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For: Nash RK, Nouvellet P, Cori A. Real-time estimation of the epidemic reproduction number: Scoping review of the applications and challenges. PLOS Digit Health 2022;1:e0000052. [PMID: 36812522 PMCID: PMC9931334 DOI: 10.1371/journal.pdig.0000052] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/27/2022] [Indexed: 12/24/2022]
Number Cited by Other Article(s)
1
Ogi-Gittins I, Steyn N, Polonsky J, Hart WS, Keita M, Ahuka-Mundeke S, Hill EM, Thompson RN. Simulation-based inference of the time-dependent reproduction number from temporally aggregated and under-reported disease incidence time series data. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2025;383:20240412. [PMID: 40172553 DOI: 10.1098/rsta.2024.0412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Revised: 12/20/2024] [Accepted: 01/03/2025] [Indexed: 04/04/2025]
2
Ravuri S, Burnor E, Routledge I, Linton NM, Thakur M, Boehm A, Wolfe M, Bischel HN, Naughton CC, Yu AT, White LA, León TM. Estimating effective reproduction numbers using wastewater data from multiple sewersheds for SARS-CoV-2 in California counties. Epidemics 2025;50:100803. [PMID: 39729960 DOI: 10.1016/j.epidem.2024.100803] [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] [Received: 06/07/2024] [Revised: 10/02/2024] [Accepted: 11/03/2024] [Indexed: 12/29/2024]  Open
3
Anazawa K. Evaluating a novel reproduction number estimation method: a comparative analysis. Sci Rep 2025;15:5423. [PMID: 39948149 PMCID: PMC11825847 DOI: 10.1038/s41598-025-89203-w] [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] [Received: 04/27/2024] [Accepted: 02/04/2025] [Indexed: 02/16/2025]  Open
4
Pang X, Han Y, Tressier E, Abdul Aziz N, Pellis L, House T, Hall I. Time-varying reproduction number estimation: fusing compartmental models with generalized additive models. J R Soc Interface 2025;22:20240518. [PMID: 39878127 PMCID: PMC11776018 DOI: 10.1098/rsif.2024.0518] [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] [Received: 07/30/2024] [Revised: 10/09/2024] [Accepted: 11/07/2024] [Indexed: 01/31/2025]  Open
5
Shi J, Zhou Y, Huang J. Unlocking the power of time-since-infection models: data augmentation for improved instantaneous reproduction number estimation. Biostatistics 2024;26:kxae054. [PMID: 40036311 PMCID: PMC11878408 DOI: 10.1093/biostatistics/kxae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 12/17/2024] [Accepted: 12/19/2024] [Indexed: 03/06/2025]  Open
6
Liu Y, Diamond C, Abbott S, Wong K, Schmidt T, Edmunds W, Pebody R, Jit M. The Impact of Public Health and Social Measures (PHSMs) on SARS-CoV-2 Transmission in the WHO European Region (2020-2022). Influenza Other Respir Viruses 2024;18:e70036. [PMID: 39724912 PMCID: PMC11671160 DOI: 10.1111/irv.70036] [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: 07/04/2024] [Revised: 10/08/2024] [Accepted: 10/15/2024] [Indexed: 12/28/2024]  Open
7
She B, Smith RL, Pytlarz I, Sundaram S, Paré PE. A framework for counterfactual analysis, strategy evaluation, and control of epidemics using reproduction number estimates. PLoS Comput Biol 2024;20:e1012569. [PMID: 39565799 PMCID: PMC11616887 DOI: 10.1371/journal.pcbi.1012569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 12/04/2024] [Accepted: 10/17/2024] [Indexed: 11/22/2024]  Open
8
Rastegar M, Nazar E, Nasehi M, Sharafi S, Fakoor V, Shakeri MT. Bayesian estimation of the time-varying reproduction number for pulmonary tuberculosis in Iran: A registry-based study from 2018 to 2022 using new smear-positive cases. Infect Dis Model 2024;9:963-974. [PMID: 38873589 PMCID: PMC11169078 DOI: 10.1016/j.idm.2024.05.003] [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: 10/23/2023] [Revised: 04/09/2024] [Accepted: 05/07/2024] [Indexed: 06/15/2024]  Open
9
Bizzotto A, Guzzetta G, Marziano V, Del Manso M, Mateo Urdiales A, Petrone D, Cannone A, Sacco C, Poletti P, Manica M, Zardini A, Trentini F, Fabiani M, Bella A, Riccardo F, Pezzotti P, Ajelli M, Merler S. Increasing situational awareness through nowcasting of the reproduction number. Front Public Health 2024;12:1430920. [PMID: 39234082 PMCID: PMC11371679 DOI: 10.3389/fpubh.2024.1430920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 08/05/2024] [Indexed: 09/06/2024]  Open
10
Hulland EN, Charpignon ML, El Hayek GY, Zhao L, Desai AN, Majumder MS. Estimating time-varying cholera transmission and oral cholera vaccine effectiveness in Haiti and Cameroon, 2021-2023. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.12.24308792. [PMID: 39185512 PMCID: PMC11343247 DOI: 10.1101/2024.06.12.24308792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
11
Eales O, McCaw JM, Shearer FM. Challenges in the case-based surveillance of infectious diseases. ROYAL SOCIETY OPEN SCIENCE 2024;11:240202. [PMID: 39205993 PMCID: PMC11349437 DOI: 10.1098/rsos.240202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 05/01/2024] [Accepted: 06/14/2024] [Indexed: 09/04/2024]
12
Ogi-Gittins I, Hart WS, Song J, Nash RK, Polonsky J, Cori A, Hill EM, Thompson RN. A simulation-based approach for estimating the time-dependent reproduction number from temporally aggregated disease incidence time series data. Epidemics 2024;47:100773. [PMID: 38781911 DOI: 10.1016/j.epidem.2024.100773] [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] [Received: 09/12/2023] [Revised: 02/29/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]  Open
13
Charniga K, Madewell ZJ, Masters NB, Asher J, Nakazawa Y, Spicknall IH. Nowcasting and forecasting the 2022 U.S. mpox outbreak: Support for public health decision making and lessons learned. Epidemics 2024;47:100755. [PMID: 38452454 DOI: 10.1016/j.epidem.2024.100755] [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] [Received: 05/04/2023] [Revised: 01/14/2024] [Accepted: 02/26/2024] [Indexed: 03/09/2024]  Open
14
Goldstein IH, Wakefield J, Minin VM. Incorporating testing volume into estimation of effective reproduction number dynamics. JOURNAL OF THE ROYAL STATISTICAL SOCIETY. SERIES A, (STATISTICS IN SOCIETY) 2024;187:436-453. [PMID: 38617598 PMCID: PMC11009926 DOI: 10.1093/jrsssa/qnad128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/04/2023] [Accepted: 09/10/2023] [Indexed: 04/16/2024]
15
Eales O, Riley S. Differences between the true reproduction number and the apparent reproduction number of an epidemic time series. Epidemics 2024;46:100742. [PMID: 38227994 DOI: 10.1016/j.epidem.2024.100742] [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: 07/10/2023] [Revised: 12/21/2023] [Accepted: 01/11/2024] [Indexed: 01/18/2024]  Open
16
Bonaldi C, Fouillet A, Sommen C, Lévy-Bruhl D, Paireau J. Monitoring the reproductive number of COVID-19 in France: Comparative estimates from three datasets. PLoS One 2023;18:e0293585. [PMID: 37906577 PMCID: PMC10617725 DOI: 10.1371/journal.pone.0293585] [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: 09/12/2022] [Accepted: 10/17/2023] [Indexed: 11/02/2023]  Open
17
Li K, Wang J, Xie J, Rui J, Abudunaibi B, Wei H, Liu H, Zhang S, Li Q, Niu Y, Chen T. Advancements in Defining and Estimating the Reproduction Number in Infectious Disease Epidemiology. China CDC Wkly 2023;5:829-834. [PMID: 37814634 PMCID: PMC10560332 DOI: 10.46234/ccdcw2023.158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/11/2023] [Indexed: 10/11/2023]  Open
18
Scire J, Huisman JS, Grosu A, Angst DC, Lison A, Li J, Maathuis MH, Bonhoeffer S, Stadler T. estimateR: an R package to estimate and monitor the effective reproductive number. BMC Bioinformatics 2023;24:310. [PMID: 37568078 PMCID: PMC10416499 DOI: 10.1186/s12859-023-05428-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 07/24/2023] [Indexed: 08/13/2023]  Open
19
Nash RK, Bhatt S, Cori A, Nouvellet P. Estimating the epidemic reproduction number from temporally aggregated incidence data: A statistical modelling approach and software tool. PLoS Comput Biol 2023;19:e1011439. [PMID: 37639484 PMCID: PMC10491397 DOI: 10.1371/journal.pcbi.1011439] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 09/08/2023] [Accepted: 08/18/2023] [Indexed: 08/31/2023]  Open
20
Sebastiani G, Spassiani I. New Insights into the Estimation of Reproduction Numbers during an Epidemic. Vaccines (Basel) 2022;10:1788. [PMID: 36366299 PMCID: PMC9694736 DOI: 10.3390/vaccines10111788] [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: 09/15/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 09/10/2024]  Open
21
Gressani O, Wallinga J, Althaus CL, Hens N, Faes C. EpiLPS: A fast and flexible Bayesian tool for estimation of the time-varying reproduction number. PLoS Comput Biol 2022;18:e1010618. [PMID: 36215319 PMCID: PMC9584461 DOI: 10.1371/journal.pcbi.1010618] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 10/20/2022] [Accepted: 09/30/2022] [Indexed: 11/17/2022]  Open
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