ArticlePLoS pathogens2018
When are pathogen genome sequences informative of transmission events?
Article in PLoS pathogens, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers, 2 of them syntheses that pooled it.
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Who cites it
70 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Marburg virus disease outbreaks, mathematical models, and disease parameters: a systematic review.The Lancet. Infectious diseases · 2024Pooled it
- Pooled it
- Lineage Diversification and Evolutionary Dynamics of theMicroorganisms · 2026Article
- Network analysis of pairwise relative tuberculosis transmission probabilities in Lima, Peru.American journal of epidemiology · 2026Article
- A statistical framework for comparing epidemic forests.PLoS computational biology · 2026Article
- Strain-level transmission inference across multi-kingdom metagenomic data using TRACS.Nature microbiology · 2026Article
- Characterizing the informativeness of pathogen genome sequence datasets about transmission between population groups.Proceedings. Biological sciences · 2026Article
- A new method to estimate factors associated with tuberculosis transmission using whole genome sequencing and other additional metadata.Epidemiologic methods · 2026Article
- Network Analysis of Pairwise Relative Tuberculosis Transmission Probabilities in Lima, Peru.medRxiv : the preprint server for health sciences · 2025Article
- Incorporating Epidemiological Data into the Genomic Analysis of Partially Sampled Infectious Disease Outbreaks.Molecular biology and evolution · 2025Article
- Phylogenetic Study of Local Patterns Influenza A(H3N2) Virus Transmission in a Semi-Isolated Population in a Remote Island in Japan Between 2011 and 2013.Influenza and other respiratory viruses · 2025Article
- Bayesian estimation of transmission networks for infectious diseases.Journal of mathematical biology · 2025Article
- Classification of unsequenced Mycobacterium tuberculosis strains in a high-burden setting using a pairwise logistic regression approach.Access microbiology · 2025Article
- Severe Acute Respiratory Syndrome Coronavirus 2 Household Transmission During the Omicron Era in Massachusetts: A Prospective, Case-Ascertained Study Using Genomic Epidemiology.Open forum infectious diseases · 2024Article
- Trends in Nationally Notifiable Infectious Diseases in Humans and Animals during COVID-19 Pandemic, South Korea.Emerging infectious diseases · 2024Article
- Estimating the reproduction number and transmission heterogeneity from the size distribution of clusters of identical pathogen sequences.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis.International journal of molecular sciences · 2024Review
- Transmission Bottleneck Size Estimation from De Novo Viral Genetic Variation.Molecular biology and evolution · 2024Article
- Sorting out assortativity: When can we assess the contributions of different population groups to epidemic transmission?PloS one · 2024Article
- Shigellosis outbreak among persons experiencing homelessness-San Diego County, California, October-December 2021.Epidemiology and infection · 2023Article
10 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
Recent years have seen the development of numerous methodologies for reconstructing transmission trees in infectious disease outbreaks from densely sampled whole genome sequence data. However, a fundamental and as of yet poorly addressed limitation of such approaches is the requirement for genetic diversity to arise on epidemiological timescales. Specifically, the position of infected individuals in a transmission tree can only be resolved by genetic data if mutations have accumulated between the sampled pathogen genomes. To quantify and compare the useful genetic diversity expected from genetic data in different pathogen outbreaks, we introduce here the concept of 'transmission divergence', defined as the number of mutations separating whole genome sequences sampled from transmission pairs. Using parameter values obtained by literature review, we simulate outbreak scenarios alongside sequence evolution using two models described in the literature to describe transmission divergence of ten major outbreak-causing pathogens. We find that while mean values vary significantly between the pathogens considered, their transmission divergence is generally very low, with many outbreaks characterised by large numbers of genetically identical transmission pairs. We describe the impact of transmission divergence on our ability to reconstruct outbreaks using two outbreak reconstruction tools, the R packages outbreaker and phybreak, and demonstrate that, in agreement with previous observations, genetic sequence data of rapidly evolving pathogens such as RNA viruses can provide valuable information on individual transmission events. Conversely, sequence data of pathogens with lower mean transmission divergence, including Streptococcus pneumoniae, Shigella sonnei and Clostridium difficile, provide little to no information about individual transmission events. Our results highlight the informational limitations of genetic sequence data in certain outbreak scenarios, and demonstrate the need to expand the toolkit of outbreak reconstruction tools to integrate other types of epidemiological data.
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