurosurveillance ◽

10.2807/ese.14.32.19299-en ◽

2009 ◽

Vol 14 (32) ◽

Author(s):

C V Munayco ◽

J Gómez ◽

V A Laguna-Torres ◽

J Arrasco ◽

T J Kochel ◽

...

Keyword(s):

Influenza A ◽

Additional Data ◽

Reproduction Number ◽

Age Distribution ◽

School Age Children ◽

School Age ◽

Transmission Potential ◽

Influenza A H1n1 ◽

Specific Frequency ◽

Children And Young Adults

We present a preliminary analysis of 1,771 confirmed cases of influenza A(H1N1)v reported in Peru by 17 July including the frequency of the clinical characteristics, the spatial and age distribution of the cases and the estimate of the transmission potential. Age-specific frequency of cases was highest among school age children and young adults, with the lowest frequency of cases among seniors, a pattern that is consistent with reports from other countries. Estimates of the reproduction number lie in the range of 1.2 to 1.7, which is broadly consistent with previous estimates for this pandemic in other regions. Validation of these estimates will be possible as additional data become available.

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Spatial variability in reproduction number and doubling time across two waves of the COVID-19 pandemic in South Korea, February to July 2020

10.1101/2020.07.21.20158923 ◽

2020 ◽

Author(s):

Eunha Shim ◽

Amna Tariq ◽

Gerardo Chowell

Keyword(s):

South Korea ◽

Doubling Time ◽

Reproduction Number ◽

Control Measures ◽

List Type ◽

Transmission Potential ◽

Reproduction Numbers ◽

Gyeonggi Province ◽

The Government ◽

Second Wave

AbstractObjectivesIn South Korea, 13,745 cases of coronavirus disease (COVID-19) have been reported as of 19 July, 2020. To examine the spatiotemporal changes in the transmission potential, we present regional estimates of the doubling time and reproduction number (Rt) of COVID-19 in the country.MethodsDaily series of confirmed COVID-19 cases in the most affected regions were extracted from publicly available sources. We employed established mathematical and statistical methods to investigate the time-varying reproduction numbers of the COVID-19 in Korea and its doubling time, respectively.ResultsAt the regional level, Seoul and Gyeonggi Province have experienced the first peak of COVID-19 in early March, followed by the second wave in early June, with Rt exceeding 3.0 and mean doubling time ranging from 3.6 to 10.1 days. As of 19 July, 2020, Gyeongbuk Province and Daegu are yet to experience a second wave of the disease, where the mean Rt reached 3.5-4.4 and doubling time ranging from 2.8 to 4.6 days during the first wave.ConclusionsOur findings support the effectiveness of control measures against COVID-19 in Korea. However, the easing of the restrictions imposed by the government in May 2020 facilitated a second wave in the greater Seoul area.HighlightsSouth Korea has experienced two spatially heterogenous waves of COVID-19.Seoul and Gyeonggi Province experienced two waves of COVID-19 in March and June.In the densely populated Seoul and nearby areas, reproduction numbers exceeded 3.0.The easing of the social distancing measures resulted in the second wave.

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COVID-19: Time-Dependent Effective Reproduction Number and Sub-notification Effect Estimation Modeling (Preprint)

10.2196/preprints.23997 ◽

2020 ◽

Author(s):

Eduardo Atem De Carvalho ◽

Rogerio Atem De Carvalho

Keyword(s):

New York ◽

Reproduction Number ◽

Moving Average ◽

Real Data ◽

Time Dependent ◽

Initial Value ◽

Health Authorities ◽

Reproduction Numbers ◽

Effect Estimation ◽

The Impact

BACKGROUND Since the beginning of the COVID-19 pandemic, researchers and health authorities have sought to identify the different parameters that govern their infection and death cycles, in order to be able to make better decisions. In particular, a series of reproduction number estimation models have been presented, with different practical results. OBJECTIVE This article aims to present an effective and efficient model for estimating the Reproduction Number and to discuss the impacts of sub-notification on these calculations. METHODS The concept of Moving Average Method with Initial value (MAMI) is used, as well as a model for Rt, the Reproduction Number, is derived from experimental data. The models are applied to real data and their performance is presented. RESULTS Analyses on Rt and sub-notification effects for Germany, Italy, Sweden, United Kingdom, South Korea, and the State of New York are presented to show the performance of the methods here introduced. CONCLUSIONS We show that, with relatively simple mathematical tools, it is possible to obtain reliable values for time-dependent, incubation period-independent Reproduction Numbers (Rt). We also demonstrate that the impact of sub-notification is relatively low, after the initial phase of the epidemic cycle has passed.

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Epidemiological analysis of critically ill adult patients with pandemic influenza A(H1N1) in South Korea

Epidemiology and Infection ◽

10.1017/s0950268812001604 ◽

2012 ◽

Vol 141 (5) ◽

pp. 1070-1079 ◽

Cited By ~ 7

Author(s):

S. B. HONG ◽

E. Y. CHOI ◽

S. H. KIM ◽

G. Y. SUH ◽

M. S. PARK ◽

...

Keyword(s):

South Korea ◽

Influenza A ◽

Multivariate Logistic Regression Analysis ◽

H1n1 Influenza ◽

Epidemiological Analysis ◽

Influenza A H1n1 ◽

Failure Assessment ◽

2009 H1n1 ◽

Independent Risk Factors ◽

Chronic Comorbidities

SUMMARYA total of 245 patients with confirmed 2009 H1N1 influenza were admitted to the intensive-care units of 28 hospitals (South Korea). Their mean age was 55·3 years with 68·6% aged >50 years, and 54·7% male. Nine were obese and three were pregnant. One or more comorbidities were present in 83·7%, and nosocomial acquisition occurred in 14·3%. In total, 107 (43·7%) patients received corticosteroids and 66·1% required mechanical ventilation. Eighty (32·7%) patients died within 30 days after onset of symptoms and 99 (40·4%) within 90 days. Multivariate logistic regression analysis showed that the clinician's decision to prescribe corticosteroids, older age, Sequential Organ Failure Assessment score and nosocomial bacterial pneumonia were independent risk factors for 90-day mortality. In contrast with Western countries, critical illness in Korea in relation to 2009 H1N1 was most common in older patients with chronic comorbidities; nosocomial acquisition occurred occasionally but disease in obese or pregnant patients was uncommon.

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Transmission potential of COVID-19 in South Korea

10.1101/2020.02.27.20028829 ◽

2020 ◽

Cited By ~ 23

Author(s):

Eunha Shim ◽

Amna Tariq ◽

Wongyeong Choi ◽

Yiseul Lee ◽

Gerardo Chowell

Keyword(s):

South Korea ◽

Reproduction Number ◽

Social Distancing ◽

Transmission Potential ◽

Incidence Data ◽

Novel Coronavirus

AbstractSince the first identified individual of 2019 novel coronavirus (COVID-19) infection on Jan 20, 2020 in South Korea, the number of confirmed cases rapidly increased. As of Feb 26, 2020, 1,261 cases of COVID-19 including 12 deaths were confirmed in South Korea. Using the incidence data of COVID-19, we estimate the reproduction number at 1.5 (95% CI: 1.4-1.6), which indicates sustained transmission and support the implementation of social distancing measures to rapidly control the outbreak.

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