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Han Q, Bragazzi N, Asgary A, Orbinski J, Wu J, Kong JD. Estimation of epidemiological parameters and ascertainment rate from early transmission of COVID-19 across Africa. R Soc Open Sci 2023; 10:230316. [PMID: 37736525 PMCID: PMC10509578 DOI: 10.1098/rsos.230316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/21/2023] [Indexed: 09/23/2023]
Abstract
Country reported case counts suggested a slow spread of SARS-CoV-2 in the initial phase of the COVID-19 pandemic in Africa. Owing to inadequate public awareness, unestablished monitoring practices, limited testing and stigmas, there might exist extensive under-ascertainment of the true number of cases, especially at the beginning of the novel epidemic. We developed a compartmentalized epidemiological model to track the early epidemics in 54 African countries. Data on the reported cumulative number of cases and daily confirmed cases were used to fit the model for the time period with no or little massive national interventions yet in each country. We estimated that the mean basic reproduction number is 2.02 (s.d. 0.7), with a range between 1.12 (Zambia) and 3.64 (Nigeria). The mean overall report rate was estimated to be 5.37% (s.d. 5.71%), with the highest 30.41% in Libya and the lowest 0.02% in São Tomé and Príncipe. An average of 5.46% (s.d. 6.4%) of all infected cases were severe cases and 66.74% (s.d. 17.28%) were asymptomatic ones. The estimated low reporting rates in Africa suggested a clear need for improved reporting and surveillance systems in these countries.
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Affiliation(s)
- Qing Han
- Africa-Canada Artificial Intelligence and Data Innovation Consortium (ACADIC), York University, Keele Campus, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
- Department of Mathematics and Statistics, Laboratory for Industrial and Applied Mathematics (LIAM), York University, Keele Campus, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
| | - Nicola Bragazzi
- Department of Mathematics and Statistics, Laboratory for Industrial and Applied Mathematics (LIAM), York University, Keele Campus, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
| | - Ali Asgary
- Disaster and Emergency Management, School of Administrative Studies, Faculty of Liberal Arts and Professional Studies, York University, Keele Campus, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
| | - James Orbinski
- Dahdaleh Institute for Global Health Research, York University, Keele Campus, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
| | - Jianhong Wu
- Department of Mathematics and Statistics, Laboratory for Industrial and Applied Mathematics (LIAM), York University, Keele Campus, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
| | - Jude Dzevela Kong
- Africa-Canada Artificial Intelligence and Data Innovation Consortium (ACADIC), York University, Keele Campus, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
- Department of Mathematics and Statistics, Laboratory for Industrial and Applied Mathematics (LIAM), York University, Keele Campus, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
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Macdonald JC, Browne C, Gulbudak H. Modelling COVID-19 outbreaks in USA with distinct testing, lockdown speed and fatigue rates. R Soc Open Sci 2021; 8:210227. [PMID: 34386248 PMCID: PMC8334836 DOI: 10.1098/rsos.210227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 07/20/2021] [Indexed: 05/28/2023]
Abstract
Each state in the USA exhibited a unique response to the COVID-19 outbreak, along with variable levels of testing, leading to different actual case burdens in the country. In this study, via per capita testing dependent ascertainment rates, along with case and death data, we fit a minimal epidemic model for each state. We estimate infection-level responsive lockdown/self-quarantine entry and exit rates (representing government and behavioural reaction), along with the true number of cases as of 31 May 2020. Ultimately, we provide error-corrected estimates for commonly used metrics such as infection fatality ratio and overall case ascertainment for all 55 states and territories considered, along with the USA in aggregate, in order to correlate outbreak severity with first wave intervention attributes and suggest potential management strategies for future outbreaks. We observe a theoretically predicted inverse proportionality relation between outbreak size and lockdown rate, with scale dependent on the underlying reproduction number and simulations suggesting a critical population quarantine 'half-life' of 30 days independent of other model parameters.
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Affiliation(s)
- J. C. Macdonald
- Department of Mathematics, University of Louisiana at Lafayette, Lafayette, LA 70503-2014 USA
| | - C. Browne
- Department of Mathematics, University of Louisiana at Lafayette, Lafayette, LA 70503-2014 USA
| | - H. Gulbudak
- Department of Mathematics, University of Louisiana at Lafayette, Lafayette, LA 70503-2014 USA
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Read JM, Bridgen JRE, Cummings DAT, Ho A, Jewell CP. Novel coronavirus 2019-nCoV (COVID-19): early estimation of epidemiological parameters and epidemic size estimates. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200265. [PMID: 34053269 PMCID: PMC8165596 DOI: 10.1098/rstb.2020.0265] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2020] [Indexed: 12/15/2022] Open
Abstract
Since it was first identified, the epidemic scale of the recently emerged novel coronavirus (2019-nCoV) in Wuhan, China, has increased rapidly, with cases arising across China and other countries and regions. Using a transmission model, we estimate a basic reproductive number of 3.11 (95% CI, 2.39-4.13), indicating that 58-76% of transmissions must be prevented to stop increasing. We also estimate a case ascertainment rate in Wuhan of 5.0% (95% CI, 3.6-7.4). The true size of the epidemic may be significantly greater than the published case counts suggest, with our model estimating 21 022 (prediction interval, 11 090-33 490) total infections in Wuhan between 1 and 22 January. We discuss our findings in the light of more recent information. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.
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Affiliation(s)
- Jonathan M. Read
- Centre for Health Informatics, Computing and Statistics, Lancaster Medical School, Lancaster University, Lancaster LA1 4AT, UK
| | - Jessica R. E. Bridgen
- Centre for Health Informatics, Computing and Statistics, Lancaster Medical School, Lancaster University, Lancaster LA1 4AT, UK
| | - Derek A. T. Cummings
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
| | - Antonia Ho
- Medical Research Council - University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Chris P. Jewell
- Centre for Health Informatics, Computing and Statistics, Lancaster Medical School, Lancaster University, Lancaster LA1 4AT, UK
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Read JM, Bridgen JRE, Cummings DAT, Ho A, Jewell CP. Novel coronavirus 2019-nCoV (COVID-19): early estimation of epidemiological parameters and epidemic size estimates. Philos Trans R Soc Lond B Biol Sci 2021. [PMID: 34053269 DOI: 10.1101/2020.01.23.20018549] [Citation(s) in RCA: 258] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
Since it was first identified, the epidemic scale of the recently emerged novel coronavirus (2019-nCoV) in Wuhan, China, has increased rapidly, with cases arising across China and other countries and regions. Using a transmission model, we estimate a basic reproductive number of 3.11 (95% CI, 2.39-4.13), indicating that 58-76% of transmissions must be prevented to stop increasing. We also estimate a case ascertainment rate in Wuhan of 5.0% (95% CI, 3.6-7.4). The true size of the epidemic may be significantly greater than the published case counts suggest, with our model estimating 21 022 (prediction interval, 11 090-33 490) total infections in Wuhan between 1 and 22 January. We discuss our findings in the light of more recent information. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.
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Affiliation(s)
- Jonathan M Read
- Centre for Health Informatics, Computing and Statistics, Lancaster Medical School, Lancaster University, Lancaster LA1 4AT, UK
| | - Jessica R E Bridgen
- Centre for Health Informatics, Computing and Statistics, Lancaster Medical School, Lancaster University, Lancaster LA1 4AT, UK
| | - Derek A T Cummings
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
| | - Antonia Ho
- Medical Research Council - University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Chris P Jewell
- Centre for Health Informatics, Computing and Statistics, Lancaster Medical School, Lancaster University, Lancaster LA1 4AT, UK
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