ReviewPathogens (Basel, Switzerland)2022
Methods Combining Genomic and Epidemiological Data in the Reconstruction of Transmission Trees: A Systematic Review.
Review in Pathogens (Basel, Switzerland), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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
16 citing papers in PubMed.
- A statistical framework for comparing epidemic forests.PLoS computational biology · 2026Article
- Fast hospital discharge rates blur within-hospital 'transmission footprint' in bacterial genomes, as showcased with Staphylococcus aureus.PLoS computational biology · 2026Article
- Unwelcome neighbours: Tracking the transmission of Streptococcus equi in the United Kingdom horse population.Equine veterinary journal · 2026Article
- Genomic and ecological systems-thinking framework for pathogenicFrontiers in public health · 2026Article
- Generalizing an outbreak cluster detection method for two groups: an application to rabies.Royal Society open science · 2025Article
- The NOSTRA model: Coherent estimation of infection sources in the case of possible nosocomial transmission.PLoS computational biology · 2025Article
- Incorporating Epidemiological Data into the Genomic Analysis of Partially Sampled Infectious Disease Outbreaks.Molecular biology and evolution · 2025Article
- Bayesian estimation of transmission networks for infectious diseases.Journal of mathematical biology · 2025Article
- AMRomics: a scalable workflow to analyze large microbial genome collections.BMC genomics · 2024Article
- Genetic diversity and evolutionary dynamics of the Omicron variant of SARS-CoV-2 in Morocco.Pathogens and global health · 2024Article
- Transmission Bottleneck Size Estimation from De Novo Viral Genetic Variation.Molecular biology and evolution · 2024Article
- Inference of Infectious Disease Transmission through a Relaxed Bottleneck Using Multiple Genomes Per Host.Molecular biology and evolution · 2024Article
- Sorting out assortativity: When can we assess the contributions of different population groups to epidemic transmission?PloS one · 2024Article
- Complex norovirus transmission dynamics at hospital wards revealed by deep sequencing.Journal of clinical microbiology · 2023Article
- Unveiling invisible farm-to-farm PRRSV-2 transmission links and routes through transmission tree and network analysis.Evolutionary applications · 2023Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In order to better understand transmission dynamics and appropriately target control and preventive measures, studies have aimed to identify who-infected-whom in actual outbreaks. Numerous reconstruction methods exist, each with their own assumptions, types of data, and inference strategy. Thus, selecting a method can be difficult. Following PRISMA guidelines, we systematically reviewed the literature for methods combing epidemiological and genomic data in transmission tree reconstruction. We identified 22 methods from the 41 selected articles. We defined three families according to how genomic data was handled: a non-phylogenetic family, a sequential phylogenetic family, and a simultaneous phylogenetic family. We discussed methods according to the data needed as well as the underlying sequence mutation, within-host evolution, transmission, and case observation. In the non-phylogenetic family consisting of eight methods, pairwise genetic distances were estimated. In the phylogenetic families, transmission trees were inferred from phylogenetic trees either simultaneously (nine methods) or sequentially (five methods). While a majority of methods (17/22) modeled the transmission process, few (8/22) took into account imperfect case detection. Within-host evolution was generally (7/8) modeled as a coalescent process. These practical and theoretical considerations were highlighted in order to help select the appropriate method for an outbreak.
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.