Biology subjects

Brunker, K.

Publications and source records attributed to Brunker, K..

8 recordsLinked to original sources

bioRxiv2026

Lateral flow devices can fast-track rabies virus genomic surveillance

Viral genomic data can resolve rabies transmission and guide outbreak response, but surveillance is often limited less by sequencing capacity than by getting suitable specimens from remote collection sites to a laboratory, a process that can take months. Here, we show that lateral flow devices (LFDs) used for rabies diagnosis can also serve as genomic specimens, integrating diagnosis and genomic sampling into a single workflow without additional specimen collection. We evaluated LFDs and FTA cards for rabies virus genome recovery under laboratory and field conditions. During surveillance across the island provinces of MIMAROPA, Philippines, the Bionote LFD had 99.1% sensitivity and 100% specificity against the gold-standard direct fluorescent antibody test (n = 319), with results available a median of 1 day after sampling versus 5 days for DFAT confirmation. Under laboratory conditions simulating field storage (ambient temperature or 37 degrees Celsius for up to 21 days), both residual LFD material and FTA cards supported near-complete genome sequencing, although genome recovery declined with storage duration, particularly at elevated temperatures. Consistent with this, field-collected LFDs yielded near-complete genomes up to 23 days of ambient storage but only partial genomes after 29-77 days, indicating a practical window of around three weeks for use. Repurposing LFDs already embedded in diagnostic workflows offers a practical route to decentralised genomic surveillance without additional sample collection or a cold chain. FTA cards provide a complementary preservation option, while further optimisation of specimen preparation, extraction and storage could improve genome recovery and extend the sequencing window.

molecular biology↗

bioRxiv2026

One Health genomic surveillance reveals structured urban rabies transmission and major surveillance gaps

Persistent local foci remain a barrier to eliminating dog-mediated rabies. The processes sustaining micro-scale transmission, particularly in complex urban systems, remain poorly understood. We apply an integrated One Health genomic epidemiology framework to reconstruct a decade-long rabies virus (RABV) epidemic in Arequipa, Peru. Combining 133 new whole genomes with existing data, we produce the most comprehensive canine RABV dataset in Latin America and use whole-genome-informed phylogenetic, phylodynamic, and landscape analyses, to trace the epidemic from its first detection in 2015. Transmission was dominated by a single lineage estimated to be introduced around 2012, which spread for approximately 3 years before detection. We find that only 1-2% of infections are routinely detected, revealing extensive cryptic transmission and undermining case-based metrics for verifying disease freedom. Additional regional and transboundary introductions were detected, but only one resulted in sustained transmission. Within Arequipa city, transmission is highly structured, concentrated in densely populated and socioeconomically deprived areas, and shaped by urban connectivity, with roads and dry water channels facilitating spread and rivers acting as partial barriers. Together, our findings demonstrate that rabies persistence reflects interacting processes across spatial scales and support genomic-informed, spatially targeted surveillance and control strategies.

evolutionary biology↗

bioRxiv2026

A simple method of estimating rabies outbreak sizes from phylogenies

The ability to estimate the size of a disease outbreak is beneficial both for coordinating an outbreak response and for retrospectively evaluating the effectiveness of response measures and surveillance. Methods such as seroprevalence surveys and epidemiological modelling can be used for this purpose, but are not suitable for every outbreak. We develop a simple formula to estimate the proportion of outbreak cases sequenced, using only the per-generation substitution rate and the length of a phylogenetic tree. This proportion can then be used to estimate the outbreak size. We validate this method using subsampled data from fully observed simulated outbreaks, and then apply it to an ongoing rabies outbreak in the Philippines. We find that this method produces accurate estimates of outbreak size and can be applied to outbreaks with substitution rates and R0 values within the estimated range for rabies. We estimated that approximately 19% of cases from the outbreak in the Philippines had been sequenced, suggesting better than average case detection, with a resulting outbreak size estimate consistent with previous analyses. With this method and the associated R package POSER (https://github.com/RowanDurrant/poser), we aim to make rabies outbreak size estimation more accessible, but further work is required to improve its applicability to other diseases.

genetics↗

bioRxiv2024

Genomic Characterization of a Dog-Mediated Rabies Outbreak in El Pedregal, Arequipa, Peru

BackgroundRabies, a re-emerging zoonosis with the highest known human case fatality rate, has been largely absent from Peru, except for endemic circulation in the Puno region on the Bolivian border and re-emergence in Arequipa City in 2015, where it has persisted. In 2021, an outbreak occurred in the rapidly expanding city of El Pedregal near Arequipa, followed by more cases in 2022 after nearly a year of epidemiological silence. While currently under control, questions persist regarding the origin of the El Pedregal outbreak and implications for maintaining rabies control in Peru. MethodsWe sequenced 25 dog rabies virus (RABV) genomes from the El Pedregal outbreak (n=11) and Arequipa City (n=14) from 2021-2023 using Nanopore sequencing in Peru. Historical genomes from Puno (n=4, 2010-2012) and Arequipa (n=5, 2015-2019), were sequenced using an Illumina approach in the UK. In total, 34 RABV genomes were analyzed, including archived and newly obtained samples. The genomes were analyzed phylogenetically to understand the outbreaks context and origins. ResultsPhylogenomic analysis identified two genetic clusters in El Pedregal: 2021 cases stemmed from a single introduction unrelated to Arequipa cases, while the 2022 sequence suggested a new introduction from Arequipa rather than persistence. In relation to canine RABV diversity in Latin America, all new sequences belonged to a new minor clade, Cosmopolitan Am5, sharing relatives from Bolivia, Argentina, and Brazil. ConclusionGenomic insights into the El Pedregal outbreak revealed multiple introductions over a 2-year window. Eco-epidemiological conditions, including migratory worker patterns, suggest human-mediated movement drove introductions. Despite outbreak containment, El Pedregal remains at risk of dog-mediated rabies due to ongoing circulation in Arequipa, Puno, and Bolivia. Human-mediated movement of dogs presents a major risk for rabies re-emergence in Peru, jeopardizing regional dog-mediated rabies control. Additional sequence data is needed for comprehensive phylogenetic analyses.

genomics↗

bioRxiv2023

Examining the molecular clock hypothesis for the contemporary evolution of the rabies virus

The molecular clock hypothesis assumes that mutations accumulate on an organisms genome at a constant rate over time, but this assumption does not always hold true. While modelling approaches exist to accommodate deviations from a strict molecular clock, assumptions about rate variation may not fully represent the underlying evolutionary processes. There is considerable variability in rabies virus (RABV) incubation periods, ranging from days to over a year, during which viral replication may be reduced. This prompts the question of whether modelling RABV on a per infection generation basis might be more appropriate. We investigate how variable incubation periods affect root-to-tip divergence under per-unit time and per-generation models of mutation. Additionally, we assess how well these models represent root-to-tip divergence in time-stamped RABV sequences. We find that at low substitution rates (<1 substitution per genome per generation) divergence patterns between these models are difficult to distinguish, while above this threshold differences become apparent across a range of sampling rates. Using a Tanzanian RABV dataset, we calculate the mean substitution rate to be 0.17 substitutions per genome per generation. At RABVs substitution rate, the per-generation substitution model is unlikely to represent rabies evolution substantially differently than the molecular clock model when examining contemporary outbreaks; over enough generations for any divergence to accumulate, extreme incubation periods average out. However, measuring substitution rates per-generation holds potential in applications such as inferring transmission trees and predicting lineage emergence. Author SummaryRabies is a neglected disease that kills around 60,000 people each year. After entering the body, the incubation period of the virus is usually less than one month, but can sometimes span months to years. While we normally assume a virus accumulates mutations at a constant rate, it is possible that rabies occasional long incubation periods mean that mutations accumulate at varying rates if the virus replicates (and thus mutates) more slowly during the incubation period. We compared how the rabies virus evolves over time using two simulation models where mutations either occur per unit time or per infection generation. We also calculated the mean substitution rate per infection generation, which can be useful for inferring linkage between related rabies cases. We found that at realistic substitution rates for the rabies virus, we could not distinguish between the two models. Our calculations show that in most generations no mutations are expected to occur. Thus, over a time period long enough to observe genetic divergence, occasional long incubation periods would be "cancelled out" by shorter than average incubation periods, meaning that the two models are almost equivalent. However our work suggests that modelling substitution rates per generation may be useful for epidemiological inference.

microbiology↗

bioRxiv2021

Spatial scale of transmission explains how acute infections circulate at low prevalence

Fundamental questions remain about the regulation of acute pathogens in the absence of acquired immunity. This is especially true for canine rabies, a universally fatal zoonosis. From tracing rabies transmission in a population of 50,000 dogs in Tanzania between 2002-2016 we unravel the processes through which rabies is regulated and persists, fitting individual-based models to spatially-resolved data to investigate the mechanisms modulating transmission and the scale over which they operate. We find that while prevalence never exceeds 0.15%, we detect significant susceptible depletion at local scales commensurate with rabid dog movement, reducing transmission through clustering of rabies deaths and individuals incubating infection. Individual variation in rabid dog behaviour facilitates virus dispersal and co-circulation of lineages, enabling metapopulation persistence. These mechanisms likely operate in many pathogens circulating in spatially structured populations, with important implications for prediction and control, yet are unobservable unless the scale of host interactions is identified. One-Sentence SummaryIdentifying the spatial scale of contact reveals the mechanisms that limit the size of rabies outbreaks and that are critical for predicting transmission dynamics.

ecology↗

bioRxiv2021

Making Genomic Surveillance Deliver: A Lineage Classification and Nomenclature System to Inform Rabies Virus Elimination

The availability of pathogen sequence data and use of genomic surveillance is rapidly increasing. Genomic tools and classification systems need updating to reflect this. Here, rabies virus is used as an example to showcase the potential value of updated genomic tools to enhance surveillance to better understand epidemiological dynamics and improve disease control. Previous studies have described the evolutionary history of rabies virus; however, the resulting taxonomy lacks the definition necessary to identify incursions, lineage turnover and transmission routes at high resolution. Here we propose a lineage classification system based on the dynamic nomenclature used for SARS-CoV-2, defining a lineage by phylogenetic methods, for tracking virus spread and comparing sequences across geographic areas. We demonstrate this system through application to the globally distributed Cosmopolitan clade of rabies virus, defining 73 total lineages within the clade, beyond the 22 previously reported. We further show how integration of this tool with a new rabies virus sequence data resource (RABV-GLUE) enables rapid application, for example, highlighting lineage dynamics relevant to control and elimination programmes, such as identifying importations and their sources, and areas of persistence and transmission, including transboundary incursions. This system and the tools developed should be useful for coordinating and targeting control programmes and monitoring progress as we work towards eliminating dog-mediated rabies, as well as having potential for broad application to the surveillance of other viruses. Author SummaryThe importance of the ability to track the diversity and spread of viruses in a universal way that can be clearly communicated has been highlighted during the SARS-CoV-2 pandemic. This, accompanied with the increase in the availability and use of pathogen sequence data, means the development of new genomic tools and classification systems can strengthen outbreak response and disease control. Here, we present an easy-to-use objective and transferable classification tool for tracking viruses at high resolution. We use rabies virus, a neglected zoonotic disease that causes around 59,000 human deaths each year, as an example use case of this tool. Applying our tool to a global clade of rabies virus, we find an over 200% increase in the definition at which we can classify the virus, allowing us to identify areas of persistence and transmission that were not previously apparent, and patterns of virus spread. Insights from the application of this tool should prove valuable in targeting vaccination campaigns and improving surveillance as countries work towards the elimination of dog-mediated rabies.

genomics↗

bioRxiv2016

Surveillance to Establish Elimination of Transmission and Freedom from Dog-mediated Rabies

BackgroundWith a global target set for zero human deaths from dog-mediated rabies by 2030 and some regional programmes close to eliminating canine rabies, there is an urgent need for enhanced surveillance strategies suitable for declaring freedom from disease and elimination of transmission with known confidence.\n\nMethodsUsing exhaustive contact tracing across settings in Tanzania we generated detailed data on rabies incidence, rabid dog biting behaviour and health-seeking behaviour of bite victims. Using these data we compared case detection of sampling-based and enhanced surveillance methodologies and investigated elimination verification procedures.\n\nFindingsWe demonstrate that patients presenting to clinics with bite injuries are sensitive sentinels for identifying dog rabies cases. Triage of patients based on bite history criteria and investigation of suspicious incidents can confirm >10% of dog rabies cases and is an affordable approach that will enable validation of disease freedom following two years without case detection. Approaches based on sampling the dog population without using bite-injury follow-up were found to be neither sensitive nor cost-effective.\n\nInterpretationThe low prevalence of rabies, and short window in which disease can be detected, preclude sampling-based surveillance. Instead, active case finding guided by bite-patient triage is needed as elimination is approached. Our proposed methodology is affordable, practical and supports the goal of eliminating human rabies deaths by improving administration of lifesaving post-exposure prophylaxis for genuinely exposed but untreated contacts. Moreover, joint investigations by public health and veterinary workers will strengthen intersectoral partnerships and capacity for control of emerging zoonoses.

epidemiology↗