1
|
Zheng W, Tan Y, Zhao Z, Chen J, Dong X, Chen X. "Low-risk groups" deserve more attention than "high-risk groups" in imported COVID-19 cases. Front Med (Lausanne) 2023; 10:1293747. [PMID: 38098851 PMCID: PMC10720434 DOI: 10.3389/fmed.2023.1293747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/14/2023] [Indexed: 12/17/2023] Open
Abstract
Objective To estimate the optimal quarantine period for inbound travelers and identify key risk factors to provide scientific reference for emerging infectious diseases. Methods A parametric survival analysis model was used to calculate the time interval between entry and first positive nucleic acid test of imported cases in Guangzhou, to identify the influencing factors. And the COVID-19 epidemic risk prediction model based on multiple risk factors among inbound travelers was constructed. Results The approximate 95th percentile of the time interval was 14 days. Multivariate analysis found that the mean time interval for inbound travelers in entry/exit high-risk occupations was 29% shorter (OR 0.29, 95% CI 0.18-0.46, p < 0.0001) than that of low-risk occupations, those from Africa were 37% shorter (OR 0.37, 95% CI 0.17-0.78, p = 0.01) than those from Asia, those who were fully vaccinated were 1.88 times higher (OR 1.88, 95% CI 1.13-3.12, p = 0.01) than that of those who were unvaccinated, and those in other VOC periods were lower than in the Delta period. Decision tree analysis showed that a combined entry/exit low-risk occupation group with Delta period could create a high indigenous epidemic risk by 0.24. Conclusion Different strata of imported cases can result in varying degrees of risk of indigenous outbreaks. "low-risk groups" with entry/exit low-risk occupations, fully vaccinated, or from Asia deserve more attention than "high-risk groups."
Collapse
Affiliation(s)
- Wanshan Zheng
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Ying Tan
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Zedi Zhao
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Jin Chen
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Xiaomei Dong
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Xiongfei Chen
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| |
Collapse
|
2
|
Lei H, Yang M, Dong Z, Hu K, Chen T, Yang L, Zhang N, Duan X, Yang S, Wang D, Shu Y, Li Y. Indoor relative humidity shapes influenza seasonality in temperate and subtropical climates in China. Int J Infect Dis 2023; 126:54-63. [PMID: 36427703 DOI: 10.1016/j.ijid.2022.11.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVES The aim of this study was to explore whether indoor or outdoor relative humidity (RH) modulates the influenza epidemic transmission in temperate and subtropical climates. METHODS In this study, the daily temperature and RH in 1558 households from March 2017 to January 2019 in five cities across both temperate and subtropical regions in China were collected. City-level outdoor temperature and RH from 2013 to 2019 were collected from the weather stations. We first estimated the effective reproduction number (Rt) of influenza and then used time-series analyses to explore the relationship between indoor/outdoor RH/absolute humidity and the Rt of influenza. Furthermore, we expanded the measured 1-year indoor temperature and the RH data into 5 years and used the same method to examine the relationship between indoor/outdoor RH and the Rt of influenza. RESULTS Indoor RH displayed a seasonal pattern, with highs during the summer months and lows during the winter months, whereas outdoor RH fluctuated with no consistent pattern in subtropical regions. The Rt of influenza followed a U-shaped relationship with indoor RH in both temperate and subtropical regions, whereas a U-shaped relationship was not observed between outdoor RH and Rt. In addition, indoor RH may be a better indicator for Rt of influenza than indoor absolute humidity. CONCLUSION The findings indicated that indoor RH may be the driver of influenza seasonality in both temperate and subtropical locations in China.
Collapse
Affiliation(s)
- Hao Lei
- School of Public Health, Zhejiang University, Hangzhou, P.R. China
| | - Mengya Yang
- School of Public Health, Zhejiang University, Hangzhou, P.R. China
| | - Zhaomin Dong
- School of Space and Environment, Beihang University, Beijing, China
| | - Kejia Hu
- School of Public Health, Zhejiang University, Hangzhou, P.R. China
| | - Tao Chen
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, P.R. China
| | - Lei Yang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, P.R. China
| | - Nan Zhang
- Beijing Key Laboratory of Green Built Environment and Energy Efficient Technology, Beijing University of Technology, Beijing, P.R. China
| | - Xiaoli Duan
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, China
| | - Shigui Yang
- School of Public Health, Zhejiang University, Hangzhou, P.R. China
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, P.R. China
| | - Yuelong Shu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, P.R. China
| | - Yuguo Li
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, P.R. China
| |
Collapse
|
3
|
Yadav SK, Kumar V, Akhter Y. Modeling Global COVID-19 Dissemination Data After the Emergence of Omicron Variant Using Multipronged Approaches. Curr Microbiol 2022; 79:286. [PMID: 35947199 PMCID: PMC9363856 DOI: 10.1007/s00284-022-02985-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/21/2022] [Indexed: 11/26/2022]
Abstract
The COVID-19 pandemic has followed a wave pattern, with an increase in new cases followed by a drop. Several factors influence this pattern, including vaccination efficacy over time, human behavior, infection management measures used, emergence of novel variants of SARS-CoV-2, and the size of the vulnerable population, among others. In this study, we used three statistical approaches to analyze COVID-19 dissemination data collected from 15 November 2021 to 09 January 2022 for the prediction of further spread and to determine the behavior of the pandemic in the top 12 countries by infection incidence at that time, namely Distribution Fitting, Time Series Modeling, and Epidemiological Modeling. We fitted various theoretical distributions to data sets from different countries, yielding the best-fit distribution for the most accurate interpretation and prediction of the disease spread. Several time series models were fitted to the data of the studied countries using the expert modeler to obtain the best fitting models. Finally, we estimated the infection rates (β), recovery rates (γ), and Basic Reproduction Numbers ([Formula: see text]) for the countries using the compartmental model SIR (Susceptible-Infectious-Recovered). Following more research on this, our findings may be validated and interpreted. Therefore, the most refined information may be used to develop the best policies for breaking the disease's chain of transmission by implementing suppressive measures such as vaccination, which will also aid in the prevention of future waves of infection.
Collapse
Affiliation(s)
- Subhash Kumar Yadav
- Department of Statistics, School of Physical & Decision Science, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025, India.
| | - Vinit Kumar
- Department of Library & Information Science, School of Information Science & Technology, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025, India
| | - Yusuf Akhter
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025, India.
| |
Collapse
|
4
|
Zachreson C, Chang S, Harding N, Prokopenko M. The effects of local homogeneity assumptions in metapopulation models of infectious disease. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211919. [PMID: 35845852 PMCID: PMC9277238 DOI: 10.1098/rsos.211919] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 06/23/2022] [Indexed: 05/10/2023]
Abstract
Computational models of infectious disease can be broadly categorized into two types: individual-based (agent-based) or compartmental models. While there are clear conceptual distinctions between these methodologies, a fair comparison of the approaches is difficult to achieve. Here, we carry out such a comparison by building a set of compartmental metapopulation models from an agent-based representation of a real population. By adjusting the compartmental model to approximately match the dynamics of the agent-based model, we identify two key qualitative properties of the individual-based dynamics which are lost upon aggregation into metapopulations. These are (i) the local depletion of susceptibility to infection and (ii) decoupling of different regional groups due to correlation between commuting behaviours and contact rates. The first of these effects is a general consequence of aggregating small, closely connected groups (i.e. families) into larger homogeneous metapopulations. The second can be interpreted as a consequence of aggregating two distinct types of individuals: school children, who travel short distances but have many potentially infectious contacts, and adults, who travel further but tend to have fewer contacts capable of transmitting infection. Our results could be generalized to other types of correlations between the characteristics of individuals and the behaviours that distinguish them.
Collapse
Affiliation(s)
- Cameron Zachreson
- School of Computing and Information Systems, The University of Melbourne, Melbourne, Australia
- Centre for Complex Systems, Faculty of Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Sheryl Chang
- Centre for Complex Systems, Faculty of Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Nathan Harding
- Centre for Complex Systems, Faculty of Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Mikhail Prokopenko
- Centre for Complex Systems, Faculty of Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, New South Wales 2145, Australia
| |
Collapse
|
5
|
Zachreson C, Chang S, Harding N, Prokopenko M. The effects of local homogeneity assumptions in metapopulation models of infectious disease. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211919. [PMID: 35845852 DOI: 10.5281/zenodo.6486795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 06/23/2022] [Indexed: 05/25/2023]
Abstract
Computational models of infectious disease can be broadly categorized into two types: individual-based (agent-based) or compartmental models. While there are clear conceptual distinctions between these methodologies, a fair comparison of the approaches is difficult to achieve. Here, we carry out such a comparison by building a set of compartmental metapopulation models from an agent-based representation of a real population. By adjusting the compartmental model to approximately match the dynamics of the agent-based model, we identify two key qualitative properties of the individual-based dynamics which are lost upon aggregation into metapopulations. These are (i) the local depletion of susceptibility to infection and (ii) decoupling of different regional groups due to correlation between commuting behaviours and contact rates. The first of these effects is a general consequence of aggregating small, closely connected groups (i.e. families) into larger homogeneous metapopulations. The second can be interpreted as a consequence of aggregating two distinct types of individuals: school children, who travel short distances but have many potentially infectious contacts, and adults, who travel further but tend to have fewer contacts capable of transmitting infection. Our results could be generalized to other types of correlations between the characteristics of individuals and the behaviours that distinguish them.
Collapse
Affiliation(s)
- Cameron Zachreson
- School of Computing and Information Systems, The University of Melbourne, Melbourne, Australia
- Centre for Complex Systems, Faculty of Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Sheryl Chang
- Centre for Complex Systems, Faculty of Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Nathan Harding
- Centre for Complex Systems, Faculty of Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Mikhail Prokopenko
- Centre for Complex Systems, Faculty of Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, New South Wales 2145, Australia
| |
Collapse
|
6
|
Ma P, Tang X, Zhang L, Wang X, Wang W, Zhang X, Wang S, Zhou N. Influenza A and B outbreaks differed in their associations with climate conditions in Shenzhen, China. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2022; 66:163-173. [PMID: 34693474 PMCID: PMC8542503 DOI: 10.1007/s00484-021-02204-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 10/04/2021] [Accepted: 10/07/2021] [Indexed: 05/20/2023]
Abstract
Under the variant climate conditions in the transitional regions between tropics and subtropics, the impacts of climate factors on influenza subtypes have rarely been evaluated. With the available influenza A (Flu-A) and influenza B (Flu-B) outbreak data in Shenzhen, China, which is an excellent example of a transitional marine climate, the associations of multiple climate variables with these outbreaks were explored in this study. Daily laboratory-confirmed influenza virus and climate data were collected from 2009 to 2015. Potential impacts of daily mean/maximum/minimum temperatures (T/Tmax/Tmin), relative humidity (RH), wind velocity (V), and diurnal temperature range (DTR) were analyzed using the distributed lag nonlinear model (DLNM) and generalized additive model (GAM). Under its local climate partitions, Flu-A mainly prevailed in summer months (May to June), and a second peak appeared in early winter (December to January). Flu-B outbreaks usually occurred in transitional seasons, especially in autumn. Although low temperature caused an instant increase in both Flu-A and Flu-B risks, its effect could persist for up to 10 days for Flu-B and peak at 17 C (relative risk (RR) = 14.16, 95% CI: 7.46-26.88). For both subtypes, moderate-high temperature (28 C) had a significant but delayed effect on influenza, especially for Flu-A (RR = 26.20, 95% CI: 13.22-51.20). The Flu-A virus was sensitive to RH higher than 76%, while higher Flu-B risks were observed at both low (< 65%) and high (> 83%) humidity. Flu-A was active for a short term after exposure to large DTR (e.g., DTR = 10 C, RR = 12.45, 95% CI: 6.50-23.87), whereas Flu-B mainly circulated under stable temperatures. Although the overall wind speed in Shenzhen was low, moderate wind (2-3 m/s) was found to favor the outbreaks of both subtypes. This study revealed the thresholds of various climatic variables promoting influenza outbreaks, as well as the distinctions between the flu subtypes. These data can be helpful in predicting seasonal influenza outbreaks and minimizing the impacts, based on integrated forecast systems coupled with short-term climate models.
Collapse
Affiliation(s)
- Pan Ma
- Plateau Atmosphere and Environment Key Laboratory of Sichuan Province, College of Atmospheric Science, Chengdu University of Information Technology, Chengdu, 610225, Sichuan, China.
| | - Xiaoxin Tang
- Shenzhen National Climate Observatory, Shenzhen Meteorological Bureau, Shenzhen, 518000, China
| | - Li Zhang
- Shenzhen National Climate Observatory, Shenzhen Meteorological Bureau, Shenzhen, 518000, China
| | - Xinzi Wang
- Plateau Atmosphere and Environment Key Laboratory of Sichuan Province, College of Atmospheric Science, Chengdu University of Information Technology, Chengdu, 610225, Sichuan, China
| | - Weimin Wang
- Shangluo Meteorological Bureau, Shangluo, 726000, Shanxi, China
| | - Xiaoling Zhang
- Plateau Atmosphere and Environment Key Laboratory of Sichuan Province, College of Atmospheric Science, Chengdu University of Information Technology, Chengdu, 610225, Sichuan, China
| | - Shigong Wang
- Plateau Atmosphere and Environment Key Laboratory of Sichuan Province, College of Atmospheric Science, Chengdu University of Information Technology, Chengdu, 610225, Sichuan, China
| | - Ning Zhou
- The First Hospital of Lanzhou, Lanzhou, 730000, Gansu, China
| |
Collapse
|
7
|
Yadav SK, Akhter Y. Statistical Modeling for the Prediction of Infectious Disease Dissemination With Special Reference to COVID-19 Spread. Front Public Health 2021; 9:645405. [PMID: 34222166 PMCID: PMC8242242 DOI: 10.3389/fpubh.2021.645405] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/06/2021] [Indexed: 12/24/2022] Open
Abstract
In this review, we have discussed the different statistical modeling and prediction techniques for various infectious diseases including the recent pandemic of COVID-19. The distribution fitting, time series modeling along with predictive monitoring approaches, and epidemiological modeling are illustrated. When the epidemiology data is sufficient to fit with the required sample size, the normal distribution in general or other theoretical distributions are fitted and the best-fitted distribution is chosen for the prediction of the spread of the disease. The infectious diseases develop over time and we have data on the single variable that is the number of infections that happened, therefore, time series models are fitted and the prediction is done based on the best-fitted model. Monitoring approaches may also be applied to time series models which could estimate the parameters more precisely. In epidemiological modeling, more biological parameters are incorporated in the models and the forecasting of the disease spread is carried out. We came up with, how to improve the existing modeling methods, the use of fuzzy variables, and detection of fraud in the available data. Ultimately, we have reviewed the results of recent statistical modeling efforts to predict the course of COVID-19 spread.
Collapse
Affiliation(s)
- Subhash Kumar Yadav
- Department of Statistics, School of Physical and Decision Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Yusuf Akhter
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| |
Collapse
|
8
|
Dhouib W, Maatoug J, Ayouni I, Zammit N, Ghammem R, Fredj SB, Ghannem H. The incubation period during the pandemic of COVID-19: a systematic review and meta-analysis. Syst Rev 2021; 10:101. [PMID: 33832511 PMCID: PMC8031340 DOI: 10.1186/s13643-021-01648-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 03/22/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The aim of our study was to determine through a systematic review and meta-analysis the incubation period of COVID-19. It was conducted based on the preferred reporting items for systematic reviews and meta-analyses (PRISMA). Criteria for eligibility were all published population-based primary literature in PubMed interface and the Science Direct, dealing with incubation period of COVID-19, written in English, since December 2019 to December 2020. We estimated the mean of the incubation period using meta-analysis, taking into account between-study heterogeneity, and the analysis with moderator variables. RESULTS This review included 42 studies done predominantly in China. The mean and median incubation period were of maximum 8 days and 12 days respectively. In various parametric models, the 95th percentiles were in the range 10.3-16 days. The highest 99th percentile would be as long as 20.4 days. Out of the 10 included studies in the meta-analysis, 8 were conducted in China, 1 in Singapore, and 1 in Argentina. The pooled mean incubation period was 6.2 (95% CI 5.4, 7.0) days. The heterogeneity (I2 77.1%; p < 0.001) was decreased when we included the study quality and the method of calculation used as moderator variables (I2 0%). The mean incubation period ranged from 5.2 (95% CI 4.4 to 5.9) to 6.65 days (95% CI 6.0 to 7.2). CONCLUSIONS This work provides additional evidence of incubation period for COVID-19 and showed that it is prudent not to dismiss the possibility of incubation periods up to 14 days at this stage of the epidemic.
Collapse
Affiliation(s)
- Wafa Dhouib
- Department of Epidemiology and Preventive Medicine, University of Sousse, Sousse, Tunisia.
| | - Jihen Maatoug
- Department of Epidemiology and Preventive Medicine, University of Sousse, Sousse, Tunisia
| | - Imen Ayouni
- Department of Epidemiology and Preventive Medicine, University of Sousse, Sousse, Tunisia
| | - Nawel Zammit
- Department of Epidemiology and Preventive Medicine, University of Sousse, Sousse, Tunisia
| | - Rim Ghammem
- Department of Epidemiology and Preventive Medicine, University of Sousse, Sousse, Tunisia
| | - Sihem Ben Fredj
- Department of Epidemiology and Preventive Medicine, University of Sousse, Sousse, Tunisia
| | - Hassen Ghannem
- Department of Epidemiology and Preventive Medicine, University of Sousse, Sousse, Tunisia
| |
Collapse
|
9
|
Fonseca-Rodríguez O, Sheridan SC, Lundevaller EH, Schumann B. Effect of extreme hot and cold weather on cause-specific hospitalizations in Sweden: A time series analysis. ENVIRONMENTAL RESEARCH 2021; 193:110535. [PMID: 33271141 DOI: 10.1016/j.envres.2020.110535] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 11/18/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Considering that several meteorological variables can contribute to weather vulnerability, the estimation of their synergetic effects on health is particularly useful. The spatial synoptic classification (SSC) has been used in biometeorological applications to estimate the effect of the entire suite of weather conditions on human morbidity and mortality. In this study, we assessed the relationships between extremely hot and dry (dry tropical plus, DT+) and hot and moist (moist tropical plus, MT+) weather types in summer and extremely cold and dry (dry polar plus, DP+) and cold and moist (moist polar, MP+) weather types in winter and cardiovascular and respiratory hospitalizations by age and sex. Time-series quasi-Poisson regression with distributed lags was used to assess the relationship between oppressive weather types and daily hospitalizations over 14 subsequent days in the extended summer (May to August) and 28 subsequent days during the extended winter (November to March) over 24 years in 4 Swedish locations from 1991 to 2014. In summer, exposure to hot weather types appeared to reduce cardiovascular hospitalizations while increased the risk of hospitalizations for respiratory diseases, mainly related to MT+. In winter, the effect of cold weather on both cause-specific hospitalizations was small; however, MP+ was related to a delayed increase in cardiovascular hospitalizations, whilst MP+ and DP + increased the risk of hospitalizations due to respiratory diseases. This study provides useful information for the staff of hospitals and elderly care centers who can help to implement protective measures for patients and residents. Also, our results could be helpful for vulnerable people who can adopt protective measures to reduce health risks.
Collapse
Affiliation(s)
- Osvaldo Fonseca-Rodríguez
- Department of Epidemiology and Global Health, Umeå University, 901 85, Umeå, Sweden; Centre for Demographic and Ageing Research, Umeå University, 901 87, Umeå, Sweden.
| | - Scott C Sheridan
- Department of Geography, Kent State University, Kent, OH, 44242, USA.
| | | | - Barbara Schumann
- Department of Epidemiology and Global Health, Umeå University, 901 85, Umeå, Sweden; Centre for Demographic and Ageing Research, Umeå University, 901 87, Umeå, Sweden.
| |
Collapse
|
10
|
Pak D, Liu J, Ning J, Gómez G, Shen Y. Analyzing left-truncated and right-censored infectious disease cohort data with interval-censored infection onset. Stat Med 2020; 40:287-298. [PMID: 33086432 DOI: 10.1002/sim.8774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 08/18/2020] [Accepted: 09/26/2020] [Indexed: 11/10/2022]
Abstract
In an infectious disease cohort study, individuals who have been infected with a pathogen are often recruited for follow up. The period between infection and the onset of symptomatic disease, referred to as the incubation period, is of interest because of its importance on disease surveillance and control. However, the incubation period is often difficult to ascertain due to the uncertainty associated with asymptomatic infection onset time. An additional complication is that the observed infected subjects are likely to have longer incubation periods due to the prevalent sampling. In this article, we demonstrate how to estimate the distribution of the incubation period with the uncertain infection onset, subject to left-truncation and right-censoring. We employ a family of sufficiently general parametric models, the generalized odds-rate class of regression models, for the underlying incubation period and its correlation with covariates. In simulation studies, we assess the finite sample performance of the model fitting and hazard function estimation. The proposed method is illustrated on data from the HIV/AIDS study on injection drug users admitted to a detoxification program in Badalona, Spain.
Collapse
Affiliation(s)
- Daewoo Pak
- Department of Information & Statistics, Yonsei University, Wonju, Korea.,Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jun Liu
- Department of Plastic Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jing Ning
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Guadalupe Gómez
- Departament d'Estadística i Investigació Operativa and Barcelona Graduate School of Mathematics BGSMath, Universitat Politécnica de Catalunya, Barcelona, Spain
| | - Yu Shen
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| |
Collapse
|
11
|
Lu QB, Zhang Y, Liu MJ, Zhang HY, Jalali N, Zhang AR, Li JC, Zhao H, Song QQ, Zhao TS, Zhao J, Liu HY, Du J, Teng AY, Zhou ZW, Zhou SX, Che TL, Wang T, Yang T, Guan XG, Peng XF, Wang YN, Zhang YY, Lv SM, Liu BC, Shi WQ, Zhang XA, Duan XG, Liu W, Yang Y, Fang LQ. Epidemiological parameters of COVID-19 and its implication for infectivity among patients in China, 1 January to 11 February 2020. Euro Surveill 2020; 25:2000250. [PMID: 33034281 PMCID: PMC7545819 DOI: 10.2807/1560-7917.es.2020.25.40.2000250] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 07/14/2020] [Indexed: 01/08/2023] Open
Abstract
BackgroundThe natural history of disease in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remained obscure during the early pandemic.AimOur objective was to estimate epidemiological parameters of coronavirus disease (COVID-19) and assess the relative infectivity of the incubation period.MethodsWe estimated the distributions of four epidemiological parameters of SARS-CoV-2 transmission using a large database of COVID-19 cases and potential transmission pairs of cases, and assessed their heterogeneity by demographics, epidemic phase and geographical region. We further calculated the time of peak infectivity and quantified the proportion of secondary infections during the incubation period.ResultsThe median incubation period was 7.2 (95% confidence interval (CI): 6.9‒7.5) days. The median serial and generation intervals were similar, 4.7 (95% CI: 4.2‒5.3) and 4.6 (95% CI: 4.2‒5.1) days, respectively. Paediatric cases < 18 years had a longer incubation period than adult age groups (p = 0.007). The median incubation period increased from 4.4 days before 25 January to 11.5 days after 31 January (p < 0.001), whereas the median serial (generation) interval contracted from 5.9 (4.8) days before 25 January to 3.4 (3.7) days after. The median time from symptom onset to discharge was also shortened from 18.3 before 22 January to 14.1 days after. Peak infectivity occurred 1 day before symptom onset on average, and the incubation period accounted for 70% of transmission.ConclusionThe high infectivity during the incubation period led to short generation and serial intervals, necessitating aggressive control measures such as early case finding and quarantine of close contacts.
Collapse
Affiliation(s)
- Qing-Bin Lu
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, China
- These authors contributed equally to this manuscript
| | - Yong Zhang
- These authors contributed equally to this manuscript
- School of Mathematical Sciences, Beijing Normal University, Beijing, China
| | - Ming-Jin Liu
- Department of Biostatistics, College of Public Health and Health Professions, and Emerging Pathogens Institute, University of Florida, Gainesville, United States
| | - Hai-Yang Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Neda Jalali
- Department of Biostatistics, College of Public Health and Health Professions, and Emerging Pathogens Institute, University of Florida, Gainesville, United States
| | - An-Ran Zhang
- Department of Biostatistics, College of Public Health and Health Professions, and Emerging Pathogens Institute, University of Florida, Gainesville, United States
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jia-Chen Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Han Zhao
- School of Mathematical Sciences, Beijing Normal University, Beijing, China
| | - Qian-Qian Song
- School of Mathematical Sciences, Beijing Normal University, Beijing, China
| | - Tian-Shuo Zhao
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, China
| | - Jing Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Han-Yu Liu
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, China
| | - Juan Du
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, China
| | - Ai-Ying Teng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zi-Wei Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shi-Xia Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tian-Le Che
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tao Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tong Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiu-Gang Guan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xue-Fang Peng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yu-Na Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yuan-Yuan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shou-Ming Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bao-Cheng Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Wen-Qiang Shi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiao-Ai Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiao-Gang Duan
- School of Statistics, Beijing Normal University, Beijing, China
- These senior authors contributed equally to this manuscript
| | - Wei Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- These senior authors contributed equally to this manuscript
| | - Yang Yang
- Department of Biostatistics, College of Public Health and Health Professions, and Emerging Pathogens Institute, University of Florida, Gainesville, United States
- These senior authors contributed equally to this manuscript
| | - Li-Qun Fang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- These senior authors contributed equally to this manuscript
| |
Collapse
|
12
|
Dai J, Yang L, Zhao J. Probable Longer Incubation Period for Elderly COVID-19 Cases: Analysis of 180 Contact Tracing Data in Hubei Province, China. Risk Manag Healthc Policy 2020; 13:1111-1117. [PMID: 32848488 PMCID: PMC7429221 DOI: 10.2147/rmhp.s257907] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 07/21/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Factors associated with the incubation period of COVID-19 are not fully known. The aim of this study was to estimate the incubation period of COVID-19 using epidemiological contact tracing data, and to explore whether there were different incubation periods among different age gr1oups. METHODS We collected contact tracing data in a municipality in Hubei province during the full outbreak period of COVID-19. The exposure periods were inferred from the history of travel in Wuhan and/or history of exposure to confirmed cases. The incubation periods were estimated using parametric accelerated failure time models accounting for interval censoring of exposures. RESULTS The incubation period of COVID-19 follows a Weibull distribution and has a median of 5.8 days with a bootstrap 95% CI: 5.4-6.7 days. Of the symptomatic cases, 95% showed symptoms by 14.3 days (95% CI: 13.0-15.7), and 99% showed symptoms by 18.7 days (95% CI: 16.7-20.9). The incubation periods were not found significantly different between male and female. Elderly cases had significant longer incubation periods than young age cases (HR 1.49 with 95% CI: 1.09-2.05). The median incubation period was estimated at 4.0 days (95% CI: 3.5-4.4) for cases aged under 30, 5.8 days (95% CI: 5.6-6.0) for cases aged between 30 and 59, and 7.7 days (95% CI: 6.9-8.4) for cases aged greater than or equal to 60. CONCLUSION The current practice of a 14-day quarantine period in many regions is reasonable for any age. Older people infected with SARS-CoV2 have longer incubation period than that of younger people. Thus, more attention should be paid to asymptomatic elderly people who had a history of exposure.
Collapse
Affiliation(s)
- Jingyi Dai
- Department of Infectious Diseases, The Third People’s Hospital of Kunming City, Kunming, Yunnan Province, People’s Republic of China
| | - Lin Yang
- School of Public Health and Management, Hubei University of Medicine, Shiyan, Hubei Province, People’s Republic of China
| | - Jun Zhao
- School of Public Health and Management, Hubei University of Medicine, Shiyan, Hubei Province, People’s Republic of China
| |
Collapse
|
13
|
Estimation of incubation period and serial interval of COVID-19: analysis of 178 cases and 131 transmission chains in Hubei province, China. Epidemiol Infect 2020; 148:e117. [PMID: 32594928 PMCID: PMC7324649 DOI: 10.1017/s0950268820001338] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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.
Collapse
|
14
|
An J, Jiang Y, Shi B, Wu D, Wu W. Low-Cost Battery-Powered and User-Friendly Real-Time Quantitative PCR System for the Detection of Multigene. MICROMACHINES 2020; 11:mi11040435. [PMID: 32326194 PMCID: PMC7231343 DOI: 10.3390/mi11040435] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/09/2020] [Accepted: 04/15/2020] [Indexed: 12/25/2022]
Abstract
Real-time polymerase chain reaction (PCR) is the standard for nucleic acid detection and plays an important role in many fields. A new chip design is proposed in this study to avoid the use of expensive instruments for hydrophobic treatment of the surface, and a new injection method solves the issue of bubbles formed during the temperature cycle. We built a battery-powered real-time PCR device to follow polymerase chain reaction using fluorescence detection and developed an independently designed electromechanical control system and a fluorescence analysis software to control the temperature cycle, the photoelectric detection coupling, and the automatic analysis of the experimental data. The microchips and the temperature cycling system cost USD 100. All the elements of the device are available through open access, and there are no technical barriers. The simple structure and manipulation allows beginners to build instruments and perform PCR tests after only a short tutorial. The device is used for analysis of the amplification curve and the melting curve of multiple target genes to demonstrate that our instrument has the same accuracy and stability as a commercial instrument.
Collapse
Affiliation(s)
- Junru An
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China; (J.A.); (Y.J.); (B.S.); (D.W.)
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Yangyang Jiang
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China; (J.A.); (Y.J.); (B.S.); (D.W.)
| | - Bing Shi
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China; (J.A.); (Y.J.); (B.S.); (D.W.)
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Di Wu
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China; (J.A.); (Y.J.); (B.S.); (D.W.)
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Wenming Wu
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China; (J.A.); (Y.J.); (B.S.); (D.W.)
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
- Correspondence: ; Tel.: +86-431-8670-8159
| |
Collapse
|
15
|
|
16
|
Zhou L, Li Q, Uyeki TM. Estimated Incubation Period and Serial Interval for Human-to-Human Influenza A(H7N9) Virus Transmission. Emerg Infect Dis 2019; 25:1982-1983. [PMID: 31264568 PMCID: PMC6759274 DOI: 10.3201/eid2510.190117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We estimated the incubation period and serial interval for human-to-human–transmitted avian influenza A(H7N9) virus infection using case-patient clusters from epidemics in China during 2013–2017. The median incubation period was 4 days and serial interval 9 days. China’s 10-day monitoring period for close contacts of case-patients should detect most secondary infections.
Collapse
|
17
|
Wang X, Wu P, Pei Y, Tsang TK, Gu D, Wang W, Zhang J, Horby PW, Uyeki TM, Cowling BJ, Yu H. Assessment of Human-to-Human Transmissibility of Avian Influenza A(H7N9) Virus Across 5 Waves by Analyzing Clusters of Case Patients in Mainland China, 2013-2017. Clin Infect Dis 2019; 68:623-631. [PMID: 29961834 PMCID: PMC6355824 DOI: 10.1093/cid/ciy541] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/28/2018] [Indexed: 12/14/2022] Open
Abstract
Background The 2016-17 epidemic of human infections with avian influenza A(H7N9) virus was alarming, due to the surge in reported cases across a wide geographic area and the emergence of highly-pathogenic A(H7N9) viruses. Our study aimed to assess whether the human-to-human transmission risk of A(H7N9) virus has changed across the 5 waves since 2013. Methods Data on human cases and clusters of A(H7N9) virus infection were collected from the World Health Organization, open access national and provincial reports, informal online sources, and published literature. We compared the epidemiological characteristics of sporadic and cluster cases, estimated the relative risk (RR) of infection in blood relatives and non-blood relatives, and estimated the bounds on the effective reproductive number (Re) across waves from 2013 through September 2017. Results We identified 40 human clusters of A(H7N9) virus infection, with a median cluster size of 2 (range 2-3). The overall RR of infection in blood relatives versus non-blood relatives was 1.65 (95% confidence interval [CI]: 0.88, 3.09), and was not significantly different across waves (χ2 = 2.66, P = .617). The upper limit of Re for A(H7N9) virus was 0.12 (95% CI: 0.10, 0.14) and was not significantly different across waves (χ2 = 1.52, P = .822). Conclusions The small cluster size and low Re suggest that human-to-human transmissibility of A(H7N9) virus has not changed over time and remains limited to date. Continuous assessment of A(H7N9) virus infections and human case clusters is of crucial importance for public health.
Collapse
Affiliation(s)
- Xiling Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai
| | - Peng Wu
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Yao Pei
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai
| | - Tim K Tsang
- Department of Biostatistics, College of Public Health and Health Professions & College of Medicine, University of Florida, Gainesville
| | - Dantong Gu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai
| | - Wei Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai
| | - Juanjuan Zhang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai
| | - Peter W Horby
- Center for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Timothy M Uyeki
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Benjamin J Cowling
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai
| |
Collapse
|
18
|
Dai Q, Ma W, Huang H, Xu K, Qi X, Yu H, Deng F, Bao C, Huo X. The effect of ambient temperature on the activity of influenza and influenza like illness in Jiangsu Province, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 645:684-691. [PMID: 30031326 DOI: 10.1016/j.scitotenv.2018.07.065] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 04/15/2023]
Abstract
OBJECTIVE We aimed to evaluate and quantify the association between ambient temperature and activity of influenza like illness (ILI) and influenza in Jiangsu Province, China. METHOD Daily data of meteorology, influenza-like illness and detected influenza virus from 1 April 2013 to 27 March 2016 were collected. Distributed lag non-linear model (DLNM) was used to quantify the exposure-lag-response of ILI and influenza activity to daily average temperature. RESULT Influenza A virus (Flu-A) circulated throughout the year with two peaks at -4 °C and 28 °C respectively, while influenza B (Flu-B) viruses were usually tested positive in winter or early spring and peaked at 5 °C. The lag-response curves revealed that the RR of ILI increased with time and peaked 1 day later at low temperature (3 °C), however, the maximum RR of ILI caused by high temperature (26 °C) appeared immediately on day 0, the similar phenomena of immediate effect to ILI at high temperature were also observed in the lag-response curve for Flu-A or Flu-B. CONCLUSION ILI and Flu-A experienced two peaks of circulates at both low and high temperature in Jiangsu. The influenza viruses activity did drive up the rising of ILI%, particularly the activity of Flu-A which circulated throughout the year played a crucial role. Regional homogeneity was the relatively mainstream in aspects of cumulative association between influenza activity and temperature in Jiangsu Province.
Collapse
Affiliation(s)
- Qigang Dai
- Jiangsu Provincial Center for Disease Control and Prevention, China
| | - Wang Ma
- The First Affiliated Hospital with Nanjing Medical University, China
| | - Haodi Huang
- Jiangsu Provincial Center for Disease Control and Prevention, China
| | - Ke Xu
- Jiangsu Provincial Center for Disease Control and Prevention, China
| | - Xian Qi
- Jiangsu Provincial Center for Disease Control and Prevention, China
| | - Huiyan Yu
- Jiangsu Provincial Center for Disease Control and Prevention, China
| | - Fei Deng
- Jiangsu Provincial Center for Disease Control and Prevention, China
| | - Changjun Bao
- Jiangsu Provincial Center for Disease Control and Prevention, China
| | - Xiang Huo
- Jiangsu Provincial Center for Disease Control and Prevention, China.
| |
Collapse
|
19
|
Artois J, Jiang H, Wang X, Qin Y, Pearcy M, Lai S, Shi Y, Zhang J, Peng Z, Zheng J, He Y, Dhingra MS, von Dobschuetz S, Guo F, Martin V, Kalpravidh W, Claes F, Robinson T, Hay SI, Xiao X, Feng L, Gilbert M, Yu H. Changing Geographic Patterns and Risk Factors for Avian Influenza A(H7N9) Infections in Humans, China. Emerg Infect Dis 2018; 24:87-94. [PMID: 29260681 PMCID: PMC5749478 DOI: 10.3201/eid2401.171393] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The fifth epidemic wave of avian influenza A(H7N9) virus in China during 2016–2017 demonstrated a geographic range expansion and caused more human cases than any previous wave. The factors that may explain the recent range expansion and surge in incidence remain unknown. We investigated the effect of anthropogenic, poultry, and wetland variables on all epidemic waves. Poultry predictor variables became much more important in the last 2 epidemic waves than they were previously, supporting the assumption of much wider H7N9 transmission in the chicken reservoir. We show that the future range expansion of H7N9 to northern China may increase the risk of H7N9 epidemic peaks coinciding in time and space with those of seasonal influenza, leading to a higher risk of reassortments than before, although the risk is still low so far.
Collapse
|
20
|
The temporal distribution of new H7N9 avian influenza infections based on laboratory-confirmed cases in Mainland China, 2013-2017. Sci Rep 2018; 8:4051. [PMID: 29511257 PMCID: PMC5840377 DOI: 10.1038/s41598-018-22410-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 02/22/2018] [Indexed: 12/12/2022] Open
Abstract
In this study, estimates of the growth rate of new infections, based on the growth rate of new laboratory-confirmed cases, were used to provide a statistical basis for in-depth research into the epidemiological patterns of H7N9 epidemics. The incubation period, interval from onset to laboratory confirmation, and confirmation time for all laboratory-confirmed cases of H7N9 avian influenza in Mainland China, occurring between January 2013 and June 2017, were used as the statistical data. Stochastic processes theory and maximum likelihood were used to calculate the growth rate of new infections. Time-series analysis was then performed to assess correlations between the time series of new infections and new laboratory-confirmed cases. The rate of new infections showed significant seasonal fluctuation. Laboratory confirmation was delayed by a period of time longer than that of the infection (average delay, 13 days; standard deviation, 6.8 days). At the lags of −7.5 and −15 days, respectively, the time-series of new infections and new confirmed cases were significantly correlated; the cross correlation coefficients (CCFs) were 0.61 and 0.16, respectively. The temporal distribution characteristics of new infections and new laboratory-confirmed cases were similar and strongly correlated.
Collapse
|
21
|
Virlogeux V, Feng L, Tsang TK, Jiang H, Fang VJ, Qin Y, Wu P, Wang X, Zheng J, Lau EHY, Peng Z, Yang J, Cowling BJ, Yu H. Evaluation of animal-to-human and human-to-human transmission of influenza A (H7N9) virus in China, 2013-15. Sci Rep 2018; 8:552. [PMID: 29323268 PMCID: PMC5765021 DOI: 10.1038/s41598-017-17335-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 11/23/2017] [Indexed: 11/09/2022] Open
Abstract
A novel avian-origin influenza A(H7N9) virus emerged in China in March 2013 and by 27 September 2017 a total of 1533 laboratory-confirmed cases have been reported. Occurrences of animal-to-human and human-to-human transmission have been previously identified, and the force of human-to-human transmission is an important component of risk assessment. In this study, we constructed an ecological model to evaluate the animal-to-human and human-to-human transmission of H7N9 during the first three epidemic waves in spring 2013, winter/spring 2013-2014 and winter/spring 2014-2015 in China based on 149 laboratory-confirmed urban cases. Our analysis of patterns in incidence in major cities allowed us to estimate a mean incubation period in humans of 2.6 days (95% credibility interval, CrI: 1.4-3.1) and an effective reproduction number Re of 0.23 (95% CrI: 0.05-0.47) for the first wave, 0.16 (95% CrI: 0.01-0.41) for the second wave, and 0.16 (95% CrI: 0.01-0.45) for the third wave without a significant difference between waves. There was a significant decrease in the incidence of H7N9 cases after live poultry market closures in various major cities. Our analytic framework can be used for continued assessment of the risk of human to human transmission of A(H7N9) virus as human infections continue to occur in China.
Collapse
Affiliation(s)
- Victor Virlogeux
- Department of Biology, Ecole Normale Supérieure de Lyon, Lyon, France.,Cancer Research Center of Lyon, UMR Inserm U1052, CNRS 5286, Lyon, France.,School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Luzhao Feng
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Tim K Tsang
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Hui Jiang
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Vicky J Fang
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Ying Qin
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Peng Wu
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Xiling Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Xuhui District, Shanghai, 200032, China
| | - Jiandong Zheng
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Eric H Y Lau
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Zhibin Peng
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Juan Yang
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Benjamin J Cowling
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Xuhui District, Shanghai, 200032, China.
| |
Collapse
|
22
|
Liu B, Havers FP, Zhou L, Zhong H, Wang X, Mao S, Li H, Ren R, Xiang N, Shu Y, Zhou S, Liu F, Chen E, Zhang Y, Widdowson MA, Li Q, Feng Z. Clusters of Human Infections With Avian Influenza A(H7N9) Virus in China, March 2013 to June 2015. J Infect Dis 2017; 216:S548-S554. [PMID: 28934462 DOI: 10.1093/infdis/jix098] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Multiple clusters of human infections with novel avian influenza A(H7N9) virus have occurred since the virus was first identified in spring 2013. However, in many situations it is unclear whether these clusters result from person-to-person transmission or exposure to a common infectious source. We analyzed the possibility of person-to-person transmission in each cluster and developed a framework to assess the likelihood that person-to-person transmission had occurred. We described 21 clusters with 22 infected contact cases that were identified by the Chinese Center for Disease Control and Prevention from March 2013 through June 2015. Based on detailed epidemiological information and the timing of the contact case patients' exposures to infected persons and to poultry during their potential incubation period, we graded the likelihood of person-to-person transmission as probable, possible, or unlikely. We found that person-to-person transmission probably occurred 12 times and possibly occurred 4 times; it was unlikely in 6 clusters. Probable nosocomial transmission is likely to have occurred in 2 clusters. Limited person-to-person transmission is likely to have occurred on multiple occasions since the H7N9 virus was first identified. However, these transmission events represented a small fraction of all identified cases of H7N9 human infection, and sustained person-to-person transmission was not documented.
Collapse
Affiliation(s)
- Bo Liu
- Public Health Emergency Center
| | - Fiona P Havers
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Haojie Zhong
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou
| | - Xianjun Wang
- Shandong Provincial Center for Disease Control and Prevention, Jinan
| | - Shenghua Mao
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai
| | - Hai Li
- Guangxi Provincial Center for Disease Control and Prevention, Nanning
| | | | | | - Yuelong Shu
- Institute for Viral Disease Control and Prevention
| | - Suizan Zhou
- China Office, US Centers for Disease Control and Prevention, Beijing
| | - Fuqiang Liu
- Hunan Provincial Center for Disease Control and Prevention, Changsha City
| | - Enfu Chen
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | | | - Marc-Alain Widdowson
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Qun Li
- Public Health Emergency Center
| | - Zijian Feng
- Chinese Center for Disease Control and Prevention
| |
Collapse
|
23
|
Virlogeux V, Fang VJ, Park M, Wu JT, Cowling BJ. Comparison of incubation period distribution of human infections with MERS-CoV in South Korea and Saudi Arabia. Sci Rep 2016; 6:35839. [PMID: 27775012 PMCID: PMC5075793 DOI: 10.1038/srep35839] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 10/05/2016] [Indexed: 11/16/2022] Open
Abstract
The incubation period is an important epidemiologic distribution, it is often incorporated in case definitions, used to determine appropriate quarantine periods, and is an input to mathematical modeling studies. Middle East Respiratory Syndrome coronavirus (MERS) is an emerging infectious disease in the Arabian Peninsula. There was a large outbreak of MERS in South Korea in 2015. We examined the incubation period distribution of MERS coronavirus infection for cases in South Korea and in Saudi Arabia. Using parametric and nonparametric methods, we estimated a mean incubation period of 6.9 days (95% credibility interval: 6.3–7.5) for cases in South Korea and 5.0 days (95% credibility interval: 4.0–6.6) among cases in Saudi Arabia. In a log-linear regression model, the mean incubation period was 1.42 times longer (95% credibility interval: 1.18–1.71) among cases in South Korea compared to Saudi Arabia. The variation that we identified in the incubation period distribution between locations could be associated with differences in ascertainment or reporting of exposure dates and illness onset dates, differences in the source or mode of infection, or environmental differences.
Collapse
Affiliation(s)
- Victor Virlogeux
- Department of Biology, Ecole Normale Supérieure de Lyon, Lyon, France.,WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.,Cancer Research Center of Lyon, UMR Inserm U1052, CNRS 5286, Lyon, France
| | - Vicky J Fang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Minah Park
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Joseph T Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| |
Collapse
|
24
|
Virlogeux V, Yang J, Fang VJ, Feng L, Tsang TK, Jiang H, Wu P, Zheng J, Lau EHY, Qin Y, Peng Z, Peiris JSM, Yu H, Cowling BJ. Association between the Severity of Influenza A(H7N9) Virus Infections and Length of the Incubation Period. PLoS One 2016; 11:e0148506. [PMID: 26885816 PMCID: PMC4757028 DOI: 10.1371/journal.pone.0148506] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/19/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND In early 2013, a novel avian-origin influenza A(H7N9) virus emerged in China, and has caused sporadic human infections. The incubation period is the delay from infection until onset of symptoms, and varies from person to person. Few previous studies have examined whether the duration of the incubation period correlates with subsequent disease severity. METHODS AND FINDINGS We analyzed data of period of exposure on 395 human cases of laboratory-confirmed influenza A(H7N9) virus infection in China in a Bayesian framework using a Weibull distribution. We found a longer incubation period for the 173 fatal cases with a mean of 3.7 days (95% credibility interval, CrI: 3.4-4.1), compared to a mean of 3.3 days (95% CrI: 2.9-3.6) for the 222 non-fatal cases, and the difference in means was marginally significant at 0.47 days (95% CrI: -0.04, 0.99). There was a statistically significant correlation between a longer incubation period and an increased risk of death after adjustment for age, sex, geographical location and underlying medical conditions (adjusted odds ratio 1.70 per day increase in incubation period; 95% credibility interval 1.47-1.97). CONCLUSIONS We found a significant association between a longer incubation period and a greater risk of death among human H7N9 cases. The underlying biological mechanisms leading to this association deserve further exploration.
Collapse
Affiliation(s)
- Victor Virlogeux
- Department of Biology, Ecole Normale Supérieure de Lyon, 15 parvis René Descartes, 69007 Lyon, France
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong Special Administrative Region, China
| | - Juan Yang
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, 155# Changbai Road, Beijing, 102206, China
| | - Vicky J. Fang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong Special Administrative Region, China
| | - Luzhao Feng
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, 155# Changbai Road, Beijing, 102206, China
| | - Tim K. Tsang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong Special Administrative Region, China
| | - Hui Jiang
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, 155# Changbai Road, Beijing, 102206, China
| | - Peng Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong Special Administrative Region, China
| | - Jiandong Zheng
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, 155# Changbai Road, Beijing, 102206, China
| | - Eric H. Y. Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong Special Administrative Region, China
| | - Ying Qin
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, 155# Changbai Road, Beijing, 102206, China
| | - Zhibin Peng
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, 155# Changbai Road, Beijing, 102206, China
| | - J. S. Malik Peiris
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong Special Administrative Region, China
| | - Hongjie Yu
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, 155# Changbai Road, Beijing, 102206, China
- * E-mail:
| | - Benjamin J. Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong Special Administrative Region, China
| |
Collapse
|