Biology subjects

Hall, R. J.

Publications and source records attributed to Hall, R. J..

25 records · Page 2Linked to original sources

bioRxiv2020

Reactivation of latent infections with migration shapes population-level disease dynamics

Annual migration is common across animal taxa and can dramatically shape the spatial and temporal patterns of infectious disease. Although migration can decrease infection prevalence in some contexts, these energetically costly long-distance movements can also have immunosuppressive effects that may interact with transmission processes in complex ways. Here we develop a mechanistic model for the reactivation of latent infections driven by physiological changes or energetic costs associated with migration (i.e., "migratory relapse") and its effects on disease dynamics. We determine conditions under which migratory relapse can amplify or reduce infection prevalence across pathogen and host traits (e.g., infectious periods, virulence, overwinter survival, timing of relapse) and transmission phenologies. We show that relapse at either the start or end of migration can dramatically increase prevalence across the annual cycle and may be crucial for maintaining pathogens with low transmissibility and short infectious periods in migratory populations. Conversely, relapse at the start of migration can reduce the prevalence of highly virulent pathogens by amplifying culling of infected hosts during costly migration, especially for highly transmissible pathogens and those transmitted during migration or the breeding season. Our study provides a mechanistic foundation for understanding the spatiotemporal patterns of relapsing infections in migratory hosts, with implications for zoonotic surveillance and understanding how infection patterns will respond to shifts in migratory propensity associated with environmental change. Further, our work suggests incorporating within-host processes into population-level models of pathogen transmission may be crucial for reconciling the range of migration-infection relationships observed across migratory species.

ecology↗

bioRxiv2020

Light pollution affects West Nile virus exposure risk across Florida.

Emerging infectious diseases (EIDs), including zoonotic arboviruses, present a global health threat. Multiple components of human land use change have been linked to arboviral emergence, but one pervasive factor that has received comparatively little attention is light pollution. Although often considered a component of built environments, artificial light at night (ALAN) outpaces the growth and spatial extent of urbanization, and thus affects areas where human population density and anthropogenic land changes are modest. West Nile virus (WNV) emergence has been described as peri-urban, but recent research suggests that its relative ubiquity in human-altered environments might actually be due to ALAN. Indeed, we found previously that experimental ALAN exposure enhanced avian competence to transmit WNV to mosquitoes. In the present study, we asked whether such organismal effects manifest ecologically by determining whether WNV exposure among sentinel chickens in Florida is related to local ALAN conditions. We found strong support for a nonlinear relationship between ALAN and WNV exposure in chickens with peak WNV risk occurring at low ALAN levels. Importantly, effects of ALAN on WNV exposure were stronger than other aspects of urbanization; only ambient temperature in the month prior to sampling had a comparable effect to ALAN. These results represent the first field evidence that ALAN might affect infectious disease exposure risk. We advocate for further research on how ALAN influences zoonotic risk, as well as efforts to study alternative nighttime lighting methods to reduce such risk. Significance StatementLight pollution associated with human development is a globally pervasive and rapidly expanding anthropogenic stressor; but despite documented effects on host immune functions and vector behaviors, how it affects infectious disease risk is unknown. Using data from the Florida Department of Health arbovirus surveillance program, we show that light pollution is a stronger predictor of variation in West Nile virus (WNV) exposure risk than many other previously implicated anthropogenic and natural environmental variables. Light pollution effects are nonlinear, so risk is highest in areas with dim light pollution. Our results highlight a new way that light pollution might affect human and wildlife health.

ecology↗

bioRxiv2019

Simulating the evolutionary trajectories of metabolic pathways for insect symbionts in the Sodalis genus

1Insect-bacterial symbioses are ubiquitous, but there is still much to uncover about how these relationships establish, persist and evolve. The tsetse endosymbiont Sodalis glossinidius displays intriguing metabolic adaptations to its microenvironment, but the process by which this relationship evolved remains to be elucidated. The recent chance discovery of the free-living secies of the Sodalis genus, S. praecaptivus, provides a serendipitous starting point from which to investigate the evolution of this symbiosis. Here, we present a flux balance model for S. praecaptivus. Metabolic modelling is used in combination with a multi-objective evolutionary algorithm to explore the trajectories that S. glossinidius may have undertaken after becoming internalised. The time-dependent loss of key genes is shown to influence the evolved populations, providing possible targets for future in vitro genetic manipulation. This method provides an unusually detailed perspective on possible evolutionary trajectories for S. glossinidius in this fundamental process of evolutionary and ecological change.

evolutionary biology↗

bioRxiv2019

Mosquito species and age influence thermal performance of traits relevant to malaria transmission

Models predicting disease transmission are a vital tool in the control of mosquito populations and malaria reduction as they can target intervention efforts. We compared the performance of temperature-dependent transmission models when mosquito life history traits were allowed to change across the lifespan of Anopheles stephensi, the urban malaria mosquito, to models parameterized with commonly derived estimates of lifetime trait values. We conducted an experiment on adult female An. stephensi to generate daily per capita values for lifespan, egg production, and biting rate at six constant temperatures. Both temperature and age significantly affected trait values. Further, we found quantitative and qualitative differences between temperature-trait relationships estimated based on daily rates versus directly observed lifetime values. Incorporating these temperature-trait relationships into an expression governing transmission suitability, relative R0(T), model resulted in minor differences in the breadth of suitable temperatures for Plasmodium falciparum transmission between the two models constructed from only An. stephensi trait data, but a substantial increase in breadth compared to a previously published model consisting of trait data from multiple mosquito species. Overall this work highlights the importance of considering how mosquito trait values vary with mosquito age and mosquito species when generating temperature-based environmental suitability predictions of transmission.

ecology↗

bioRxiv2019

Highly-accurate long-read sequencing improves variant detection and assembly of a human genome

The major DNA sequencing technologies in use today produce either highly-accurate short reads or noisy long reads. We developed a protocol based on single-molecule, circular consensus sequencing (CCS) to generate highly-accurate (99.8%) long reads averaging 13.5 kb and applied it to sequence the well-characterized human HG002/NA24385. We optimized existing tools to comprehensively detect variants, achieving precision and recall above 99.91% for SNVs, 95.98% for indels, and 95.99% for structural variants. We estimate that 2,434 discordances are correctable mistakes in the high-quality Genome in a Bottle benchmark. Nearly all (99.64%) variants are phased into haplotypes, which further improves variant detection. De novo assembly produces a highly contiguous and accurate genome with contig N50 above 15 Mb and concordance of 99.998%. CCS reads match short reads for small variant detection, while enabling structural variant detection and de novo assembly at similar contiguity and markedly higher concordance than noisy long reads.

genomics↗

bioRxiv2018

FALCON-Phase: Integrating PacBio and Hi-C data for phased diploid genomes

Haplotype-resolved genome assemblies are important for understanding how combinations of variants impact phenotypes. These assemblies can be created in various ways, such as use of tissues that contain single-haplotype (haploid) genomes, or by co-sequencing of parental genomes, but these approaches can be impractical in many situations. We present FALCON-Phase, which integrates long-read sequencing data and ultra-long-range Hi-C chromatin interaction data of a diploid individual to create high-quality, phased diploid genome assemblies. The method was evaluated by application to three datasets, including human, cattle, and zebra finch, for which high-quality, fully haplotype resolved assemblies were available for benchmarking. Phasing algorithm accuracy was affected by heterozygosity of the individual sequenced, with higher accuracy for cattle and zebra finch (>97%) compared to human (82%). In addition, scaffolding with the same Hi-C chromatin contact data resulted in phased chromosome-scale scaffolds.

genomics↗

bioRxiv2018

Light Pollution Increases West Nile Virus Competence in a Ubiquitous Passerine Reservoir Species

One sentence summaryLight pollution increases host infectiousness.\n\nAbstractLight pollution is a growing problem, but its impacts on infectious disease risk have not been considered. Previous research has revealed that dim light at night (dLAN) dysregulates various immune functions and biorhythms, which hints that dLAN could change the risk of disease epidemics. Here, we demonstrate that dLAN enhances infectiousness of the house sparrow (Passer domesticus), an urban-dwelling avian host of West Nile virus (WNV). Sparrows exposed to dLAN maintained viral titers above the transmission threshold to a biting vector (105 plaque-forming units) for two days longer than controls but did not die at higher rates. A mathematical model revealed that such effects could increase WNV outbreak potential by ~41%. dLAN likely affects other host and vector traits relevant to transmission, so additional research is needed to advise management of zoonotic diseases in light polluted areas.

pathology↗