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COVID-19 pandemic dynamics in South Africa and epidemiological characteristics of three variants of concern (Beta, Delta, and Omicron).
Yang, Wan; Shaman, Jeffrey L.
  • Yang W; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, United States.
  • Shaman JL; Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, United States.
Elife ; 112022 08 09.
Article in English | MEDLINE | ID: covidwho-2067161
ABSTRACT
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Pandemics / COVID-19 Type of study: Observational study / Prognostic study Topics: Vaccines / Variants Limits: Humans Country/Region as subject: Africa / North America Language: English Year: 2022 Document Type: Article Affiliation country: ELife.78933

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Pandemics / COVID-19 Type of study: Observational study / Prognostic study Topics: Vaccines / Variants Limits: Humans Country/Region as subject: Africa / North America Language: English Year: 2022 Document Type: Article Affiliation country: ELife.78933