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Shared Genomic Variants: Identification of Transmission Routes Using Pathogen Deep-Sequence Data.

Colin J Worby, Marc Lipsitch, William P Hanage

American Journal of Epidemiology

|November 18, 2017

Summary

Deep sequencing pathogen genomes enhances communicable disease outbreak investigations. Analyzing shared genomic variants and phylogenetic distance accurately identifies transmission routes, improving infection control strategies.

Keywords:

Ebola virus epidemics genomics infection control infectious disease outbreaks molecular epidemiology

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Area of Science:

Genomics
Epidemiology
Infectious Disease Outbreak Analysis

Background:

Pathogen genome sequencing is crucial for understanding communicable disease outbreaks.
Genomic data reveals transmission patterns but individual infection routes remain uncertain.
Deep sequencing offers potential for higher resolution in transmission route identification.

Purpose of the Study:

To investigate the utility of deep sequence data for resolving pathogen transmission routes.
To assess methods for identifying transmission routes using shared genomic variants and genetic distance.
To develop and apply a hybrid approach incorporating phylogenetic distance.

Main Methods:

Analysis of shared genomic variants between pathogen samples.
Assessment of genetic distance metrics for transmission inference.
Development of a hybrid approach combining shared variants and phylogenetic distance.
Application of methods to genomic data from the 2014 Ebola outbreak.

Main Results:

Shared genomic variants provide significant additional information for identifying transmission routes.
Shared-variant approaches yield highly accurate, though potentially few, links, especially with small transmission bottlenecks.
The hybrid approach enhances resolution in transmission route identification.
Several likely transmission routes were identified during the 2014 Ebola outbreak.

Conclusions:

Deep sequencing data, particularly shared variants and phylogenetic distance, significantly improves the resolution of pathogen transmission routes.
The proposed hybrid method offers a powerful tool for epidemiologic investigations.
Genomic data is a vital component of modern outbreak investigation and analysis.