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The Spread of SARS-CoV-2 Variant Omicron with a Doubling Time of 2.0–3.3 Days Can Be Explained by Immune Evasion

Omicron, the novel highly mutated SARS-CoV-2 Variant of Concern (VOC, Pango lineage B.1.1.529) was first collected in early November 2021 in South Africa. By the end of November 2021, it had spread and approached fixation in South Africa, and had been detected on all continents. We analyzed the expo...

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Autores principales: Grabowski, Frederic, Kochańczyk, Marek, Lipniacki, Tomasz
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8875689/
https://www.ncbi.nlm.nih.gov/pubmed/35215887
http://dx.doi.org/10.3390/v14020294
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author Grabowski, Frederic
Kochańczyk, Marek
Lipniacki, Tomasz
author_facet Grabowski, Frederic
Kochańczyk, Marek
Lipniacki, Tomasz
author_sort Grabowski, Frederic
collection PubMed
description Omicron, the novel highly mutated SARS-CoV-2 Variant of Concern (VOC, Pango lineage B.1.1.529) was first collected in early November 2021 in South Africa. By the end of November 2021, it had spread and approached fixation in South Africa, and had been detected on all continents. We analyzed the exponential growth of Omicron over four-week periods in the two most populated of South Africa’s provinces, Gauteng and KwaZulu-Natal, arriving at the doubling time estimates of, respectively, 3.3 days (95% CI: 3.2–3.4 days) and 2.7 days (95% CI: 2.3–3.3 days). Similar or even shorter doubling times were observed in other locations: Australia (3.0 days), New York State (2.5 days), UK (2.4 days), and Denmark (2.0 days). Log–linear regression suggests that the spread began in Gauteng around 11 October 2021; however, due to presumable stochasticity in the initial spread, this estimate can be inaccurate. Phylogenetics-based analysis indicates that the Omicron strain started to diverge between 6 October and 29 October 2021. We estimated that the weekly growth of the ratio of Omicron to Delta is in the range of 7.2–10.2, considerably higher than the growth of the ratio of Delta to Alpha (estimated to be in in the range of 2.5–4.2), and Alpha to pre-existing strains (estimated to be in the range of 1.8–2.7). High relative growth does not necessarily imply higher Omicron infectivity. A two-strain SEIR model suggests that the growth advantage of Omicron may stem from immune evasion, which permits this VOC to infect both recovered and fully vaccinated individuals. As we demonstrated within the model, immune evasion is more concerning than increased transmissibility, because it can facilitate larger epidemic outbreaks.
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spelling pubmed-88756892022-02-26 The Spread of SARS-CoV-2 Variant Omicron with a Doubling Time of 2.0–3.3 Days Can Be Explained by Immune Evasion Grabowski, Frederic Kochańczyk, Marek Lipniacki, Tomasz Viruses Communication Omicron, the novel highly mutated SARS-CoV-2 Variant of Concern (VOC, Pango lineage B.1.1.529) was first collected in early November 2021 in South Africa. By the end of November 2021, it had spread and approached fixation in South Africa, and had been detected on all continents. We analyzed the exponential growth of Omicron over four-week periods in the two most populated of South Africa’s provinces, Gauteng and KwaZulu-Natal, arriving at the doubling time estimates of, respectively, 3.3 days (95% CI: 3.2–3.4 days) and 2.7 days (95% CI: 2.3–3.3 days). Similar or even shorter doubling times were observed in other locations: Australia (3.0 days), New York State (2.5 days), UK (2.4 days), and Denmark (2.0 days). Log–linear regression suggests that the spread began in Gauteng around 11 October 2021; however, due to presumable stochasticity in the initial spread, this estimate can be inaccurate. Phylogenetics-based analysis indicates that the Omicron strain started to diverge between 6 October and 29 October 2021. We estimated that the weekly growth of the ratio of Omicron to Delta is in the range of 7.2–10.2, considerably higher than the growth of the ratio of Delta to Alpha (estimated to be in in the range of 2.5–4.2), and Alpha to pre-existing strains (estimated to be in the range of 1.8–2.7). High relative growth does not necessarily imply higher Omicron infectivity. A two-strain SEIR model suggests that the growth advantage of Omicron may stem from immune evasion, which permits this VOC to infect both recovered and fully vaccinated individuals. As we demonstrated within the model, immune evasion is more concerning than increased transmissibility, because it can facilitate larger epidemic outbreaks. MDPI 2022-01-30 /pmc/articles/PMC8875689/ /pubmed/35215887 http://dx.doi.org/10.3390/v14020294 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Communication
Grabowski, Frederic
Kochańczyk, Marek
Lipniacki, Tomasz
The Spread of SARS-CoV-2 Variant Omicron with a Doubling Time of 2.0–3.3 Days Can Be Explained by Immune Evasion
title The Spread of SARS-CoV-2 Variant Omicron with a Doubling Time of 2.0–3.3 Days Can Be Explained by Immune Evasion
title_full The Spread of SARS-CoV-2 Variant Omicron with a Doubling Time of 2.0–3.3 Days Can Be Explained by Immune Evasion
title_fullStr The Spread of SARS-CoV-2 Variant Omicron with a Doubling Time of 2.0–3.3 Days Can Be Explained by Immune Evasion
title_full_unstemmed The Spread of SARS-CoV-2 Variant Omicron with a Doubling Time of 2.0–3.3 Days Can Be Explained by Immune Evasion
title_short The Spread of SARS-CoV-2 Variant Omicron with a Doubling Time of 2.0–3.3 Days Can Be Explained by Immune Evasion
title_sort spread of sars-cov-2 variant omicron with a doubling time of 2.0–3.3 days can be explained by immune evasion
topic Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8875689/
https://www.ncbi.nlm.nih.gov/pubmed/35215887
http://dx.doi.org/10.3390/v14020294
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