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Wang Z, Xu M, Yang Z, Jin Y, Zhang Y. Comparing the Performance of Three Computational Methods for Estimating the Effective Reproduction Number. J Comput Biol 2024; 31:128-146. [PMID: 38227389 DOI: 10.1089/cmb.2023.0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024] Open
Abstract
The effective reproduction number ( R t ) is one of the most important epidemiological parameters, providing suggestions for monitoring the development trend of diseases and also for adjusting the prevention and control policies. However, a few studies have focused on the performance of some common computational methods for Rt. The purpose of this article is to compare the performance of three computational methods for Rt: the time-dependent (TD) method, the new time-varying (NT) method, and the sequential Bayesian (SB) method. Four evaluation methods-accuracy, correlation coefficient, similarity based on trend, and dynamic time warping distance-were used to compare the effectiveness of three computational methods for Rt under different time lags and time windows. The results showed that the NT method was a better choice for real-time monitoring and analysis of the epidemic in the middle and late stages of the infectious disease. The TD method could reflect the change of the number of cases stably and accurately, and was more suitable for monitoring the change of Rt during the whole process of the epidemic outbreak. When the data were relatively stable, the SB method could also provide a reliable estimate for Rt, while the error would increase when the fluctuation in the number of cases increased. The results would provide suggestions for selecting appropriate Rt estimation methods and making policy adjustments more timely and effectively according to the change of Rt.
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Affiliation(s)
- Zihan Wang
- School of Mathematical Sciences, Beijing Normal University, Beijing, China
| | - Mengxia Xu
- School of Mathematical Sciences, Beijing Normal University, Beijing, China
| | - Zonglin Yang
- School of Mathematical Sciences, Beijing Normal University, Beijing, China
| | - Yu Jin
- College of Education for the Future, Beijing Normal University, Beijing, China
| | - Yong Zhang
- School of Mathematical Sciences, Beijing Normal University, Beijing, China
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Chapman LAC, Aubry M, Maset N, Russell TW, Knock ES, Lees JA, Mallet HP, Cao-Lormeau VM, Kucharski AJ. Impact of vaccinations, boosters and lockdowns on COVID-19 waves in French Polynesia. Nat Commun 2023; 14:7330. [PMID: 37957160 PMCID: PMC10643399 DOI: 10.1038/s41467-023-43002-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Estimating the impact of vaccination and non-pharmaceutical interventions on COVID-19 incidence is complicated by several factors, including successive emergence of SARS-CoV-2 variants of concern and changing population immunity from vaccination and infection. We develop an age-structured multi-strain COVID-19 transmission model and inference framework to estimate vaccination and non-pharmaceutical intervention impact accounting for these factors. We apply this framework to COVID-19 waves in French Polynesia and estimate that the vaccination programme averted 34.8% (95% credible interval: 34.5-35.2%) of 223,000 symptomatic cases, 49.6% (48.7-50.5%) of 5830 hospitalisations and 64.2% (63.1-65.3%) of 1540 hospital deaths that would have occurred in a scenario without vaccination up to May 2022. We estimate the booster campaign contributed 4.5%, 1.9%, and 0.4% to overall reductions in cases, hospitalisations, and deaths. Our results suggest that removing lockdowns during the first two waves would have had non-linear effects on incidence by altering accumulation of population immunity. Our estimates of vaccination and booster impact differ from those for other countries due to differences in age structure, previous exposure levels and timing of variant introduction relative to vaccination, emphasising the importance of detailed analysis that accounts for these factors.
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Affiliation(s)
- Lloyd A C Chapman
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK.
- Department of Mathematics and Statistics, Lancaster University, Lancaster, UK.
| | - Maite Aubry
- Laboratoire de recherche sur les infections virales émergentes, Institut Louis Malardé, Tahiti, French Polynesia
| | - Noémie Maset
- Cellule Epi-surveillance Plateforme COVID-19, Tahiti, French Polynesia
| | - Timothy W Russell
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Edward S Knock
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - John A Lees
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Cambridgeshire, UK
| | | | - Van-Mai Cao-Lormeau
- Laboratoire de recherche sur les infections virales émergentes, Institut Louis Malardé, Tahiti, French Polynesia
| | - Adam J Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Laboratoire de recherche sur les infections virales émergentes, Institut Louis Malardé, Tahiti, French Polynesia
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Xu X, Wu Y, Kummer AG, Zhao Y, Hu Z, Wang Y, Liu H, Ajelli M, Yu H. Assessing changes in incubation period, serial interval, and generation time of SARS-CoV-2 variants of concern: a systematic review and meta-analysis. BMC Med 2023; 21:374. [PMID: 37775772 PMCID: PMC10541713 DOI: 10.1186/s12916-023-03070-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/05/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND After the first COVID-19 wave caused by the ancestral lineage, the pandemic has been fueled from the continuous emergence of new SARS-CoV-2 variants. Understanding key time-to-event periods for each emerging variant of concern is critical as it can provide insights into the future trajectory of the virus and help inform outbreak preparedness and response planning. Here, we aim to examine how the incubation period, serial interval, and generation time have changed from the ancestral SARS-CoV-2 lineage to different variants of concern. METHODS We conducted a systematic review and meta-analysis that synthesized the estimates of incubation period, serial interval, and generation time (both realized and intrinsic) for the ancestral lineage, Alpha, Beta, and Omicron variants of SARS-CoV-2. RESULTS Our study included 280 records obtained from 147 household studies, contact tracing studies, or studies where epidemiological links were known. With each emerging variant, we found a progressive shortening of each of the analyzed key time-to-event periods, although we did not find statistically significant differences between the Omicron subvariants. We found that Omicron BA.1 had the shortest pooled estimates for the incubation period (3.49 days, 95% CI: 3.13-4.86 days), Omicron BA.5 for the serial interval (2.37 days, 95% CI: 1.71-3.04 days), and Omicron BA.1 for the realized generation time (2.99 days, 95% CI: 2.48-3.49 days). Only one estimate for the intrinsic generation time was available for Omicron subvariants: 6.84 days (95% CrI: 5.72-8.60 days) for Omicron BA.1. The ancestral lineage had the highest pooled estimates for each investigated key time-to-event period. We also observed shorter pooled estimates for the serial interval compared to the incubation period across the virus lineages. When pooling the estimates across different virus lineages, we found considerable heterogeneities (I2 > 80%; I2 refers to the percentage of total variation across studies that is due to heterogeneity rather than chance), possibly resulting from heterogeneities between the different study populations (e.g., deployed interventions, social behavior, demographic characteristics). CONCLUSIONS Our study supports the importance of conducting contact tracing and epidemiological investigations to monitor changes in SARS-CoV-2 transmission patterns. Our findings highlight a progressive shortening of the incubation period, serial interval, and generation time, which can lead to epidemics that spread faster, with larger peak incidence, and harder to control. We also consistently found a shorter serial interval than incubation period, suggesting that a key feature of SARS-CoV-2 is the potential for pre-symptomatic transmission. These observations are instrumental to plan for future COVID-19 waves.
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Affiliation(s)
- Xiangyanyu Xu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Yanpeng Wu
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Allisandra G Kummer
- Laboratory of Computational Epidemiology and Public Health, Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | - Yuchen Zhao
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Zexin Hu
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Yan Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Hengcong Liu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Marco Ajelli
- Laboratory of Computational Epidemiology and Public Health, Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA.
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China.
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.
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Lippiello E, Petrillo G, Baccari S, de Arcangelis L. Estimating generation time of SARS-CoV-2 variants in Italy from the daily incidence rate. Sci Rep 2023; 13:11543. [PMID: 37460598 DOI: 10.1038/s41598-023-38327-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 07/06/2023] [Indexed: 07/20/2023] Open
Abstract
The identification of the transmission parameters of a virus is fundamental to identify the optimal public health strategy. These parameters can present significant changes over time caused by genetic mutations or viral recombination, making their continuous monitoring fundamental. Here we present a method, suitable for this task, which uses as unique information the daily number of reported cases. The method is based on a time since infection model where transmission parameters are obtained by means of an efficient maximization procedure of the likelihood. Applying the method to SARS-CoV-2 data in Italy, we find an average generation time [Formula: see text] days, during the temporal window when the majority of infections can be attributed to the Omicron variants. At the same time we find a significantly larger value [Formula: see text] days, in the temporal window when spreading was dominated by the Delta variant. We are also able to show that the presence of the Omicron variant, characterized by a shorter [Formula: see text], was already detectable in the first weeks of December 2021, in full agreement with results provided by sequences of SARS-CoV-2 genomes reported in national databases. Our results therefore show that the novel approach can indicate the existence of virus variants, resulting particularly useful in situations when information about genomic sequencing is not yet available. At the same time, we find that the standard deviation of the generation time does not significantly change among variants.
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Affiliation(s)
- Eugenio Lippiello
- Department of Mathematics and Physics, University of Campania "L. Vanvitelli", Viale Lincoln, 5, 81100, Caserta, Italy.
| | - Giuseppe Petrillo
- The Institute of Statistical Mathematics, Research Organization of Information and Systems, Tokyo, Japan
| | - Silvio Baccari
- Department of Mathematics and Physics, University of Campania "L. Vanvitelli", Viale Lincoln, 5, 81100, Caserta, Italy
| | - Lucilla de Arcangelis
- Department of Mathematics and Physics, University of Campania "L. Vanvitelli", Viale Lincoln, 5, 81100, Caserta, Italy
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Madewell ZJ, Yang Y, Longini IM, Halloran ME, Vespignani A, Dean NE. Rapid review and meta-analysis of serial intervals for SARS-CoV-2 Delta and Omicron variants. BMC Infect Dis 2023; 23:429. [PMID: 37365505 DOI: 10.1186/s12879-023-08407-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/20/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND The serial interval is the period of time between symptom onset in the primary case and symptom onset in the secondary case. Understanding the serial interval is important for determining transmission dynamics of infectious diseases like COVID-19, including the reproduction number and secondary attack rates, which could influence control measures. Early meta-analyses of COVID-19 reported serial intervals of 5.2 days (95% CI: 4.9-5.5) for the original wild-type variant and 5.2 days (95% CI: 4.87-5.47) for Alpha variant. The serial interval has been shown to decrease over the course of an epidemic for other respiratory diseases, which may be due to accumulating viral mutations and implementation of more effective nonpharmaceutical interventions. We therefore aggregated the literature to estimate serial intervals for Delta and Omicron variants. METHODS This study followed Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines. A systematic literature search was conducted of PubMed, Scopus, Cochrane Library, ScienceDirect, and preprint server medRxiv for articles published from April 4, 2021, through May 23, 2023. Search terms were: ("serial interval" or "generation time"), ("Omicron" or "Delta"), and ("SARS-CoV-2" or "COVID-19"). Meta-analyses were done for Delta and Omicron variants using a restricted maximum-likelihood estimator model with a random effect for each study. Pooled average estimates and 95% confidence intervals (95% CI) are reported. RESULTS There were 46,648 primary/secondary case pairs included for the meta-analysis of Delta and 18,324 for Omicron. Mean serial interval for included studies ranged from 2.3-5.8 days for Delta and 2.1-4.8 days for Omicron. The pooled mean serial interval for Delta was 3.9 days (95% CI: 3.4-4.3) (20 studies) and Omicron was 3.2 days (95% CI: 2.9-3.5) (20 studies). Mean estimated serial interval for BA.1 was 3.3 days (95% CI: 2.8-3.7) (11 studies), BA.2 was 2.9 days (95% CI: 2.7-3.1) (six studies), and BA.5 was 2.3 days (95% CI: 1.6-3.1) (three studies). CONCLUSIONS Serial interval estimates for Delta and Omicron were shorter than ancestral SARS-CoV-2 variants. More recent Omicron subvariants had even shorter serial intervals suggesting serial intervals may be shortening over time. This suggests more rapid transmission from one generation of cases to the next, consistent with the observed faster growth dynamic of these variants compared to their ancestors. Additional changes to the serial interval may occur as SARS-CoV-2 continues to circulate and evolve. Changes to population immunity (due to infection and/or vaccination) may further modify it.
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Affiliation(s)
- Zachary J Madewell
- Department of Biostatistics, University of Florida, Gainesville, FL, USA.
| | - Yang Yang
- Department of Statistics, University of Georgia, Athens, GA, USA
| | - Ira M Longini
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - M Elizabeth Halloran
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Alessandro Vespignani
- Laboratory for the Modeling of Biological and Socio-Technical Systems, Northeastern University, Boston, MA, USA
| | - Natalie E Dean
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
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Guo Z, Zhao S, Yam CHK, Li C, Jiang X, Chow TY, Chong KC, Yeoh EK. Estimating the serial intervals of SARS-CoV-2 Omicron BA.4, BA.5, and BA.2.12.1 variants in Hong Kong. Influenza Other Respir Viruses 2023; 17:e13105. [PMID: 36824395 PMCID: PMC9942273 DOI: 10.1111/irv.13105] [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: 11/18/2022] [Revised: 01/12/2023] [Accepted: 01/15/2023] [Indexed: 02/10/2023] Open
Abstract
Empirical evidence on the epidemiological characteristics of the emerged SARS-CoV-2 variants could shed light on the transmission potential of the virus and strategic outbreak control planning. In this study, by using contact tracing data collected during an Omicron-predominant epidemic phase in Hong Kong, we estimated the mean serial interval of SARS-CoV-2 Omicron BA.4, BA.5, and BA.2.12.1 variants at 2.8 days (95% credible interval [CrI]: 1.5, 6.7), 2.7 days (95% CrI: 2.1, 3.6), and 4.4 days (95% CrI: 2.6, 7.5), respectively, with adjustment for right truncation and sampling bias. The short serial interval for the current circulating variant indicated that outbreak mitigations through contact tracing and case isolation would be quite challenging.
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Affiliation(s)
- Zihao Guo
- JC School of Public Health and Primary Care, Faculty of MedicineChinese University of Hong KongHong KongChina
| | - Shi Zhao
- JC School of Public Health and Primary Care, Faculty of MedicineChinese University of Hong KongHong KongChina,Centre for Health Systems and Policy Research, Faculty of MedicineChinese University of Hong KongHong KongChina
| | - Carrie Ho Kwan Yam
- JC School of Public Health and Primary Care, Faculty of MedicineChinese University of Hong KongHong KongChina,Centre for Health Systems and Policy Research, Faculty of MedicineChinese University of Hong KongHong KongChina
| | - Conglu Li
- JC School of Public Health and Primary Care, Faculty of MedicineChinese University of Hong KongHong KongChina
| | - Xiaoting Jiang
- JC School of Public Health and Primary Care, Faculty of MedicineChinese University of Hong KongHong KongChina
| | - Tsz Yu Chow
- JC School of Public Health and Primary Care, Faculty of MedicineChinese University of Hong KongHong KongChina,Centre for Health Systems and Policy Research, Faculty of MedicineChinese University of Hong KongHong KongChina
| | - Ka Chun Chong
- JC School of Public Health and Primary Care, Faculty of MedicineChinese University of Hong KongHong KongChina,Centre for Health Systems and Policy Research, Faculty of MedicineChinese University of Hong KongHong KongChina
| | - Eng Kiong Yeoh
- JC School of Public Health and Primary Care, Faculty of MedicineChinese University of Hong KongHong KongChina,Centre for Health Systems and Policy Research, Faculty of MedicineChinese University of Hong KongHong KongChina
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an der Heiden M, Buchholz U. Serial interval in households infected with SARS-CoV-2 variant B.1.1.529 (Omicron) is even shorter compared to Delta. Epidemiol Infect 2022; 150:e165. [PMID: 35929470 PMCID: PMC9530378 DOI: 10.1017/s0950268822001248] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/01/2022] [Accepted: 06/29/2022] [Indexed: 11/05/2022] Open
Affiliation(s)
| | - Udo Buchholz
- Department for Infectious Disease Epidemiology, Robert Koch-Institute, Berlin, Germany
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