Biology subjects

Diaz, E. W.

Publications and source records attributed to Diaz, E. W..

5 recordsLinked to original sources

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↗

bioRxiv2025

Cave dogs around major urban areas threaten rabies elimination program

BackgroundIn the city of Arequipa, Peru, the government has implemented control measures against dog rabies virus since the detection of its reintroduction in 2015. The city was previously considered free of animal reservoirs other than owned and stray dogs within its urban boundaries. However, multiple reports from peri-urban residents have suggested the presence of feral dogs living in caves on the citys outskirts. We aim to document the presence and dietary patterns of feral dogs adjacent to the city margins. MethodsWe conducted monthly field visits to four peri-urban localities in eastern Arequipa, an area where the presence of feral dogs had been previously reported. Dog caves were identified by tracking footprints and other field signs left by dogs, and their locations were georeferenced. Each cave was revisited monthly three times to record the presence of live and dead dogs, and puppies. Fecal samples collected around the caves were analyzed to assess dietary patterns. ResultsWe observed that feral dogs use caves for resting, hiding, and reproduction-- some of which appear to be constructed by the dogs themselves. The high number of puppies and dead adult dogs indicates a high population turnover. Dietary analysis revealed that these dogs feed on local fauna, including birds, rodents, cats, sheep, and, notably, other dogs. ConclusionsThese unowned, cave-dwelling dogs are not reached by mass rabies vaccination or sterilization programs. Moreover, they exist outside the jurisdiction of health inspectors responsible for rabies surveillance, resulting in a lack of data on rabies infection in this subpopulation. Our findings highlight the need for integrated One Health strategies to address the challenges posed by feral dog populations in rabies elimination efforts.

ecology↗

bioRxiv2025

Highly Dynamic Population of Owned Dogs and Implications for Zoonosis Control

BackgroundDomestic dogs are known carriers of a variety of zoonotic pathogens significant to public health including leishmaniasis, echinococcosis, and, the most lethal, rabies. Control efforts for rabies and other diseases focus on the removal of infected individuals and mass treatment or vaccination to reduce incidence and raise immunity in the susceptible population. However, the complex population dynamics surrounding free-roaming dogs in many developing countries complicate these control methods. While rabies vaccination coverage of 70% or higher, of the dog population at risk, performed annually, should be sufficient to maintain coverage above the critical threshold, rapid population turnover and growth could reduce effective coverage. Our objective was to investigate the impact of dog population dynamics on rabies control activities in a rabies-endemic city. MethodologyUsing data from annual door-to-door surveys in urban and periurban areas, we collected household information (e.g., number of residents), respondent characteristics (e.g., education level), and dog-related data (e.g., vaccination status). These variables were analyzed to evaluate changes in the dog population and vaccination coverage. A compartmental Susceptible - Exposed - Infectious - Vaccinated (SEIV) mathematical model was utilized to estimate the effects of population dynamics on herd immunity against rabies. FindingsWe found that the highly dynamic dog population in Arequipa and its rapid expansion hampers herd immunity, counteracting the efforts made in yearly vaccination campaigns and leading to underestimates of the human to dog ratios ([~]4:1 vs 6:1). Moreover, there are significant differences in dog population trends within urban and periurban areas indicating that different strategies or coverage vaccination targets might be needed. This study also introduces an important variable of interest: transient dogs, a population with extremely high turnover (less than one year), which causes an important drop in vaccination coverage that has thus far gone undetected. ConclusionsStabilizing the free-roaming domestic dog population by lowering both mortality and birth rates may help improve the efficacy of current mass vaccination programs. Additionally, the population dynamic parameters, on which we base our models, must be regularly refined to best represent the current status of disease risk and population immunity. By using a One Health approach we can understand and address the dynamics of dog populations, and better control zoonotic diseases like rabies, ultimately improving public health.

ecology↗

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↗

bioRxiv2024

Estimation of free-roaming dog populations using Google Street View: A Validation Study

Free-roaming dogs play a central role in carrying zoonotic pathogens such as rabies virus, Echinococcus granulosus, and Leishmania spp. The control and elimination of these pathogens require quantitative knowledge of dog populations. Thus, estimating the dog population is fundamental for planning, implementing, and evaluating public health programs. However, dog population estimation is time-consuming, requires many field personnel, may be inaccurate and unreliable, and is not without danger. Our objective was to validate a remote methodology for estimating the population of free-roaming dogs using Google Street View (GSV). Our target populations were free-roaming dogs from Arequipa, Peru, a rabies-affected area. Adopting a citizen science approach, and using social media, we recruited online citizen scientists from Arequipa and other regions and trained them to use GSV to identify and count free-roaming dogs in 26 urban and periurban communities. We used correlation metrics and negative binomial models to compare the counts of dogs identified in the GSV imagery with accurate counts of free-roaming owned dogs estimated via door-to-door surveys. In total, citizen scientists detected 868 dogs using GSV and using door-to-door surveys we estimated 909 free-roaming dogs across those 26 communities (Pearsons coefficient was r=0.73, p < 0.001). Our model predicted that for each free-roaming dog detected with GSV in urban areas, there were 1.03 owned dogs with free access to the street (p < 0.001). The type of community, urban versus periurban, did not have an important effect on the model, but fitting the models in periurban communities was difficult because of the sparsity of high-resolution GSV images in those areas. Using GSV imagery for estimating dog populations is a promising tool in urban areas. Citizen scientists can help to generate information for disease control programs in places with insufficient resources.

ecology↗