COVID-19 pandemic dynamics in South Africa and epidemiological characteristics of three variants of concern (Beta, Delta, and Omicron).
COVID-19 pandemic dynamics in South Africa and epidemiological characteristics of three variants of concern (Beta, Delta, and Omicron).
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DOI：
10.7554/elife.78933
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发表时间：
2022-08-09
期刊：
影响因子：
7.7
通讯作者：
Shaman, Jeffrey L.
中科院分区：
文献类型：
--
作者：
Yang, Wan;Shaman, Jeffrey L.
严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 相关变种 (VOC) 是 2019 年新型冠状病毒病 (COVID-19) 大流行的关键驱动因素。为了更好地了解不同的流行病学特征，我们在这里应用模型推理系统来重建南非的 SARS-CoV-2 传播动态，该国到 2022 年 2 月经历了三次 VOC 大流行浪潮（即 Beta、Delta 和 Omicron BA.1）。我们估计了 2020 年 3 月至 2022 年 2 月期间南非九个省份的关键流行病学数量，同时考虑了检测率的变化、感染季节性、非药物干预和疫苗接种。模型验证表明，估计的基础感染率和关键参数（例如感染检出率和感染死亡风险）与独立的流行病学数据和调查一致。此外，回顾性预测可以捕捉模型训练期之外的流行病轨迹。因此，这些详细的、经过验证的模型推断估计能够量化三种主要 SARS-CoV-2 VOC（即 Beta、Delta 和 Omicron BA.1）的免疫侵蚀潜力和传播性。这些发现有助于阐明不断变化的 COVID-19 动态并为未来的公共卫生规划提供信息。
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) have been key drivers of new coronavirus disease 2019 (COVID-19) pandemic waves. To better understand variant epidemiologic characteristics, here we apply a model-inference system to reconstruct SARS-CoV-2 transmission dynamics in South Africa, a country that has experienced three VOC pandemic waves (i.e. Beta, Delta, and Omicron BA.1) by February 2022. We estimate key epidemiologic quantities in each of the nine South African provinces during March 2020 to February 2022, while accounting for changing detection rates, infection seasonality, nonpharmaceutical interventions, and vaccination. Model validation shows that estimated underlying infection rates and key parameters (e.g. infection-detection rate and infection-fatality risk) are in line with independent epidemiological data and investigations. In addition, retrospective predictions capture pandemic trajectories beyond the model training period. These detailed, validated model-inference estimates thus enable quantification of both the immune erosion potential and transmissibility of three major SARS-CoV-2 VOCs, that is, Beta, Delta, and Omicron BA.1. These findings help elucidate changing COVID-19 dynamics and inform future public health planning.