The rapid replacement of the SARS-CoV-2 Delta variant by Omicron (B.1.1.529) in England.
Sci Transl Med
; 14(652): eabo5395, 2022 07 06.
Article
in English
| MEDLINE | ID: covidwho-1949956
ABSTRACT
The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.529 (Omicron) variant caused international concern due to its rapid spread in Southern Africa. It was unknown whether this variant would replace or coexist with (either transiently or long term) the then-dominant Delta variant on its introduction to England. We developed a set of hierarchical logistic growth models to describe changes in the frequency of S gene target failure (SGTF) PCR tests, a proxy for Omicron. The doubling time of SGTF cases peaked at 1.56 days (95% CI 1.49 to 1.63) on 5 December, whereas triple-positive cases were halving every 5.82 days (95% CI 5.11 to 6.67) going into Christmas 2021. We were unable to characterize the replacement of Delta by Omicron with a single rate. The replacement rate decreased by 53.56% (95% CrI 45.38 to 61.01) between 14 and 15 December, meaning the competitive advantage of Omicron approximately halved. Preceding the changepoint, Omicron was replacing Delta 16.24% (95% CrI 9.72 to 23.41) faster in those with two or more vaccine doses, indicative of vaccine escape being a substantial component of competitive advantage. Despite the slowdown, Delta was almost entirely replaced in England within a month of the first sequenced domestic case. The synchrony of changepoints across regions at various stages of Omicron epidemics suggests that the growth rate advantage was not attenuated because of biological mechanisms related to strain competition. The step change in replacement could have resulted from behavioral changes, potentially elicited by public health messaging or policies, that differentially affected Omicron.
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Epidemics
/
COVID-19
Type of study:
Observational study
Topics:
Vaccines
/
Variants
Limits:
Humans
Country/Region as subject:
Europa
Language:
English
Journal:
Sci Transl Med
Journal subject:
Science
/
Medicine
Year:
2022
Document Type:
Article
Affiliation country:
Scitranslmed.abo5395
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