scholarly journals Transmission interval estimates suggest pre-symptomatic spread of COVID-19

2020 ◽  
Author(s):  
Lauren C. Tindale ◽  
Michelle Coombe ◽  
Jessica E. Stockdale ◽  
Emma S. Garlock ◽  
Wing Yin Venus Lau ◽  
...  
Keyword(s):  
Incubation Period ◽  
Basic Reproduction Number ◽  
Reproduction Number ◽  
Interval Estimates ◽  
Secondary Infections ◽  
Serial Interval ◽  
Incubation Periods ◽  
Key Variables ◽  
The Mean ◽  
Interval Distribution

AbstractBackgroundAs the COVID-19 epidemic is spreading, incoming data allows us to quantify values of key variables that determine the transmission and the effort required to control the epidemic. We determine the incubation period and serial interval distribution for transmission clusters in Singapore and in Tianjin. We infer the basic reproduction number and identify the extent of pre-symptomatic transmission.MethodsWe collected outbreak information from Singapore and Tianjin, China, reported from Jan.19-Feb.26 and Jan.21-Feb.27, respectively. We estimated incubation periods and serial intervals in both populations.ResultsThe mean incubation period was 7.1 (6.13, 8.25) days for Singapore and 9 (7.92, 10.2) days for Tianjin. Both datasets had shorter incubation periods for earlier-occurring cases. The mean serial interval was 4.56 (2.69, 6.42) days for Singapore and 4.22 (3.43, 5.01) for Tianjin. We inferred that early in the outbreaks, infection was transmitted on average 2.55 and 2.89 days before symptom onset (Singapore, Tianjin). The estimated basic reproduction number for Singapore was 1.97 (1.45, 2.48) secondary cases per infective; for Tianjin it was 1.87 (1.65, 2.09) secondary cases per infective.ConclusionsEstimated serial intervals are shorter than incubation periods in both Singapore and Tianjin, suggesting that pre-symptomatic transmission is occurring. Shorter serial intervals lead to lower estimates of R0, which suggest that half of all secondary infections should be prevented to control spread.

scholarly journals The basic reproduction number and prediction of the epidemic size of the novel coronavirus (COVID-19) in Shahroud, Iran

2020 ◽  
Vol 148 ◽  
Author(s):  
A. Khosravi ◽  
R. Chaman ◽  
M. Rohani-Rasaf ◽  
F. Zare ◽  
S. Mehravaran ◽  
...  
Keyword(s):  
Basic Reproduction Number ◽  
Reproduction Number ◽  
Early Stage ◽  
Screening Tests ◽  
The Novel ◽  
Epidemic Size ◽  
Serial Interval ◽  
Novel Coronavirus ◽  
Interval Distribution ◽  
The Basic Reproduction Number

Abstract The aim of this study was to estimate the basic reproduction number (R0) of COVID-19 in the early stage of the epidemic and predict the expected number of new cases in Shahroud in Northeastern Iran. The R0 of COVID-19 was estimated using the serial interval distribution and the number of incidence cases. The 30-day probable incidence and cumulative incidence were predicted using the assumption that daily incidence follows a Poisson distribution determined by daily infectiousness. Data analysis was done using ‘earlyR’ and ‘projections’ packages in R software. The maximum-likelihood value of R0 was 2.7 (95% confidence interval (CI): 2.1−3.4) for the COVID-19 epidemic in the early 14 days and decreased to 1.13 (95% CI 1.03–1.25) by the end of day 42. The expected average number of new cases in Shahroud was 9.0 ± 3.8 cases/day, which means an estimated total of 271 (95% CI: 178–383) new cases for the period between 02 April to 03 May 2020. By day 67 (27 April), the effective reproduction number (Rt), which had a descending trend and was around 1, reduced to 0.70. Based on the Rt for the last 21 days (days 46–67 of the epidemic), the prediction for 27 April to 26 May is a mean daily cases of 2.9 ± 2.0 with 87 (48–136) new cases. In order to maintain R below 1, we strongly recommend enforcing and continuing the current preventive measures, restricting travel and providing screening tests for a larger proportion of the population.

scholarly journals Epidemiologic Characteristics of COVID-19 in Guizhou, China

2020 ◽  
Author(s):  
Kaike Ping ◽  
Mingyu Lei ◽  
Yun Gou ◽  
Ying Tao ◽  
Yan Huang
Keyword(s):  
Incubation Period ◽  
Basic Reproduction Number ◽  
Reproduction Number ◽  
Demographic Characteristics ◽  
Guizhou Province ◽  
Serial Interval ◽  
Epidemiologic Characteristics

AbstractAt the end of 2019, a coronavirus disease 2019 (COVID-19) outbroke in Wuhan, China, and spread to Guizhou province on January of 2020. To acquire the epidemiologic characteristics of COVID-19 in Guizhou, China, we collected data on 162 laboratory-confirmed cases related to COVID-19. We described the demographic characteristics of the cases and estimated the incubation period, serial interval and basic reproduction number. With an estimation of 8 days incubation period and 6 days serial interval, our results indicate that there may exist infectiousness during the incubation period for 2019-nCoV. This increases the difficulty of screening or identifying cases related to COVID-19.

scholarly journals Serial interval and basic reproduction number of SARS-CoV-2 Omicron variant in South Korea

2021 ◽  
Author(s):  
Dasom Kim ◽  
Jisoo Jo ◽  
Jun-Sik Lim ◽  
Sukhyun Ryu
Keyword(s):  
South Korea ◽  
Basic Reproduction Number ◽  
Reproduction Number ◽  
Credible Interval ◽  
Serial Interval ◽  
Community Transmission ◽  
The Mean ◽  
The Basic Reproduction Number

South Korea is experiencing the community transmission of the SARS-CoV-2 Omicron variant (B.1.1.529). We estimated that the mean of the serial interval was 2.22 days, and the basic reproduction number was 1.90 (95% Credible Interval, 1.50-2.43) for the Omicron variant outbreak in South Korea.

scholarly journals The basic reproduction number and prediction of the epidemic size of the novel coronavirus (COVID-19) in Shahroud, Iran

2020 ◽  
Author(s):  
Ahmad Khosravi ◽  
Reza Chaman ◽  
Marzieh Rohani-Rasaf ◽  
Fariba Zare ◽  
Shiva Mehravaran ◽  
...  
Keyword(s):  
Basic Reproduction Number ◽  
Reproduction Number ◽  
Early Stage ◽  
Screening Tests ◽  
The Novel ◽  
Epidemic Size ◽  
Serial Interval ◽  
Novel Coronavirus ◽  
Interval Distribution ◽  
The Basic Reproduction Number

AbstractObjectivesTo estimate the basic reproduction number (R0) of COVID-19 in the early stage of the epidemic and predict the expected number of new cases in Shahroud, Northeast of Iran.MethodsThe R0 of COVID-19 was estimated using the serial interval distribution and the number of incidence cases. The serial interval was fit with a gamma distribution. The probable incidence and cumulative incidence in the next 30 days were predicted using the assumption that daily incidence follows a Poisson distribution determined by daily infectiousness. Data analysis was done using “earlyR” and “projections” packages in R software.ResultsThe maximum-likelihood value of R0 was 2.7 (95% confidence interval (CI): 2.1 to 3.4) for the COVID-19 epidemic in the early 14 days and decreased to 1.13 (95% CI: 1.03 to 1.25) by the end of the day 41. The expected average number of new cases in Shahroud is 9.0±3.8 case/day, which means an estimated total of 271 (95% CI: 178-383) new cases in the next 30 days.ConclusionsIt is essential to reduce the R0 to values below one. Therefore, we strongly recommend enforcing and continuing the current preventive measures, restricting travel, and providing screening tests for a larger proportion of the population.

scholarly journals Early reports of epidemiological parameters of the COVID-19 pandemic

2021 ◽  
Vol 12 (2) ◽  
pp. 65-81
Author(s):  
Keeley Allen ◽  
Ame Elizabeth Parry ◽  
Kathryn Glass
Keyword(s):  
Incubation Period ◽  
Reproduction Number ◽  
Rapid Assessment ◽  
Control Measures ◽  
Inclusion Criteria ◽  
Early Analysis ◽  
Outbreak Response ◽  
Median Length ◽  
Serial Interval ◽  
The Mean

Background: The emergence of a new pathogen requires a rapid assessment of its transmissibility, to inform appropriate public health interventions. Methods: The peer-reviewed literature published between 1 January and 30 April 2020 on COVID-19 in PubMed was searched. Estimates of the incubation period, serial interval and reproduction number for COVID-19 were obtained and compared. Results: A total of 86 studies met the inclusion criteria. Of these, 33 estimated the mean incubation period (4–7 days) and 15 included estimates of the serial interval (mean 4–8 days; median length 4–5 days). Fifty-two studies estimated the reproduction number. Although reproduction number estimates ranged from 0.3 to 14.8, in 33 studies (63%), they fell between 2 and 3. Discussion: Studies calculating the incubation period and effective reproduction number were published from the beginning of the pandemic until the end of the study period (30 April 2020); however, most of the studies calculating the serial interval were published in April 2020. The calculated incubation period was similar over the study period and in different settings, whereas estimates of the serial interval and effective reproduction number were setting-specific. Estimates of the serial interval were shorter at the end of the study period as increasing evidence of pre-symptomatic transmission was documented and as jurisdictions enacted outbreak control measures. Estimates of the effective reproduction number varied with the setting and the underlying model assumptions. Early analysis of epidemic parameters provides vital information to inform the outbreak response.

scholarly journals Dynamics of a scrapie outbreak in a flock of Romanov sheep – estimation of transmission parameters

2003 ◽  
Vol 131 (2) ◽  
pp. 1015-1022 ◽  
Author(s):  
T. J. HAGENAARS ◽  
C. A. DONNELLY ◽  
N. M. FERGUSON ◽  
R. M. ANDERSON
Keyword(s):  
Incubation Period ◽  
Basic Reproduction Number ◽  
Reproduction Number ◽  
Transmission Parameters ◽  
Environmental Reservoir ◽  
The Mean ◽  
Range Of Values ◽  
Transmission Models ◽  
The Basic Reproduction Number

Knowledge of epidemiological mechanisms and parameters underlying scrapie transmission in sheep flocks remains very limited at present. Here we introduce a method for fitting stochastic transmission models to outbreak data to estimate bounds on key transmission parameters. We apply this method to data describing an outbreak of scrapie in a closed flock of Romanov sheep. The main findings are that the relative infectiousness of infected animals in this outbreak becomes appreciable early into disease incubation and that the mean incubation period is less than 1·5 years. We also find that the data are consistent with a broad range of values for the basic reproduction number R0 and describe how the boundaries of this range depend on assumptions about the mean incubation period and the contribution to transmission of a long-lived environmental reservoir of infectivity.

scholarly journals First Consistent Determination of the Basic Reproduction Number for the First Covid-19 Wave in 71 Countries from the SIR-Epidemics Model with a Constant Ratio of Recovery to Infection Rate

2020 ◽  
pp. 37-43
Author(s):  
R. Schlickeiser ◽  
M. Kröger
Keyword(s):  
Infection Rate ◽  
Basic Reproduction Number ◽  
Reproduction Number ◽  
Simple Relation ◽  
Reproduction Numbers ◽  
Serial Interval ◽  
Reproduction Factor ◽  
Interval Distribution ◽  
The Basic Reproduction Number

The box-shaped serial interval distribution and the analytical solution of the Susceptible Infectious-Recovered (SIR)-epidemics model with a constant time-independent ratio of the recovery (μ0) to infection rate (a0) are used to calculate the effective reproduction factor and the basic reproduction number R0. The latter depends on the positively valued net infection number x = 13.5(a0 − μ0) as R0(x) = x(1 − e−x)−1 which for all values of x is greater unity. This dependence differs from the simple relation R0 = a0/μ0. With the earlier determination of the values of k and a0 of the Covid-19 pandemic waves in 71 countries the net infection rates and the basic reproduction numbers for these countries are calculated.

scholarly journals Subcritical Transmission in the Early Stage of COVID-19 in Korea

2021 ◽  
Vol 18 (3) ◽  
pp. 1265
Author(s):  
Yong Sul Won ◽  
Jong-Hoon Kim ◽  
Chi Young Ahn ◽  
Hyojung Lee
Keyword(s):  
Incubation Period ◽  
Early Stage ◽  
Probability Distributions ◽  
Likelihood Estimation ◽  
Contact Tracing ◽  
Statistical Characterization ◽  
Serial Interval ◽  
Imported Cases ◽  
The Mean ◽  
Reporting Delays

While the coronavirus disease 2019 (COVID-19) outbreak has been ongoing in Korea since January 2020, there were limited transmissions during the early stages of the outbreak. In the present study, we aimed to provide a statistical characterization of COVID-19 transmissions that led to this small outbreak. We collated the individual data of the first 28 confirmed cases reported from 20 January to 10 February 2020. We estimated key epidemiological parameters such as reporting delay (i.e., time from symptom onset to confirmation), incubation period, and serial interval by fitting probability distributions to the data based on the maximum likelihood estimation. We also estimated the basic reproduction number (R0) using the renewal equation, which allows for the transmissibility to differ between imported and locally transmitted cases. There were 16 imported and 12 locally transmitted cases, and secondary transmissions per case were higher for the imported cases than the locally transmitted cases (nine vs. three cases). The mean reporting delays were estimated to be 6.76 days (95% CI: 4.53, 9.28) and 2.57 days (95% CI: 1.57, 4.23) for imported and locally transmitted cases, respectively. The mean incubation period was estimated to be 5.53 days (95% CI: 3.98, 8.09) and was shorter than the mean serial interval of 6.45 days (95% CI: 4.32, 9.65). The R0 was estimated to be 0.40 (95% CI: 0.16, 0.99), accounting for the local and imported cases. The fewer secondary cases and shorter reporting delays for the locally transmitted cases suggest that contact tracing of imported cases was effective at reducing further transmissions, which helped to keep R0 below one and the overall transmissions small.

scholarly journals Quantifying TB transmission: a systematic review of reproduction number and serial interval estimates for tuberculosis

2018 ◽  
Vol 146 (12) ◽  
pp. 1478-1494 ◽  
Author(s):  
Y. Ma ◽  
C. R. Horsburgh ◽  
L. F. White ◽  
H. E. Jenkins
Keyword(s):  
Systematic Review ◽  
Parameter Estimation ◽  
The Netherlands ◽  
Cause Of Death ◽  
Reproduction Number ◽  
Reproductive Number ◽  
Interval Estimates ◽  
Transmission Parameters ◽  
Serial Interval ◽  
Number Of Publications

AbstractTuberculosis (TB) is the leading global infectious cause of death. Understanding TB transmission is critical to creating policies and monitoring the disease with the end goal of TB elimination. To our knowledge, there has been no systematic review of key transmission parameters for TB. We carried out a systematic review of the published literature to identify studies estimating either of the two key TB transmission parameters: the serial interval (SI) and the reproductive number. We identified five publications that estimated the SI and 56 publications that estimated the reproductive number. The SI estimates from four studies were: 0.57, 1.42, 1.44 and 1.65 years; the fifth paper presented age-specific estimates ranging from 20 to 30 years (for infants <1 year old) to <5 years (for adults). The reproductive number estimates ranged from 0.24 in the Netherlands (during 1933–2007) to 4.3 in China in 2012. We found a limited number of publications and many high TB burden settings were not represented. Certain features of TB dynamics, such as slow transmission, complicated parameter estimation, require novel methods. Additional efforts to estimate these parameters for TB are needed so that we can monitor and evaluate interventions designed to achieve TB elimination.

scholarly journals Estimation of incubation period and serial interval of COVID-19: analysis of 178 cases and 131 transmission chains in Hubei province, China

2020 ◽  
Vol 148 ◽  
Author(s):  
Lin Yang ◽  
Jingyi Dai ◽  
Jun Zhao ◽  
Yunfu Wang ◽  
Pingji Deng ◽  
...  
Keyword(s):  
Incubation Period ◽  
Failure Time ◽  
Age Groups ◽  
Hubei Province ◽  
Interval Censoring ◽  
Contact Tracing ◽  
Considerable Proportion ◽  
Outbreak Period ◽  
Serial Interval ◽  
Incubation Periods

Abstract A novel coronavirus disease, designated as COVID-19, has become a pandemic worldwide. This study aims to estimate the incubation period and serial interval of COVID-19. We collected contact tracing data in a municipality in Hubei province during a full outbreak period. The date of infection and infector–infectee pairs were inferred from the history of travel in Wuhan or exposed to confirmed cases. The incubation periods and serial intervals were estimated using parametric accelerated failure time models, accounting for interval censoring of the exposures. Our estimated median incubation period of COVID-19 is 5.4 days (bootstrapped 95% confidence interval (CI) 4.8–6.0), and the 2.5th and 97.5th percentiles are 1 and 15 days, respectively; while the estimated serial interval of COVID-19 falls within the range of −4 to 13 days with 95% confidence and has a median of 4.6 days (95% CI 3.7–5.5). Ninety-five per cent of symptomatic cases showed symptoms by 13.7 days (95% CI 12.5–14.9). The incubation periods and serial intervals were not significantly different between male and female, and among age groups. Our results suggest a considerable proportion of secondary transmission occurred prior to symptom onset. And the current practice of 14-day quarantine period in many regions is reasonable.

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