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.

Highlights

  • Received: 9 December 2021Understanding transmission dynamics is pivotal in controlling and preventing infectious diseases

  • We systematically reviewed the literature for methods combining genomic and epiWe systematically reviewed the literature for methods combining genomic and demiological data to reconstruct transmission trees

  • We systematically reviewed the literature for methods combining genomic and epidemiological data to reconstruct transmission trees

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Summary

Introduction

Received: 9 December 2021Understanding transmission dynamics is pivotal in controlling and preventing infectious diseases. Studies have aimed to reconstruct transmission trees depicting transmission histories of actual outbreaks in order to draw conclusions on how the disease spread [1,2]. Nodes represent infected hosts (i.e., entities that the pathogen can infect, e.g., individuals or groups of individuals like farms in a foot-and-mouth disease (FMD) outbreak [5]), connected by transmission events represented by directed edges [6]. One way to infer transmission history in an outbreak has been the use of contact tracing methods, in which infected individuals are interrogated regarding time of symptom onset, duration of disease, and potential exposures to pathogen [7]. S.M.; Hayama, Y.; Bradhurst, R.; Yamamoto, T.; Tsutsui, T.; Stevenson, M.A. Reconstructing foot-and-mouth disease outbreaks: A methods comparison of transmission network models.

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