ArticleeLife2023
Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks.
Article in eLife, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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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.
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Who cites it
14 citing papers in PubMed, 11 citations in OpenAlex.
- SARS-CoV-2 intra-host variation shows evidence of transmission and convergent evolution in a university surveillance cohort.Microbial genomics · 2026Article
- Investigating Bacillus anthracis genomic diversity and trait-specific lineages in an endemic area in northern Tanzania through a combination of traditional and culture-free sequencing approaches.PLoS neglected tropical diseases · 2026Article
- Genomic and Phylogenetic Dissection of SARS-CoV-2 Transmission Networks in Healthcare Workers.International journal of microbiology · 2026Article
- Oxford Nanopore Sequencing in pediatric emergency infectious diseases: from rapid diagnosis to precision medicine.Frontiers in cellular and infection microbiology · 2026Review
- SARS-CoV-2 Intra-host Variation Shows Evidence of Transmission and Convergent Evolution in a University Surveillance Cohort.bioRxiv : the preprint server for biology · 2025Article
- InvestigatingbioRxiv : the preprint server for biology · 2025Article
- Musculoskeletal biomarkers in health and disease: implications for the aging spine-a review for spinal surgeons by the SRS adult spinal deformity task force on senescence.Spine deformity · 2025Review
- Article
- Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater.Nature communications · 2024Article
- Inference of Infectious Disease Transmission through a Relaxed Bottleneck Using Multiple Genomes Per Host.Molecular biology and evolution · 2024Article
- VIPERA: Viral Intra-Patient Evolution Reporting and Analysis.Virus evolution · 2024Article
- Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks.eLife · 2023Article
- Intra- and interhost genomic diversity of monkeypox virus.Journal of medical virology · 2023Article
- Within-host genetic diversity of SARS-CoV-2 in the context of large-scale hospital-associated genomic surveillance.medRxiv : the preprint server for health sciences · 2022Article
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Authors and funding
13 authors at 5 institutions in 2 countries.
Funding
Abstract
Accurate inference of who infected whom in an infectious disease outbreak is critical for the delivery of effective infection prevention and control. The increased resolution of pathogen whole-genome sequencing has significantly improved our ability to infer transmission events. Despite this, transmission inference often remains limited by the lack of genomic variation between the source case and infected contacts. Although within-host genetic diversity is common among a wide variety of pathogens, conventional whole-genome sequencing phylogenetic approaches exclusively use consensus sequences, which consider only the most prevalent nucleotide at each position and therefore fail to capture low-frequency variation within samples. We hypothesized that including within-sample variation in a phylogenetic model would help to identify who infected whom in instances in which this was previously impossible. Using whole-genome sequences from SARS-CoV-2 multi-institutional outbreaks as an example, we show how within-sample diversity is partially maintained among repeated serial samples from the same host, it can transmitted between those cases with known epidemiological links, and how this improves phylogenetic inference and our understanding of who infected whom. Our technique is applicable to other infectious diseases and has immediate clinical utility in infection prevention and control.
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