ArticleMolecular biology and evolution2018
PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity.
Article in Molecular biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers.
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101 citing papers in PubMed, 179 citations in OpenAlex.
- Demographics of sources of HIV-1 transmission in Zambia: a molecular epidemiology analysis in the HPTN 071 PopART study.The Lancet. Microbe · 2024Trial
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- Ultrasensitive single-genome sequencing reveals strong purifying selection in acute HIV-1 infection.bioRxiv : the preprint server for biology · 2026Article
- The tree labeling polytope: A unified approach to ancestral reconstruction problems.Cell systems · 2026Article
- Strain-level transmission inference across multi-kingdom metagenomic data using TRACS.Nature microbiology · 2026Article
- Unpacking sources of transmission in HIV prevention trials with deep-sequence pathogen data.Nature communications · 2026Article
- The age and sex dynamics of heterosexual HIV transmission in Zambia: an HPTN 071 (PopART) phylogenetic and modelling study.medRxiv : the preprint server for health sciences · 2026Article
- Phylogenetics and molecular evolution to understand and curb the HIV pandemic.Nature reviews. Microbiology · 2026Review
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- A graph homomorphism approach for unraveling histories of metastatic cancers and viral outbreaks under evolutionary constraints.Nature communications · 2025Article
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- HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data.BMC bioinformatics · 2025Article
- Population sequencing for phylogenetic diversity and transmission analyses.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- ScITree: Scalable Bayesian inference of transmission tree from epidemiological and genomic data.PLoS computational biology · 2025Article
- Integrated population clustering and genomic epidemiology with PopPIPE.Microbial genomics · 2025Article
- Genetically distinct within-host subpopulations of hepatitis C virus persist after Direct-Acting Antiviral treatment failure.PLoS pathogens · 2025Article
- Quantifying prevalence and risk factors of HIV multiple infection in Uganda from population-based deep-sequence data.PLoS pathogens · 2025Article
- Addressing data management and analysis challenges in viral genomics: The Swiss HIV cohort study viral next generation sequencing database.PLOS digital health · 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
41 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors at 5 institutions in 2 countries.
Funding
Abstract
A central feature of pathogen genomics is that different infectious particles (virions and bacterial cells) within an infected individual may be genetically distinct, with patterns of relatedness among infectious particles being the result of both within-host evolution and transmission from one host to the next. Here, we present a new software tool, phyloscanner, which analyses pathogen diversity from multiple infected hosts. phyloscanner provides unprecedented resolution into the transmission process, allowing inference of the direction of transmission from sequence data alone. Multiply infected individuals are also identified, as they harbor subpopulations of infectious particles that are not connected by within-host evolution, except where recombinant types emerge. Low-level contamination is flagged and removed. We illustrate phyloscanner on both viral and bacterial pathogens, namely HIV-1 sequenced on Illumina and Roche 454 platforms, HCV sequenced with the Oxford Nanopore MinION platform, and Streptococcus pneumoniae with sequences from multiple colonies per individual. phyloscanner is available from https://github.com/BDI-pathogens/phyloscanner.
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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.