ArticlePhilosophical transactions of the Royal Society of London. Series B, Biological sciences2010
Viral phylodynamics and the search for an 'effective number of infections'.
Article in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 98 papers, 1 of them a synthesis 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
98 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Coalescent inference for infectious disease: meta-analysis of hepatitis C.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2013Pooled it
- Viral introductions and return to baseline sexual behaviors maintain low-level mpox incidence in Los Angeles.Nature communications · 2026Article
- Fast hospital discharge rates blur within-hospital 'transmission footprint' in bacterial genomes, as showcased with Staphylococcus aureus.PLoS computational biology · 2026Article
- Geographic and cross-species transmission of Mamastroviruses from multiple hosts.Animal microbiome · 2026Article
- Intensive transmission in wild, migratory birds drove rapid geographic dissemination and repeated spillovers of H5N1 into agriculture in North America.bioRxiv : the preprint server for biology · 2025Article
- Viral introductions and return to baseline sexual behaviors maintain low-level mpox incidence in Los Angeles County, USA, 2023-2024.medRxiv : the preprint server for health sciences · 2025Article
- Genomic Epidemiology for Estimating Pathogen Burden in a Population.Emerging infectious diseases · 2025Article
- Accounting for reporting delays in real-time phylodynamic analyses with preferential sampling.PLoS computational biology · 2025Article
- Evaluating ARG-estimation methods in the context of estimating population-mean polygenic score histories.Genetics · 2025Article
- The evolution and epidemiology of H3N2 canine influenza virus after 20 years in dogs.Epidemiology and infection · 2025Article
- Looking back into the Hepatitis C Virus epidemic dynamics from Unnao, India through phylogenetic approach.PloS one · 2025Article
- Evaluating ARG-estimation methods in the context of estimating population-mean polygenic score histories.bioRxiv : the preprint server for biology · 2024Article
- Interrogating Genomes and Geography to Unravel Multiyear Vesicular Stomatitis Epizootics.Viruses · 2024Article
- Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England.PLoS pathogens · 2024Article
- Deep Sequencing to Reveal Phylo-Geographic Relationships of Juquitiba Virus in Paraguay.Viruses · 2023Article
- Article
- The tumour is in the detail: Local phylogenetic, population and epidemiological dynamics of a transmissible cancer in Tasmanian devils.Evolutionary applications · 2023Article
- Estimating the fitness cost and benefit of antimicrobial resistance from pathogen genomic data.Journal of the Royal Society, Interface · 2023Article
- Resurgence of Omicron BA.2 in SARS-CoV-2 infection-naive Hong Kong.Nature communications · 2023Article
- Phylogeographic reconstruction of the emergence and spread of Powassan virus in the northeastern United States.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
38 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Information on the dynamics of the effective population size over time can be obtained from the analysis of phylogenies, through the application of time-varying coalescent models. This approach has been used to study the dynamics of many different viruses, and has demonstrated a wide variety of patterns, which have been interpreted in the context of changes over time in the 'effective number of infections', a quantity proportional to the number of infected individuals. However, for infectious diseases, the rate of coalescence is driven primarily by new transmissions i.e. the incidence, and only indirectly by the number of infected individuals through sampling effects. Using commonly used epidemiological models, we show that the coalescence rate may indeed reflect the number of infected individuals during the initial phase of exponential growth when time is scaled by infectivity, but in general, a single change in time scale cannot be used to estimate the number of infected individuals. This has important implications when integrating phylogenetic data in the context of other epidemiological data.
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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.