Phylogenetic tree shapes resolve disease transmission patterns

Abstract

The shapes of phylogenies of pathogens can reveal patterns in how an outbreak spreads. We used simple features to summarise the shapes of pathogen phylogenies. This provided enough information to distinguish outbreaks with super-spreaders, outbreaks spreading homogeneously, and those with chains of transmission.

Phylogeography, phylodynamics and transmission chains of bovine viral diarrhea virus subtype 1f in Northern Italy

“…Moreover, the geographic cluster from Bajardi and colleagues fully overlap the limited geographic distribution of BVDV-1f samples reported by our phylogeographic analysis for the recent years. According to the topology of both the phylogenetic tree and the transmission network, the introduction of BVDV-1f into Aosta Valley occurred like an outbreak, having the structure of a network with a super-spreader (Colijn and Gardy, 2014), with one index case and two distinct ways of infection. Additionally, the relationship inferred by molecular epidemiology among farms clustering in significant subclades (e.g.…”

The role of pathogen genomics in assessing disease transmission

“…Hence, intra-host and inter-host evolution change the association between transmission and phylogenetic trees. 120 Although Bayesian methods have been developed that jointly estimate transmission and phylogenetic trees and capture within host pathogen dynamics, [117][118][119] in many cases there may be too much uncertainty to resolve person to person transmission networks, even with WGS data. new capacity to provide (near) real time data on the origin and transmission dynamics of pathogens could provide a major public health benefit.…”

“…121 A growing body of statistical methods is aimed at inferring transmission networks and contact structures from pathogen genomic data, with and without contextual epidemiological information. [116][117][118][119][120] These methodological developments provide new opportunities for proactive laboratory surveillance and a better understanding of the epidemiology of high burden infectious d iseases. 3 12 65 122 123 For example, examination of the genomic diversity of Salmonella typhimurium in co-located human and animal populations in the UK showed that a large proportion of transmissions occurred between humans, challenging the current belief that human to human transmission is uncommon in the developed world.…”

A Microbiological Revolution Meets an Ancient Disease: Improving the Management of Tuberculosis with Genomics

“…However, there are indications that while genomic data alone cannot identify individual transmission events, it can provide some insight into the overall dynamics of the outbreak, including whether or not the outbreak shows evidence of a superspreader (85) and which patients are most central to the outbreak network (80). These patterns can be detected within the first several isolates from an outbreak (85), suggesting that real-time WGS may be useful in understanding an outbreak and its key players, thereby informing the public health approach to managing the situation.…”