Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2
Abstract Background The COVID-19 pandemic poses serious threats to global health, and the emerging mutation in SARS-CoV-2 genomes, e.g., the D614G substitution, is one of the major challenges of disease control. Characterizing the role of the mutation activities is of importance to understand how th...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2021-10-01
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| Series: | BMC Infectious Diseases |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12879-021-06729-w |
| _version_ | 1818908736432898048 |
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| author | Shi Zhao Jingzhi Lou Lirong Cao Hong Zheng Marc K. C. Chong Zigui Chen Renee W. Y. Chan Benny C. Y. Zee Paul K. S. Chan Maggie H. Wang |
| author_facet | Shi Zhao Jingzhi Lou Lirong Cao Hong Zheng Marc K. C. Chong Zigui Chen Renee W. Y. Chan Benny C. Y. Zee Paul K. S. Chan Maggie H. Wang |
| author_sort | Shi Zhao |
| collection | DOAJ |
| description | Abstract Background The COVID-19 pandemic poses serious threats to global health, and the emerging mutation in SARS-CoV-2 genomes, e.g., the D614G substitution, is one of the major challenges of disease control. Characterizing the role of the mutation activities is of importance to understand how the evolution of pathogen shapes the epidemiological outcomes at population scale. Methods We developed a statistical framework to reconstruct variant-specific reproduction numbers and estimate transmission advantage associated with the mutation activities marked by single substitution empirically. Using likelihood-based approach, the model is exemplified with the COVID-19 surveillance data from January 1 to June 30, 2020 in California, USA. We explore the potential of this framework to generate early warning signals for detecting transmission advantage on a real-time basis. Results The modelling framework in this study links together the mutation activity at molecular scale and COVID-19 transmissibility at population scale. We find a significant transmission advantage of COVID-19 associated with the D614G substitution, which increases the infectivity by 54% (95%CI: 36, 72). For the early alarming potentials, the analytical framework is demonstrated to detect this transmission advantage, before the mutation reaches dominance, on a real-time basis. Conclusions We reported an evidence of transmission advantage associated with D614G substitution, and highlighted the real-time estimating potentials of modelling framework. |
| first_indexed | 2024-12-19T22:15:45Z |
| format | Article |
| id | doaj.art-486435eb2dd74abcb4ff95026fb2c8c3 |
| institution | Directory Open Access Journal |
| issn | 1471-2334 |
| language | English |
| last_indexed | 2024-12-19T22:15:45Z |
| publishDate | 2021-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Infectious Diseases |
| spelling | doaj.art-486435eb2dd74abcb4ff95026fb2c8c32022-12-21T20:03:46ZengBMCBMC Infectious Diseases1471-23342021-10-012111810.1186/s12879-021-06729-wReal-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2Shi Zhao0Jingzhi Lou1Lirong Cao2Hong Zheng3Marc K. C. Chong4Zigui Chen5Renee W. Y. Chan6Benny C. Y. Zee7Paul K. S. Chan8Maggie H. Wang9JC School of Public Health and Primary Care, Chinese University of Hong KongJC School of Public Health and Primary Care, Chinese University of Hong KongJC School of Public Health and Primary Care, Chinese University of Hong KongJC School of Public Health and Primary Care, Chinese University of Hong KongJC School of Public Health and Primary Care, Chinese University of Hong KongDepartment of Microbiology, Chinese University of Hong KongDepartment of Paediatrics, Chinese University of Hong KongJC School of Public Health and Primary Care, Chinese University of Hong KongDepartment of Microbiology, Chinese University of Hong KongJC School of Public Health and Primary Care, Chinese University of Hong KongAbstract Background The COVID-19 pandemic poses serious threats to global health, and the emerging mutation in SARS-CoV-2 genomes, e.g., the D614G substitution, is one of the major challenges of disease control. Characterizing the role of the mutation activities is of importance to understand how the evolution of pathogen shapes the epidemiological outcomes at population scale. Methods We developed a statistical framework to reconstruct variant-specific reproduction numbers and estimate transmission advantage associated with the mutation activities marked by single substitution empirically. Using likelihood-based approach, the model is exemplified with the COVID-19 surveillance data from January 1 to June 30, 2020 in California, USA. We explore the potential of this framework to generate early warning signals for detecting transmission advantage on a real-time basis. Results The modelling framework in this study links together the mutation activity at molecular scale and COVID-19 transmissibility at population scale. We find a significant transmission advantage of COVID-19 associated with the D614G substitution, which increases the infectivity by 54% (95%CI: 36, 72). For the early alarming potentials, the analytical framework is demonstrated to detect this transmission advantage, before the mutation reaches dominance, on a real-time basis. Conclusions We reported an evidence of transmission advantage associated with D614G substitution, and highlighted the real-time estimating potentials of modelling framework.https://doi.org/10.1186/s12879-021-06729-wCOVID-19MutationTransmission advantageReal-time estimationStatistical modelling |
| spellingShingle | Shi Zhao Jingzhi Lou Lirong Cao Hong Zheng Marc K. C. Chong Zigui Chen Renee W. Y. Chan Benny C. Y. Zee Paul K. S. Chan Maggie H. Wang Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2 BMC Infectious Diseases COVID-19 Mutation Transmission advantage Real-time estimation Statistical modelling |
| title | Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2 |
| title_full | Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2 |
| title_fullStr | Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2 |
| title_full_unstemmed | Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2 |
| title_short | Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2 |
| title_sort | real time quantification of the transmission advantage associated with a single mutation in pathogen genomes a case study on the d614g substitution of sars cov 2 |
| topic | COVID-19 Mutation Transmission advantage Real-time estimation Statistical modelling |
| url | https://doi.org/10.1186/s12879-021-06729-w |
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