EpiMix: a novel method to estimate effective reproduction number
Transmission potential of a pathogen, often quantified by the time-varying reproduction number Rt, provides the current pace of infection for a disease and indicates whether an emerging epidemic is under control. In this study, we proposed a novel method, EpiMix, for Rt estimation, wherein we incorp...
| Main Authors: | , , , |
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| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
| Published: |
2024
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| Online Access: | https://hdl.handle.net/10356/173541 |
| _version_ | 1824453880732188672 |
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| author | Jin, Shihui Dickens, Borame Lee Lim, Jue Tao Cook, Alex R. |
| author2 | Lee Kong Chian School of Medicine (LKCMedicine) |
| author_facet | Lee Kong Chian School of Medicine (LKCMedicine) Jin, Shihui Dickens, Borame Lee Lim, Jue Tao Cook, Alex R. |
| author_sort | Jin, Shihui |
| collection | NTU |
| description | Transmission potential of a pathogen, often quantified by the time-varying reproduction number Rt, provides the current pace of infection for a disease and indicates whether an emerging epidemic is under control. In this study, we proposed a novel method, EpiMix, for Rt estimation, wherein we incorporated the impacts of exogenous factors and random effects under a Bayesian regression framework. Using Integrated Nested Laplace Approximation, EpiMix is able to efficiently generate reliable, deterministic Rt estimates. In the simulations and case studies performed, we further demonstrated the method's robustness in low-incidence scenarios, together with other merits, including its flexibility in selecting variables and tolerance of varying reporting rates. All these make EpiMix a potentially useful tool for real-time Rt estimation provided that the serial interval distribution, time series of case counts and external influencing factors are available. |
| first_indexed | 2025-02-19T03:13:27Z |
| format | Journal Article |
| id | ntu-10356/173541 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2025-02-19T03:13:27Z |
| publishDate | 2024 |
| record_format | dspace |
| spelling | ntu-10356/1735412024-02-18T15:38:14Z EpiMix: a novel method to estimate effective reproduction number Jin, Shihui Dickens, Borame Lee Lim, Jue Tao Cook, Alex R. Lee Kong Chian School of Medicine (LKCMedicine) Medicine, Health and Life Sciences Epidemics Reproduction Number Transmission potential of a pathogen, often quantified by the time-varying reproduction number Rt, provides the current pace of infection for a disease and indicates whether an emerging epidemic is under control. In this study, we proposed a novel method, EpiMix, for Rt estimation, wherein we incorporated the impacts of exogenous factors and random effects under a Bayesian regression framework. Using Integrated Nested Laplace Approximation, EpiMix is able to efficiently generate reliable, deterministic Rt estimates. In the simulations and case studies performed, we further demonstrated the method's robustness in low-incidence scenarios, together with other merits, including its flexibility in selecting variables and tolerance of varying reporting rates. All these make EpiMix a potentially useful tool for real-time Rt estimation provided that the serial interval distribution, time series of case counts and external influencing factors are available. Ministry of Education (MOE) Ministry of Health (MOH) National Medical Research Council (NMRC) Published version This research was supported by Singapore’s Ministry of Education (through a Tier 1 grant), the National University of Singapore (through a Reimagine Research grant), and the Singapore Ministry of Health’s National Medical Research Council under its National Epidemic Preparedness and Response R&D Funding Initiative (MOH-001041) Programme for Research in Epidemic Preparedness And REsponse (PREPARE). 2024-02-13T06:13:14Z 2024-02-13T06:13:14Z 2023 Journal Article Jin, S., Dickens, B. L., Lim, J. T. & Cook, A. R. (2023). EpiMix: a novel method to estimate effective reproduction number. Infectious Disease Modelling, 8(3), 704-716. https://dx.doi.org/10.1016/j.idm.2023.06.002 2468-0427 https://hdl.handle.net/10356/173541 10.1016/j.idm.2023.06.002 37416322 3 8 704 716 en MOH-001041 Infectious Disease Modelling © 2023 The Authors. Publishing services by Elsevier B.V. on behalf of KeAi Communications Co. Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). application/pdf |
| spellingShingle | Medicine, Health and Life Sciences Epidemics Reproduction Number Jin, Shihui Dickens, Borame Lee Lim, Jue Tao Cook, Alex R. EpiMix: a novel method to estimate effective reproduction number |
| title | EpiMix: a novel method to estimate effective reproduction number |
| title_full | EpiMix: a novel method to estimate effective reproduction number |
| title_fullStr | EpiMix: a novel method to estimate effective reproduction number |
| title_full_unstemmed | EpiMix: a novel method to estimate effective reproduction number |
| title_short | EpiMix: a novel method to estimate effective reproduction number |
| title_sort | epimix a novel method to estimate effective reproduction number |
| topic | Medicine, Health and Life Sciences Epidemics Reproduction Number |
| url | https://hdl.handle.net/10356/173541 |
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