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Tracking and controlling the spatiotemporal spread of SARS-CoV-2 Omicron variant in South Africa

BACKGROUND: South Africa is the focus of the current epidemic caused by Omicron. Understanding the spatiotemporal spread of Omicron in South Africa and how to control it is crucial to global countries. METHODS: To explore the spatiotemporal spread of Omicron in 9 provinces in South Africa, a provinc...

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Autores principales: Tong, Chengzhuo, Shi, Wenzhong, Zhang, Anshu, Shi, Zhicheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Published by Elsevier Ltd. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8716148/
https://www.ncbi.nlm.nih.gov/pubmed/34973454
http://dx.doi.org/10.1016/j.tmaid.2021.102252
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author Tong, Chengzhuo
Shi, Wenzhong
Zhang, Anshu
Shi, Zhicheng
author_facet Tong, Chengzhuo
Shi, Wenzhong
Zhang, Anshu
Shi, Zhicheng
author_sort Tong, Chengzhuo
collection PubMed
description BACKGROUND: South Africa is the focus of the current epidemic caused by Omicron. Understanding the spatiotemporal spread of Omicron in South Africa and how to control it is crucial to global countries. METHODS: To explore the spatiotemporal spread of Omicron in 9 provinces in South Africa, a province-level geographic prediction model of COVID-19 symptom onset risk, is proposed. RESULTS: It has been found that i) The spatiotemporal spread was relatively slow during the first stage and following the emergence of Omicron in Gauteng. The spatial spread of Omicron accelerated after it had become the dominant variant, and continued to spread from Gauteng to the neighboring provinces and main transport nodes. ii) Compared with current Alert Levels 1–4 in all provinces, the imposition of lockdown in the high-onset-risk Gauteng together with the Alert Level 1 in other 8 provinces, was found to more effectively control the spread of Omicron in South Africa. Moreover, it can reduce the spread of the Omicron epidemic in the provinces where main international airports are located to other parts of the world. iii) Due to declining vaccine efficiency over time, even when the daily vaccination rates in each province increased by 10 times, the daily overall onset risk was only reduced by 0.34%–7.86%. CONCLUSIONS: Our study has provided a comprehensive investigation concerning the spatiotemporal dynamics of Omicron and hence provided scientific findings to enable a contribution which will assist in controlling the spatiotemporal spread of Omicron by integrating the prevention measures and vaccination.
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spelling pubmed-87161482021-12-30 Tracking and controlling the spatiotemporal spread of SARS-CoV-2 Omicron variant in South Africa Tong, Chengzhuo Shi, Wenzhong Zhang, Anshu Shi, Zhicheng Travel Med Infect Dis Article BACKGROUND: South Africa is the focus of the current epidemic caused by Omicron. Understanding the spatiotemporal spread of Omicron in South Africa and how to control it is crucial to global countries. METHODS: To explore the spatiotemporal spread of Omicron in 9 provinces in South Africa, a province-level geographic prediction model of COVID-19 symptom onset risk, is proposed. RESULTS: It has been found that i) The spatiotemporal spread was relatively slow during the first stage and following the emergence of Omicron in Gauteng. The spatial spread of Omicron accelerated after it had become the dominant variant, and continued to spread from Gauteng to the neighboring provinces and main transport nodes. ii) Compared with current Alert Levels 1–4 in all provinces, the imposition of lockdown in the high-onset-risk Gauteng together with the Alert Level 1 in other 8 provinces, was found to more effectively control the spread of Omicron in South Africa. Moreover, it can reduce the spread of the Omicron epidemic in the provinces where main international airports are located to other parts of the world. iii) Due to declining vaccine efficiency over time, even when the daily vaccination rates in each province increased by 10 times, the daily overall onset risk was only reduced by 0.34%–7.86%. CONCLUSIONS: Our study has provided a comprehensive investigation concerning the spatiotemporal dynamics of Omicron and hence provided scientific findings to enable a contribution which will assist in controlling the spatiotemporal spread of Omicron by integrating the prevention measures and vaccination. Published by Elsevier Ltd. 2022 2021-12-30 /pmc/articles/PMC8716148/ /pubmed/34973454 http://dx.doi.org/10.1016/j.tmaid.2021.102252 Text en © 2021 Published by Elsevier Ltd. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
spellingShingle Article
Tong, Chengzhuo
Shi, Wenzhong
Zhang, Anshu
Shi, Zhicheng
Tracking and controlling the spatiotemporal spread of SARS-CoV-2 Omicron variant in South Africa
title Tracking and controlling the spatiotemporal spread of SARS-CoV-2 Omicron variant in South Africa
title_full Tracking and controlling the spatiotemporal spread of SARS-CoV-2 Omicron variant in South Africa
title_fullStr Tracking and controlling the spatiotemporal spread of SARS-CoV-2 Omicron variant in South Africa
title_full_unstemmed Tracking and controlling the spatiotemporal spread of SARS-CoV-2 Omicron variant in South Africa
title_short Tracking and controlling the spatiotemporal spread of SARS-CoV-2 Omicron variant in South Africa
title_sort tracking and controlling the spatiotemporal spread of sars-cov-2 omicron variant in south africa
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8716148/
https://www.ncbi.nlm.nih.gov/pubmed/34973454
http://dx.doi.org/10.1016/j.tmaid.2021.102252
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