Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2
As COVID-19 is posing a serious threat to global health, the emerging mutation in SARS-CoV-2 genomes, for example, N501Y substitution, is one of the major challenges against control of the pandemic. Characterizing the relationship between mutation activities and the risk of severe clinical outcomes...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-04-01
|
| Series: | Viruses |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1999-4915/13/4/638 |
| _version_ | 1797538322816434176 |
|---|---|
| author | Shi Zhao Jingzhi Lou Marc K. C. Chong Lirong Cao Hong Zheng Zigui Chen Renee W. Y. Chan Benny C. Y. Zee Paul K. S. Chan Maggie H. Wang |
| author_facet | Shi Zhao Jingzhi Lou Marc K. C. Chong Lirong Cao Hong Zheng Zigui Chen Renee W. Y. Chan Benny C. Y. Zee Paul K. S. Chan Maggie H. Wang |
| author_sort | Shi Zhao |
| collection | DOAJ |
| description | As COVID-19 is posing a serious threat to global health, the emerging mutation in SARS-CoV-2 genomes, for example, N501Y substitution, is one of the major challenges against control of the pandemic. Characterizing the relationship between mutation activities and the risk of severe clinical outcomes is of public health importance for informing the healthcare decision-making process. Using a likelihood-based approach, we developed a statistical framework to reconstruct a time-varying and variant-specific case fatality ratio (CFR), and to estimate changes in CFR associated with a single mutation empirically. For illustration, the statistical framework is implemented to the COVID-19 surveillance data in the United Kingdom (UK). The reconstructed instantaneous CFR gradually increased from 1.0% in September to 2.2% in November 2020 and stabilized at this level thereafter, which monitors the mortality risk of COVID-19 on a real-time basis. We identified a link between the SARS-CoV-2 mutation activity at molecular scale and COVID-19 mortality risk at population scale, and found that the 501Y variants may slightly but not significantly increase 18% of fatality risk than the preceding 501N variants. We found no statistically significant evidence of change in COVID-19 mortality risk associated with 501Y variants, and highlighted the real-time estimating potentials of the modelling framework. |
| first_indexed | 2024-03-10T12:29:50Z |
| format | Article |
| id | doaj.art-56e8eb58e8384c799d99a93373a30030 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T12:29:50Z |
| publishDate | 2021-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-56e8eb58e8384c799d99a93373a300302023-11-21T14:45:51ZengMDPI AGViruses1999-49152021-04-0113463810.3390/v13040638Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2Shi Zhao0Jingzhi Lou1Marc K. C. Chong2Lirong Cao3Hong Zheng4Zigui Chen5Renee W. Y. Chan6Benny C. Y. Zee7Paul K. S. Chan8Maggie H. Wang9JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, ChinaJC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, ChinaJC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, ChinaJC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, ChinaJC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, ChinaDepartment of Microbiology, Chinese University of Hong Kong, Hong Kong, ChinaDepartment of Pediatrics, Chinese University of Hong Kong, Hong Kong, ChinaJC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, ChinaDepartment of Microbiology, Chinese University of Hong Kong, Hong Kong, ChinaJC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, ChinaAs COVID-19 is posing a serious threat to global health, the emerging mutation in SARS-CoV-2 genomes, for example, N501Y substitution, is one of the major challenges against control of the pandemic. Characterizing the relationship between mutation activities and the risk of severe clinical outcomes is of public health importance for informing the healthcare decision-making process. Using a likelihood-based approach, we developed a statistical framework to reconstruct a time-varying and variant-specific case fatality ratio (CFR), and to estimate changes in CFR associated with a single mutation empirically. For illustration, the statistical framework is implemented to the COVID-19 surveillance data in the United Kingdom (UK). The reconstructed instantaneous CFR gradually increased from 1.0% in September to 2.2% in November 2020 and stabilized at this level thereafter, which monitors the mortality risk of COVID-19 on a real-time basis. We identified a link between the SARS-CoV-2 mutation activity at molecular scale and COVID-19 mortality risk at population scale, and found that the 501Y variants may slightly but not significantly increase 18% of fatality risk than the preceding 501N variants. We found no statistically significant evidence of change in COVID-19 mortality risk associated with 501Y variants, and highlighted the real-time estimating potentials of the modelling framework.https://www.mdpi.com/1999-4915/13/4/638COVID-19SARS-CoV-2N501Y substitutionB.1.1.7 lineagecase fatalitystatistical modelling |
| spellingShingle | Shi Zhao Jingzhi Lou Marc K. C. Chong Lirong Cao Hong Zheng Zigui Chen Renee W. Y. Chan Benny C. Y. Zee Paul K. S. Chan Maggie H. Wang Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2 Viruses COVID-19 SARS-CoV-2 N501Y substitution B.1.1.7 lineage case fatality statistical modelling |
| title | Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2 |
| title_full | Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2 |
| title_fullStr | Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2 |
| title_full_unstemmed | Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2 |
| title_short | Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2 |
| title_sort | inferring the association between the risk of covid 19 case fatality and n501y substitution in sars cov 2 |
| topic | COVID-19 SARS-CoV-2 N501Y substitution B.1.1.7 lineage case fatality statistical modelling |
| url | https://www.mdpi.com/1999-4915/13/4/638 |
| work_keys_str_mv | AT shizhao inferringtheassociationbetweentheriskofcovid19casefatalityandn501ysubstitutioninsarscov2 AT jingzhilou inferringtheassociationbetweentheriskofcovid19casefatalityandn501ysubstitutioninsarscov2 AT marckcchong inferringtheassociationbetweentheriskofcovid19casefatalityandn501ysubstitutioninsarscov2 AT lirongcao inferringtheassociationbetweentheriskofcovid19casefatalityandn501ysubstitutioninsarscov2 AT hongzheng inferringtheassociationbetweentheriskofcovid19casefatalityandn501ysubstitutioninsarscov2 AT ziguichen inferringtheassociationbetweentheriskofcovid19casefatalityandn501ysubstitutioninsarscov2 AT reneewychan inferringtheassociationbetweentheriskofcovid19casefatalityandn501ysubstitutioninsarscov2 AT bennycyzee inferringtheassociationbetweentheriskofcovid19casefatalityandn501ysubstitutioninsarscov2 AT paulkschan inferringtheassociationbetweentheriskofcovid19casefatalityandn501ysubstitutioninsarscov2 AT maggiehwang inferringtheassociationbetweentheriskofcovid19casefatalityandn501ysubstitutioninsarscov2 |