ArticleMolecular biology and evolution2014
Timing and order of transmission events is not directly reflected in a pathogen phylogeny.
Article in Molecular biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
59 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Challenges in Elucidating HIV-1 Genetic Diversity in the Middle East and North Africa: A Review Based on a Systematic Search.Viruses · 2025Pooled it
- Defining HIV-1 transmission clusters based on sequence data.AIDS (London, England) · 2017Pooled it
- Untangling the effects of within-host and between-host natural selection in viruses with applications to evolution of HIV-1 co-receptor usage.Journal of the Royal Society, Interface · 2026Article
- ScITree: Scalable Bayesian inference of transmission tree from epidemiological and genomic data.PLoS computational biology · 2025Article
- Identifying impacts of contact tracing on HIV epidemiological inference from phylogenetic data.Virus evolution · 2025Article
- Inferring Viral Transmission Time from Phylogenies for Known Transmission Pairs.Molecular biology and evolution · 2024Article
- Inference of Infectious Disease Transmission through a Relaxed Bottleneck Using Multiple Genomes Per Host.Molecular biology and evolution · 2024Article
- Methods to Estimate the Between-Population Level Effective Reproductive Number for Infectious Disease Epidemics: Foot-And-Mouth Disease (FMD) in Vietnam.Transboundary and emerging diseases · 2024Article
- Inferring viral transmission time from phylogenies for known transmission pairs.bioRxiv : the preprint server for biology · 2023Article
- ComparingEpidemiology and infection · 2023Article
- Recombination smooths the time signal disrupted by latency in within-host HIV phylogenies.Virus evolution · 2023Article
- Genome-wide association studies revealed complex genetic architecture and breeding perspective of maize ear traits.BMC plant biology · 2022Article
- Traversing missing links in the spread of HIV.eLife · 2022Article
- Combining biomarker and virus phylogenetic models improves HIV-1 epidemiological source identification.PLoS computational biology · 2022Article
- Dynamics and Dispersal of Local Human Immunodeficiency Virus Epidemics Within San Diego and Across the San Diego-Tijuana Border.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2021Article
- Incorporating Within-Host Diversity in Phylogenetic Analyses for Detecting Clusters of New HIV Diagnoses.Frontiers in microbiology · 2021Article
- Bayesian reconstruction of transmission trees from genetic sequences and uncertain infection times.Statistical applications in genetics and molecular biology · 2020Article
- Article
- Inferring transmission heterogeneity using virus genealogies: Estimation and targeted prevention.PLoS computational biology · 2020Article
- nosoi: A stochastic agent-based transmission chain simulation framework in r.Methods in ecology and evolution · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Pathogen phylogenies are often used to infer spread among hosts. There is, however, not an exact match between the pathogen phylogeny and the host transmission history. Here, we examine in detail the limitations of this relationship. First, all splits in a pathogen phylogeny of more than 1 host occur within hosts, not at the moment of transmission, predating the transmission events as described by the pretransmission interval. Second, the order in which nodes in a phylogeny occur may be reflective of the within-host dynamics rather than epidemiologic relationships. To investigate these phenomena, motivated by within-host diversity patterns, we developed a two-phase coalescent model that includes a transmission bottleneck followed by linear outgrowth to a maximum population size followed by either stabilization or decline of the population. The model predicts that the pretransmission interval shrinks compared with predictions based on constant population size or a simple transmission bottleneck. Because lineages coalesce faster in a small population, the probability of a pathogen phylogeny to resemble the transmission history depends on when after infection a donor transmits to a new host. We also show that the probability of inferring the incorrect order of multiple transmissions from the same host is high. Finally, we compare time of HIV-1 infection informed by genetic distances in phylogenies to independent biomarker data, and show that, indeed, the pretransmission interval biases phylogeny-based estimates of when transmissions occurred. We describe situations where caution is needed not to misinterpret which parts of a phylogeny that may indicate outbreaks and tight transmission clusters.
Indexed as
Identifiers
What OpenQuestion holds
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.