Real-time estimation of the epidemic reproduction number: Scoping review of the applications and challenges.
The time-varying reproduction number (Rt) is an important measure of transmissibility during outbreaks. Estimating whether and how rapidly an outbreak is growing (Rt > 1) or declining (Rt < 1) can inform the design, monitoring and adjustment of control measures in real-time. We use a popular R...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2022-06-01
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| Series: | PLOS Digital Health |
| Online Access: | https://journals.plos.org/digitalhealth/article/file?id=10.1371/journal.pdig.0000052&type=printable |
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| author | Rebecca K Nash Pierre Nouvellet Anne Cori |
| author_facet | Rebecca K Nash Pierre Nouvellet Anne Cori |
| author_sort | Rebecca K Nash |
| collection | DOAJ |
| description | The time-varying reproduction number (Rt) is an important measure of transmissibility during outbreaks. Estimating whether and how rapidly an outbreak is growing (Rt > 1) or declining (Rt < 1) can inform the design, monitoring and adjustment of control measures in real-time. We use a popular R package for Rt estimation, EpiEstim, as a case study to evaluate the contexts in which Rt estimation methods have been used and identify unmet needs which would enable broader applicability of these methods in real-time. A scoping review, complemented by a small EpiEstim user survey, highlight issues with the current approaches, including the quality of input incidence data, the inability to account for geographical factors, and other methodological issues. We summarise the methods and software developed to tackle the problems identified, but conclude that significant gaps remain which should be addressed to enable easier, more robust and applicable estimation of Rt during epidemics. |
| format | Article |
| id | doaj-art-558f27e7cc79468fafd1d0d681d3c757 |
| institution | Kabale University |
| issn | 2767-3170 |
| language | English |
| publishDate | 2022-06-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLOS Digital Health |
| spelling | doaj-art-558f27e7cc79468fafd1d0d681d3c7572025-02-05T05:33:39ZengPublic Library of Science (PLoS)PLOS Digital Health2767-31702022-06-0116e000005210.1371/journal.pdig.0000052Real-time estimation of the epidemic reproduction number: Scoping review of the applications and challenges.Rebecca K NashPierre NouvelletAnne CoriThe time-varying reproduction number (Rt) is an important measure of transmissibility during outbreaks. Estimating whether and how rapidly an outbreak is growing (Rt > 1) or declining (Rt < 1) can inform the design, monitoring and adjustment of control measures in real-time. We use a popular R package for Rt estimation, EpiEstim, as a case study to evaluate the contexts in which Rt estimation methods have been used and identify unmet needs which would enable broader applicability of these methods in real-time. A scoping review, complemented by a small EpiEstim user survey, highlight issues with the current approaches, including the quality of input incidence data, the inability to account for geographical factors, and other methodological issues. We summarise the methods and software developed to tackle the problems identified, but conclude that significant gaps remain which should be addressed to enable easier, more robust and applicable estimation of Rt during epidemics.https://journals.plos.org/digitalhealth/article/file?id=10.1371/journal.pdig.0000052&type=printable |
| spellingShingle | Rebecca K Nash Pierre Nouvellet Anne Cori Real-time estimation of the epidemic reproduction number: Scoping review of the applications and challenges. PLOS Digital Health |
| title | Real-time estimation of the epidemic reproduction number: Scoping review of the applications and challenges. |
| title_full | Real-time estimation of the epidemic reproduction number: Scoping review of the applications and challenges. |
| title_fullStr | Real-time estimation of the epidemic reproduction number: Scoping review of the applications and challenges. |
| title_full_unstemmed | Real-time estimation of the epidemic reproduction number: Scoping review of the applications and challenges. |
| title_short | Real-time estimation of the epidemic reproduction number: Scoping review of the applications and challenges. |
| title_sort | real time estimation of the epidemic reproduction number scoping review of the applications and challenges |
| url | https://journals.plos.org/digitalhealth/article/file?id=10.1371/journal.pdig.0000052&type=printable |
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