Overview
I am interested in understanding the environmental, evolutionary, and ecological factors which influence the emergence of new diseases. Within this topic, I am hoping to explore both the factors which contribute to the ability of pathogens to infect novel host species, and also the factors which allow these pathogens to establish long-term, stable transmission within their new hosts.
Broad research specialisms
Virology
Host-pathogen interactions
Qualifications
MSc in Infection Biology (with specialism in Virology) | University of Glasgow
BSc Hons in Genetics | University of Glasgow
Links
Research
Research interests
Project Title:
“Evolution and ecology of virus host shifts”
Supervisors:
Ben Longdon, Lena Wilfert, Joanne Lello (Cardiff University)
Funding Body:
NERC GW4+ DTP
Project Description:
My PhD project will use a range of different Drosophila species to investigate the factors which influence the ability of viruses to infect novel host species. Initially, the project will focus on how co-infection with multiple viruses alters infection dynamics, and will examine how this varies across a phylogenetically diverse group of host species.
Publications
Key publications | Publications by category | Publications by year
Publications by category
Journal articles
Imrie RM, Roberts KE, Longdon B (In Press). Between virus correlations in the outcome of infection across host species: evidence of virus genotype by host species interactions.
Abstract:
Between virus correlations in the outcome of infection across host species: evidence of virus genotype by host species interactions
AbstractVirus host shifts are a major source of outbreaks and emerging infectious diseases, and predicting the outcome of novel host and virus interactions remains a key challenge for virus research. The evolutionary relationships between host species can explain variation in transmission rates, virulence, and virus community composition between hosts, but the potential for different viruses to interact with host species effects has yet to be established. Here, we measure correlations in viral load of four Cripavirus isolates across experimental infections of 45 Drosophilidae host species. We find positive correlations between every pair of viruses tested, suggesting that broadly susceptible host clades could act as reservoirs and donors for certain types of viruses. Additionally, we find evidence of genotype-by-genotype interactions between viruses and host species, highlighting the importance of both host and virus traits in determining the outcome of virus host shifts. More closely related viruses tended to be more strongly correlated, providing tentative evidence that virus evolutionary relatedness may be a useful proxy for determining the likelihood of novel virus emergence, which warrants further research.Impact SummaryMany new infectious diseases are caused by viruses jumping into novel host species. Estimating the probability that jumps will occur, what the characteristics of new viruses will be, and how they are likely to evolve after jumping to new host species are major challenges. To solve these challenges, we require a detailed understanding of the interactions between different viruses and hosts, or metrics that can capture some of the variation in these interactions. Previous studies have shown that the evolutionary relationships between host species can be used to predict traits of infections in different hosts, including transmission rates and the damage caused by infection. However, the potential for different viruses to influence the patterns of these host species effects has yet to be determined. Here, we use four viruses of insects in experimental infections across 45 different fruit fly host species to begin to answer this question. We find similarities in the patterns of replication and persistence between all four viruses, suggesting susceptible groups of related hosts could act as reservoirs and donors for certain types of virus. However, we also find evidence that different virus genotypes interact in different ways with some host species. Viruses that were more closely related tended to behave in similar ways, and so we suggest that virus evolutionary relatedness may prove to be a useful metric for predicting the traits of novel infections and should be explored further in future studies.
Abstract.
Imrie RM, Roberts KE, Longdon B (2021). Between virus correlations in the outcome of infection across host species: Evidence of virus by host species interactions. Evolution Letters, 5(5), 472-483.
Publications by year
In Press
Imrie RM, Roberts KE, Longdon B (In Press). Between virus correlations in the outcome of infection across host species: evidence of virus genotype by host species interactions.
Abstract:
Between virus correlations in the outcome of infection across host species: evidence of virus genotype by host species interactions
AbstractVirus host shifts are a major source of outbreaks and emerging infectious diseases, and predicting the outcome of novel host and virus interactions remains a key challenge for virus research. The evolutionary relationships between host species can explain variation in transmission rates, virulence, and virus community composition between hosts, but the potential for different viruses to interact with host species effects has yet to be established. Here, we measure correlations in viral load of four Cripavirus isolates across experimental infections of 45 Drosophilidae host species. We find positive correlations between every pair of viruses tested, suggesting that broadly susceptible host clades could act as reservoirs and donors for certain types of viruses. Additionally, we find evidence of genotype-by-genotype interactions between viruses and host species, highlighting the importance of both host and virus traits in determining the outcome of virus host shifts. More closely related viruses tended to be more strongly correlated, providing tentative evidence that virus evolutionary relatedness may be a useful proxy for determining the likelihood of novel virus emergence, which warrants further research.Impact SummaryMany new infectious diseases are caused by viruses jumping into novel host species. Estimating the probability that jumps will occur, what the characteristics of new viruses will be, and how they are likely to evolve after jumping to new host species are major challenges. To solve these challenges, we require a detailed understanding of the interactions between different viruses and hosts, or metrics that can capture some of the variation in these interactions. Previous studies have shown that the evolutionary relationships between host species can be used to predict traits of infections in different hosts, including transmission rates and the damage caused by infection. However, the potential for different viruses to influence the patterns of these host species effects has yet to be determined. Here, we use four viruses of insects in experimental infections across 45 different fruit fly host species to begin to answer this question. We find similarities in the patterns of replication and persistence between all four viruses, suggesting susceptible groups of related hosts could act as reservoirs and donors for certain types of virus. However, we also find evidence that different virus genotypes interact in different ways with some host species. Viruses that were more closely related tended to behave in similar ways, and so we suggest that virus evolutionary relatedness may prove to be a useful metric for predicting the traits of novel infections and should be explored further in future studies.
Abstract.
Baril T, Imrie RM, Hayward A (In Press). Earl Grey: a fully automated user-friendly transposable element annotation and analysis pipeline.
Abstract:
Earl Grey: a fully automated user-friendly transposable element annotation and analysis pipeline
ABSTRACTBackgroundTransposable elements (TEs) are found in nearly all eukaryotic genomes and are implicated in a range of evolutionary processes. Despite considerable research attention on TEs, their annotation and characterisation remain challenging, particularly for non-specialists. Current methods of automated TE annotation are subject to several issues that can reduce their overall quality: (i) fragmented and overlapping TE annotations may lead to erroneous estimates of TE count and coverage; (ii) repeat models may represent small proportions of their total length, where 5’ and 3’ regions are poorly captured; (iii) resultant libraries may contain redundancy, with the same TE family represented more than once. Existing pipelines can also be challenging to install, run, and extract data from. To address these issues, we present Earl Grey: a fully automated transposable element annotation pipeline designed for the user-friendly curation and annotation of TEs in eukaryotic genome assemblies.ResultsUsing a simulated genome, three model genome assemblies, and three non-model genome assemblies, Earl Grey outperforms current widely used TE annotation methodologies in ameliorating the issues mentioned above by producing longer TE consensus sequences in non-redundant TE libraries, which are then used to produce less fragmented TE annotations without the presence of overlaps. Earl Grey scores highly in benchmarking for TE annotation (MCC: 0.99) and classification (97% correctly classified) in comparison to existing software.ConclusionsEarl Grey provides a comprehensive and fully automated TE annotation toolkit that provides researchers with paper-ready summary figures and outputs in standard formats compatible with other bioinformatics tools. Earl Grey has a modular format, with great scope for the inclusion of additional modules focussed on further quality control aspects and tailored analyses in future releases.
Abstract.
2021
Imrie RM, Roberts KE, Longdon B (2021). Between virus correlations in the outcome of infection across host species: Evidence of virus by host species interactions. Evolution Letters, 5(5), 472-483.
Ryan_Imrie Details from cache as at 2022-08-07 07:17:32
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