Potential distribution of the viral haemorrhagic septicaemia virus in the Great Lakes region

An evaluation of the ecological niche of Orf virus (Poxviridae): Challenges of distinguishing broad niches from no niches

Contagious ecthyma is a skin disease, caused by Orf virus, creating great economic threats to livestock farming worldwide. Zoonotic potential of this disease has gained recent attention owing to the re-emergence of disease in several parts of the world. Increased public health concern emphasizes the need for a predictive understanding of the geographic distributional potential of Orf virus. Here, we mapped the current distribution using occurrence records, and estimated the ecological niche in both geographical and environmental spaces. Twenty modeling experiments, resulting from two- and three-partition models, were performed to choose the candidate models that best represent the geographic distributional potential of Orf virus. For all of our models, it was possible to reject the null hypothesis of predictive performance no better than random expectations. However, statistical significance must be accompanied by sufficiently good predictive performance if a model is to be useful. In our case, omission of known distribution of the virus was noticed in all Maxent models, indicating inferior quality of our models. This conclusion was further confirmed by the independent final evaluation, using occurrence records sourced from the Centre for Agriculture and Bioscience International. Minimum volume ellipsoid (MVE) models indicated the broad range of environmental conditions under which Orf virus infections are found. The excluded climatic conditions from MVEs could not be considered as unsuitable owing to the broad distribution of Orf virus. These results suggest two possibilities: that the niche models fail to identify niche limits that constrain the virus, or that the virus has no detectable niche, as it can be found throughout the geographic distributions of its hosts. This potential limitation of component-based pathogen-only ENMs is discussed in detail.

The aquaculture disease network model (AquaNet-Mod): A simulation model to evaluate disease spread and controls for the salmonid industry in England and Wales

Infectious disease causes significant mortality in wild and farmed systems, threatening biodiversity, conservation and animal welfare, as well as food security. To mitigate impacts and inform policy, tools such as mathematical models and computer simulations are valuable for predicting the potential spread and impact of disease. This paper describes the development of the Aquaculture Disease Network Model, AquaNet-Mod, and demonstrates its application to evaluating disease epidemics and the efficacy of control, using a Viral Haemorrhagic Septicaemia (VHS) case study. AquaNet-Mod is a data-driven, stochastic, state-transition model. Disease spread can occur via four different mechanisms, i) live fish movement, ii) river based, iii) short distance mechanical and iv) distance independent mechanical. Sites transit between three disease states: susceptible, clinically infected and subclinically infected. Disease spread can be interrupted by the application of disease mitigation measures and controls such as contact tracing, culling, fallowing and surveillance. Results from a VHS case study highlight the potential for VHS to spread to 96% of sites over a 10 year time horizon if no disease controls are applied. Epidemiological impact is significantly reduced when live fish movement restrictions are placed on the most connected sites and further still, when disease controls, representative of current disease control policy in England and Wales, are applied. The importance of specific disease control measures, particularly contact tracing and disease detection rate, are also highlighted. The merit of this model for evaluation of disease spread and the efficacy of controls, in the context of policy, along with potential for further application and development of the model, for example to include economic parameters, is discussed.

Evolutionary trajectory of fish Piscine novirhabdovirus (=Viral Hemorrhagic Septicemia Virus) across its Laurentian Great Lakes history: Spatial and temporal diversification

Piscine novirhabdovirus = Viral Hemorrhagic Septicemia Virus (VHSV) first appeared in the Laurentian Great Lakes with large outbreaks from 2005 to 2006, as a new and novel RNA rhabdovirus subgenogroup (IVb) that killed >30 fish species. Interlude periods punctuated smaller more localized outbreaks in 2007, 2010, and 2017, although some fishes tested positive in the intervals. There have not been reports of outbreaks or positives from 2018, 2019, or 2020. Here, we employ a combined population genetics and phylogenetic approach to evaluate spatial and temporal evolutionary trajectory on its G-gene sequence variation, in comparison with whole-genome sequences (11,083 bp) from a subset of 44 individual isolates (including 40 newly sequenced ones). Our results show that IVb (N = 184 individual fish isolates) diversified into 36 G-gene haplotypes from 2003 to 2017, stemming from two originals ("a" and "b"). G-gene haplotypes "a" and "b" differed by just one synonymous single-nucleotide polymorphism (SNP) substitution, remained the most abundant until 2011, then disappeared. Group "a" descendants (14 haplotypes) remained most prevalent in the Upper and Central Great Lakes, with eight (51%) having nonsynonymous substitutions. Group "b" descendants primarily have occurred in the Lower Great Lakes, including 22 haplotypes, of which 15 (68%) contained nonsynonymous changes. Evolutionary patterns of the whole-genome sequences (which had 34 haplotypes among 44 isolates) appear congruent with those from the G-gene. Virus populations significantly diverged among the Upper, Central, and Lower Great Lakes, diversifying over time. Spatial divergence was apparent in the overall patterns of nucleotide substitutions, while amino acid changes increased temporally. VHSV-IVb thus significantly differentiated across its less than two decades in the Great Lakes, accompanied by declining outbreaks and virulence. Continuing diversification likely allowed the virus to persist at low levels in resident fish populations, and may facilitate its potential for further and future spread to new habitats and nonacclimated hosts.

Comparative effects of Novirhabdovirus genes on modulating constitutive transcription and innate antiviral responses, in different teleost host cell types

BACKGROUND

Infectious hematopoietic necrosis virus (IHNV) and viral hemorrhagic septicemia virus (VHSV) are highly contagious, pathogenic Novirhabdoviruses affecting fish and are thusly notifiable diseases with the World Organization for Animal Health. This study assessed the relative capacities of IHNV and VHSV genes to modulate host general transcription and explores the abilities of specific IHNV genes to interfere with the interferon pathway in heterogenous teleost cell-lines.

METHODS

Optimized protocols allowed for efficient transient transfections in EPC, BF-2, RTG-2 and RTgill-W1 cell lines of plasmids encoding IHNV (M genogroup) and VHSV (-IVb genotype) genes, including N, P, M, G and NV. Their impact on general cellular transcription was measured 48 hours post transfection (hpt) with luciferase constructs driven by a modified β-Actin promoter (pCAG). Their modulation of the innate antiviral immune response was characterized 72 hpt, using luciferase constructs measuring rainbow trout Type I IFN or MX-1 promoter augmentation, upon MAVS co-transfection.

RESULTS

M was generally confirmed as the strongest constitutive transcriptional suppressor while IHNV P, but not VHSV P, augmented constitutive transcription in fibroblastic cell types. Cell-specific effects were observed for viral G gene, with VHSV G exhibiting suppression of basal transcription in EPC and BF-2 but not in trout cells; while IHNV G was stimulatory in RTG-2, but inhibitory in RTgill-W1. NV consistently stimulated constitutive transcription, with higher augmentation patterns seen in fibroblastic compared to epithelial cells, and for IHNV NV compared to VHSV NV. The innate antiviral immune response, focusing on the IFN pathway, was silenced by IHNV M in all cell lines tested. IHNV N showed a dose-dependent suppression of type I IFN, but with minor effects on MX-1. IHNV P and G played minor IFN-inhibitory roles, consistent and dose-dependent only for G in rainbow trout cells. IHNV NV mediated a consistent stimulatory effect on either Type I IFN or MX-1, but much less pronounced in RTgill-W1.

CONCLUSIONS

This study extends our understanding of Novirhabdoviruses-host interaction, showing differential innate immune responses in heterogenous cell types. Viral regulators of innate immune signaling are identified, either as dose-dependent suppressors (such as M and N) or stimulators (mainly NV), indicating novel targets for the design of more efficient vaccination strategies.

Investigating diversity of pathogenic microbes in commercial bait trade water

The recreational bait trade is a potential pathway for pathogen introduction and spread when anglers dump bait shop sourced water into aquatic systems. Despite this possibility, and previous recognition of the importance of the bait trade in the spread of aquatic invasive species (AIS), to date there has been no region wide survey documenting pathogens in retail bait shops. In this study, we analyzed 96 environmental DNA samples from retail bait shops around the Great Lakes region to identify pathogens, targeting the V4 hypervariable region of the 16S rRNA gene. Additionally, we used samples from one site in Lake Michigan as a comparison to pathogen diversity and abundance in natural aquatic systems. Our results identified nine different groups of pathogens in the bait shop samples, including those that pose risks to both humans and fish species. Compared to wild sourced samples, the bait shops had higher relative abundance and greater taxonomic diversity. These findings suggest that the bait trade represents a potentially important pathway that could introduce and spread pathogens throughout the Great Lakes region. Improving pathogen screening and angler outreach should be used in combination to aid in preventing the future spread of high risk pathogens.

Novel Methods in Disease Biogeography: A Case Study with Heterosporosis

Disease biogeography is currently a promising field to complement epidemiology, and ecological niche modeling theory and methods are a key component. Therefore, applying the concepts and tools from ecological niche modeling to disease biogeography and epidemiology will provide biologically sound and analytically robust descriptive and predictive analyses of disease distributions. As a case study, we explored the ecologically important fish disease Heterosporosis, a relatively poorly understood disease caused by the intracellular microsporidian parasite Heterosporis sutherlandae. We explored two novel ecological niche modeling methods, the minimum-volume ellipsoid (MVE) and the Marble algorithm, which were used to reconstruct the fundamental and the realized ecological niche of H. sutherlandae, respectively. Additionally, we assessed how the management of occurrence reports can impact the output of the models. Ecological niche models were able to reconstruct a proxy of the fundamental and realized niche for this aquatic parasite, identifying specific areas suitable for Heterosporosis. We found that the conceptual and methodological advances in ecological niche modeling provide accessible tools to update the current practices of spatial epidemiology. However, careful data curation and a detailed understanding of the algorithm employed are critical for a clear definition of the assumptions implicit in the modeling process and to ensure biologically sound forecasts. In this paper, we show how sensitive MVE is to the input data, while Marble algorithm may provide detailed forecasts with a minimum of parameters. We showed that exploring algorithms of different natures such as environmental clusters, climatic envelopes, and logistic regressions (e.g., Marble, MVE, and Maxent) provide different scenarios of potential distribution. Thus, no single algorithm should be used for disease mapping. Instead, different algorithms should be employed for a more informed and complete understanding of the pathogen or parasite in question.

Accessible areas in ecological niche comparisons of invasive species: Recognized but still overlooked

Understanding biological invasions is crucial for their control and prevention. Specially, establishing whether invasive species operate within the constraint of conservative ecological niches, or if niche shifts occur at all commonly as part of the invasion process, is indispensable to identifying and anticipating potential areas of invasion. Ecological niche modeling (ENM) has been used to address such questions, but improvements and debate in study design, model evaluation, and methods are still needed to mature this field. We reanalyze data for Gray Squirrels (Sciurus carolinensis), native to North America, but invasive in Europe. Our main finding was that, when the analysis extent is established carefully based on analogous sets of environmental conditions, all evidence of niche shifts disappears, suggesting that previous reports of niche shifts for this species are artifacts of methods and interpretation, rather than biological reality. Niche conservatism should be tested only within appropriate, similar, environmental spaces that are accessible to both species or populations being compared, thus avoiding model extrapolation related to model transfers. Testing for environmental similarity between native and invaded areas is critical to identifying niche shifts during species invasion robustly, but also in applications of ENM to understanding temporal dimensions of niche dynamics.

Advances and Limitations of Disease Biogeography Using Ecological Niche Modeling

Mapping disease transmission risk is crucial in public and animal health for evidence based decision-making. Ecology and epidemiology are highly related disciplines that may contribute to improvements in mapping disease, which can be used to answer health related questions. Ecological niche modeling is increasingly used for understanding the biogeography of diseases in plants, animals, and humans. However, epidemiological applications of niche modeling approaches for disease mapping can fail to generate robust study designs, producing incomplete or incorrect inferences. This manuscript is an overview of the history and conceptual bases behind ecological niche modeling, specifically as applied to epidemiology and public health; it does not pretend to be an exhaustive and detailed description of ecological niche modeling literature and methods. Instead, this review includes selected state-of-the-science approaches and tools, providing a short guide to designing studies incorporating information on the type and quality of the input data (i.e., occurrences and environmental variables), identification and justification of the extent of the study area, and encourages users to explore and test diverse algorithms for more informed conclusions. We provide a friendly introduction to the field of disease biogeography presenting an updated guide for researchers looking to use ecological niche modeling for disease mapping. We anticipate that ecological niche modeling will soon be a critical tool for epidemiologists aiming to map disease transmission risk, forecast disease distribution under climate change scenarios, and identify landscape factors triggering outbreaks.

Realized niche shift associated with the Eurasian charophyte Nitellopsis obtusa becoming invasive in North America

Nitellopsis obtusa (starry stonewort) is a dioecious green alga native to Europe and Asia that has emerged as an aquatic invasive species in North America. Nitellopsis obtusa is rare across large portions of its native range, but has spread rapidly in northern-tier lakes in the United States, where it can interfere with recreation and may displace native species. Little is known about the invasion ecology of N. obtusa, making it difficult to forecast future expansion. Using ecological niche modeling we investigated environmental variables associated with invasion risk. We used species records, climate data, and remotely sensed environmental variables to characterize the species’ multidimensional distribution. We found that N. obtusa is exploiting novel ecological niche space in its introduced range, which may help explain its invasiveness. While the fundamental niche of N. obtusa may be stable, there appears to have been a shift in its realized niche associated with invasion in North America. Large portions of the United States are predicted to constitute highly suitable habitat for N. obtusa. Our results can inform early detection and rapid response efforts targeting N. obtusa and provide testable estimates of the physiological tolerances of this species as a baseline for future empirical research.