ArticleNature communications2025
Tracing the spatial origins and spread of SARS-CoV-2 Omicron lineages in South Africa.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
7 citing papers in PubMed.
- Understanding patterns of variant emergence and spread in an ongoing epidemic.medRxiv : the preprint server for health sciences · 2026Article
- Divergent surveillance needs and resource allocation for COVID-19 and influenza: insights from a community-based syndromic surveillance study in Shanghai (2024-2025).Frontiers in public health · 2026Article
- Evolution and viral properties of the SARS-CoV-2 BA.3.2 subvariant.Virus evolution · 2026Article
- Identification and genomic characterization of BA.3.2: a highly divergent BA.3-related SARS-CoV-2 lineage from southern Africa.Virus evolution · 2026Article
- A Pandemic-Scale Ancestral Recombination Graph for SARS-CoV-2.bioRxiv : the preprint server for biology · 2025Article
- Neutralizing and binding antibodies are a correlate of risk of COVID-19 in the CoVPN 3008 study in people with HIV.Nature communications · 2025Article
- Mutation profiling, evolution analysis, molecular dynamics simulation, and functional characterization of Omicron sub-strains.Virus research · 2025Article
Corrections and comments
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Authors and funding
32 authors.
Funding
Abstract
Since November 2021, five genetically distinct SARS-CoV-2 Omicron lineages (BA.1-BA.5) are believed to have emerged in southern Africa, with four (BA.1, BA.2, BA.4, and BA.5) spreading globally and collectively dominating SARS-CoV-2 diversity. In 2023, BA.2.86, a highly divergent BA.2 lineage that rose to prominence worldwide, was first detected in Israel and Denmark, but the subsequent diversity of South African sequences suggests it too emerged in the region. Using Bayesian phylogeographic inference, we reconstruct the origins and dispersal patterns of BA.1-BA.5 and BA.2.86. Our findings suggest that Gauteng province in South Africa likely played a key role in the emergence and/or amplification of multiple Omicron lineages, though regions with limited sampling may have also contributed. The challenge of precisely tracing these origins highlights the need for broader genomic surveillance across the region to strengthen early detection, track viral evolution, and improve preparedness for future threats.
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Registered trials
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 Socratic graph.