ArticleeLife2022
COVID-19 pandemic dynamics in South Africa and epidemiological characteristics of three variants of concern (Beta, Delta, and Omicron).
Article in eLife, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers, 1 of them a synthesis that pooled it.
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Who cites it
45 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Predictive models for health outcomes due to SARS-CoV-2, including the effect of vaccination: a systematic review.Systematic reviews · 2024Pooled it
- COVID-19's Shadow: The Effect of COVID-19 on Cytopathology Specimens Received at an Academic Laboratory in Central South Africa.Cytopathology : official journal of the British Society for Clinical Cytology · 2026Article
- Bayesian Spatio-Temporal Outbreak Detection for COVID-19 Mortality in South Africa: A Comparative Study of MCMC and Dynamic HMC Methods.Research square · 2026Article
- Accelerated Increase in Candida auris Bloodstream Infections during COVID-19 Pandemic, South Africa.Emerging infectious diseases · 2026Article
- Glycan-binding properties of SARS-CoV-2 spike proteins: interactions with aminoglycoside antibiotics.Scientific reports · 2026Article
- SARS-CoV-2 neutralising antibody profiles reveal variant specific antibody dynamics and regional differences in infection histories in Malawi.PLOS global public health · 2026Article
- Comparative evaluation of behavioral epidemic models using COVID-19 data.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Perceived stress and lower back pain amongst nurses during the SARS-CoV-2, across hospitals in Durban, South Africa.Curationis · 2025Article
- SARS-CoV-2 dynamics in New York City during March 2020-August 2023.Communications medicine · 2025Article
- SARS-CoV-2 transmission dynamics in Mozambique and Zimbabwe during the first 3 years of the pandemic.Royal Society open science · 2025Article
- Variant patterns and influence of inter-regional travel during the SARS-CoV-2 expansion in South Africa.PloS one · 2025Article
- Bayesian modeling of the effect of vaccination and the delta and omicron variants on the COVID-19 epidemic in Burkina Faso using poisson log-linear autoregressive model.Frontiers in public health · 2025Article
- A two-variant model of SARS-COV-2 transmission: estimating the characteristics of a newly emerging strain.BMC infectious diseases · 2024Article
- Update on Omicron variant and its threat to vulnerable populations.Public health in practice (Oxford, England) · 2024Review
- Reconciling the efficacy and effectiveness of masking on epidemic outcomes.Journal of the Royal Society, Interface · 2024Article
- Online public concern about allergic rhinitis and its association with COVID-19 and air quality in China: an informative epidemiological study using Baidu index.BMC public health · 2024Article
- Article
- Post-acute sequelae of SARS-CoV-2 infection in health care workers from South Africa.Oxford open immunology · 2024Article
- Adopting sustainable innovations for remote access to TB and HIV care in South Africa.PLOS global public health · 2024Article
- The impact of public transportation on the transmission of COVID-19 in Rwanda.Frontiers in public health · 2024Article
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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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.