The utility of whole-genome sequencing to identify likely transmission pairs for pathogens with slow and variable evolution.

Autor:	Wood AJ; Roslin Institute, University of Edinburgh, United Kingdom., Benton CH; Animal & Plant Health Agency, United Kingdom., Delahay RJ; Animal & Plant Health Agency, United Kingdom., Marion G; Biomathematics and Statistics Scotland, United Kingdom., Palkopoulou E; Animal & Plant Health Agency, United Kingdom., Pooley CM; Biomathematics and Statistics Scotland, United Kingdom., Smith GC; Animal & Plant Health Agency, United Kingdom., Kao RR; Roslin Institute, University of Edinburgh, United Kingdom; Royal (Dick) School of Veterinary Studies, University of Edinburgh, United Kingdom. Electronic address: rowland.kao@ed.ac.uk.
Jazyk:	angličtina
Zdroj:	Epidemics [Epidemics] 2024 Sep; Vol. 48, pp. 100787. Date of Electronic Publication: 2024 Aug 23.
DOI:	10.1016/j.epidem.2024.100787
Abstrakt:	Pathogen whole-genome sequencing (WGS) has been used to track the transmission of infectious diseases in extraordinary detail, especially for pathogens that undergo fast and steady evolution, as is the case with many RNA viruses. However, for other pathogens evolution is less predictable, making interpretation of these data to inform our understanding of their epidemiology more challenging and the value of densely collected pathogen genome data uncertain. Here, we assess the utility of WGS for one such pathogen, in the "who-infected-whom" identification problem. We study samples from hosts (130 cattle, 111 badgers) with confirmed infection of M. bovis (causing bovine Tuberculosis), which has an estimated clock rate as slow as ∼0.1-1 variations per year. For each potential pathway between hosts, we calculate the relative likelihood that such a transmission event occurred. This is informed by an epidemiological model of transmission, and host life history data. By including WGS data, we shrink the number of plausible pathways significantly, relative to those deemed likely on the basis of life history data alone. Despite our uncertainty relating to the evolution of M. bovis, the WGS data are therefore a valuable adjunct to epidemiological investigations, especially for wildlife species whose life history data are sparse. Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. (Copyright © 2024. Published by Elsevier B.V.)
Databáze:	MEDLINE
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