Distinguishing imported cases from locally acquired cases within a geographically limited genomic sample of an infectious disease
Authors:
Xavier Didelot, David Helekal, Michelle Kendall, Paolo Ribeca
Abstract:
Motivation: The ability to distinguish imported cases from locally acquired cases has important consequences for the selection of public health control strategies. Genomic data can be useful for this, for example, using a phylogeo- graphic analysis in which genomic data from multiple locations are comp red to determine likely migration events
between locations. However, these methods typically require good samples of genomes from all locations, which is rarely available.
Results: Here, we propose an alternative approach that only uses genomic data from a location of interest. By com- paring each new case with previous cases from the same location, we are able to detect imported cases, as they have a different genealogical distribution than that of locally acquired cases. We show that, when variations in the
size of the local population are accounted for, our method has good sensitivity and excellent specificity for the detection of imports. We applied our method to data simulated under the structured coalescent model and demonstrate relatively good performance even when the local population has the same size as the external population. Finally, we applied our method to several recent genomic datasets from both bacterial and viral pathogens, and show that it can, in a matter of seconds or minutes, deliver important insights on the number of imports to a geographically limited sample of a pathogen population.
Journal:
Bioinformatics