ArticleVirus evolution2021
Transmission dynamics of SARS-CoV-2 within-host diversity in two major hospital outbreaks in South Africa.
Article in Virus evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed, 39 citations in OpenAlex.
- Intra-host variation and transmission dynamics of SARS-CoV-2 Omicron outbreaks in Shandong, China.mSphere · 2025Article
- JUNIPER: Reconstructing Transmission Events from Next-Generation Sequencing Data at Scale.Research square · 2025Article
- JUNIPER: Reconstructing Transmission Events from Next-Generation Sequencing Data at Scale.medRxiv : the preprint server for health sciences · 2025Article
- Reply to: Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data.Nature communications · 2024Article
- Genomic epidemiology reveals the variation and transmission properties of SARS-CoV-2 in a single-source community outbreak.Virus evolution · 2024Article
- Article
- Inferring Viral Transmission Pathways from Within-Host Variation.medRxiv : the preprint server for health sciences · 2023Article
- SARS-CoV-2 Co-Infections and Recombinations Identified by Long-Read Single-Molecule Real-Time Sequencing.Microbiology spectrum · 2023Article
- Epidemiological inference for emerging viruses using segregating sites.Nature communications · 2023Article
- Web Resources for SARS-CoV-2 Genomic Database, Annotation, Analysis and Variant Tracking.Viruses · 2023Review
- Whole genome characterization and evolutionary analysis of bovine ephemeral fever virus isolated in Iran.Archives of microbiology · 2023Article
- Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples.PLoS pathogens · 2023Review
- Within-host genetic diversity of SARS-CoV-2 lineages in unvaccinated and vaccinated individuals.Nature communications · 2023Article
- Challenges in Harnessing Shared Within-Host Severe Acute Respiratory Syndrome Coronavirus 2 Variation for Transmission Inference.Open forum infectious diseases · 2023Article
- SARS-CoV-2 spike protein diversity at an intra-host level, among SARS-CoV-2 infected individuals in South Africa, 2020 to 2022.PloS one · 2023Article
- Lessons learned: use of WGS in real-time investigation of suspected intrahospital SARS-CoV-2 outbreaks.The Journal of hospital infection · 2023Article
- Tracking outbreak dynamics using within-host variation.Nature microbiology · 2022Article
- Understanding Early Pandemic Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in a Medical Center by Incorporating Public Sequencing Databases to Mitigate Bias.The Journal of infectious diseases · 2022Article
- Within-host diversity of SARS-CoV-2 lineages and effect of vaccination.Research square · 2022Article
- Statistical Challenges in Tracking the Evolution of SARS-CoV-2.Statistical science : a review journal of the Institute of Mathematical Statistics · 2022Article
Corrections and comments
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Authors and funding
19 authors at 7 institutions in 5 countries.
Funding
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes acute, highly transmissible respiratory infection in humans and a wide range of animal species. Its rapid global spread has resulted in a major public health emergency, necessitating commensurately rapid research to improve control strategies. In particular, the ability to effectively retrace transmission chains in outbreaks remains a major challenge, partly due to our limited understanding of the virus' underlying evolutionary dynamics within and between hosts. We used high-throughput sequencing whole-genome data coupled with bottleneck analysis to retrace the pathways of viral transmission in two nosocomial outbreaks that were previously characterised by epidemiological and phylogenetic methods. Additionally, we assessed the mutational landscape, selection pressures, and diversity at the within-host level for both outbreaks. Our findings show evidence of within-host selection and transmission of variants between samples. Both bottleneck and diversity analyses highlight within-host and consensus-level variants shared by putative source-recipient pairs in both outbreaks, suggesting that certain within-host variants in these outbreaks may have been transmitted upon infection rather than arising
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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 OpenQuestion graph.