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

Abstract

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.

Emergence of SARS-CoV-2 Omicron (B.1.1.529) variant, salient features, high global health concerns and strategies to counter it amid ongoing COVID-19 pandemic

“…Furthermore, few of the substitutions in Omicron are known to dampen the antibody binding (e.g., K417N). An improved model named as extended WKDE model has been made that performs the retrospective analysis based on the spatiotemporal information to infer the date of infection for individual cases and predict the risk of disease onset in the future ( Tong et al, 2021 ). Such more data-driven spatial prediction models need to be developed to reduce the dependence of theoretical assumptions and accurately predict the future disease onset, especially when we are combating Omicron having very high infection rates.…”

Efficient Neutralization of SARS-CoV-2 Omicron and Other VOCs by a Broad Spectrum Antibody 8G3

“…These mutations together reshaped the S confirmation, increased the stability, enhanced its binding affinity with ACE2 receptor, as well as assisted viral evasion from targeted immunotherapy [13][14][15][16] . The mutation related changes greatly affects the transmissibility of the virus, the symptoms of infection, and host immune response [17][18][19] . In addition to general immune evasion from neutralizing antibodies, Omicron also broadly caused dramatic reduction in the protective efficacy of vaccines and sera [20][21][22] [22][23][24], which leads to a reduction in the options of responding to the SARS-CoV-2 pandemic and forces the generation of more passive prevention policies.…”

Turning point: A new global COVID‐19 wave or a signal of the beginning of the end of the global COVID‐19 pandemic?

“…F I G U R E 4 Strategies to mitigate COVID-19 now and in the future [36][37][38][44][45][46][47][48]…”

“…The traditional vaccination and behavioral changes (wearing masks and reducing population density and personal contact) epidemic control model in the Olympic and paralympic games in Tokyo, Japan (at the same time as Japan's fifth pandemic wave) still apply to curb the spread of the virus in the world today, facing the Delta and Omicron variants 44 . Hierarchical management of different risk areas effectively contained the spread of Omicron in South Africa, and with daily vaccination rates increasing 10‐fold in every province of South Africa, the daily overall onset risk was only reduced by 0.34%−7.86% 45 . The spatiotemporal spread of Omicron was controlled by combining preventive measures and existing vaccines.…”