scholarly journals Mammal virus diversity estimates are unstable due to accelerating discovery effort

2021 ◽  
Author(s):  
Rory Gibb ◽  
Gregory F Albery ◽  
Nardus F Mollentze ◽  
Evan A Eskew ◽  
Liam Brierley ◽  
...  
Keyword(s):  
Current Data ◽  
Viral Diversity ◽  
Sampling Effort ◽  
Ecological Inference ◽  
Wild Mammals ◽  
Virus Diversity ◽  
Highly Sensitive ◽  
Zoonotic Risk ◽  
Association Data ◽  
Diversity Estimates

Host-virus association data form the backbone of research into eco-evolutionary drivers of viral diversity and host-level zoonotic risk. However, knowledge of the wildlife virome is inherently constrained by historical discovery effort, and there are concerns that the reliability of ecological inference from host-virus data may be undermined by taxonomic and geographical sampling biases. Here, we evaluate whether current estimates of host-level viral diversity in wild mammals are stable enough to be considered biologically meaningful, by analysing a comprehensive dataset of discovery dates of 6,571 unique mammal host-virus associations between 1930 and 2018. We show that virus discovery rates in mammal hosts are still either constant or accelerating, with little evidence of declines towards viral richness asymptotes in even highly-sampled hosts. Consequently, inference of relative viral richness across host species has been unstable over time, particularly in bats, where intensified surveillance since the early 2000s caused a rapid rearrangement of species' ranked viral richness. Our results show that comparative inference of host-level virus diversity across mammals is highly sensitive to even short-term changes in sampling effort. We advise caution to avoid overinterpreting patterns in current data, since our findings suggest that an analysis conducted today could feasibly draw quite different conclusions than one conducted only a decade ago.

scholarly journals Mammal virus diversity estimates are unstable due to accelerating discovery effort

2022 ◽  
Vol 18 (1) ◽  
Author(s):  
Rory Gibb ◽  
Gregory F. Albery ◽  
Nardus Mollentze ◽  
Evan A. Eskew ◽  
Liam Brierley ◽  
...  
Keyword(s):  
Host Species ◽  
Current Knowledge ◽  
Current Data ◽  
Viral Diversity ◽  
Sampling Effort ◽  
Ecological Inference ◽  
Wild Mammals ◽  
Virus Diversity ◽  
Zoonotic Risk ◽  
Association Data

Host-virus association data underpin research into the distribution and eco-evolutionary correlates of viral diversity and zoonotic risk across host species. However, current knowledge of the wildlife virome is inherently constrained by historical discovery effort, and there are concerns that the reliability of ecological inference from host-virus data may be undermined by taxonomic and geographical sampling biases. Here, we evaluate whether current estimates of host-level viral diversity in wild mammals are stable enough to be considered biologically meaningful, by analysing a comprehensive dataset of discovery dates of 6571 unique mammal host-virus associations between 1930 and 2018. We show that virus discovery rates in mammal hosts are either constant or accelerating, with little evidence of declines towards viral richness asymptotes, even in highly sampled hosts. Consequently, inference of relative viral richness across host species has been unstable over time, particularly in bats, where intensified surveillance since the early 2000s caused a rapid rearrangement of species' ranked viral richness. Our results illustrate that comparative inference of host-level virus diversity across mammals is highly sensitive to even short-term changes in sampling effort. We advise caution to avoid overinterpreting patterns in current data, since it is feasible that an analysis conducted today could draw quite different conclusions than one conducted only a decade ago.

Enzootic Activity of Chlamydia in Farms Located in a Hotspot Area for Zoonosis Emergence

2021 ◽  
Author(s):  
Ezequiel Andres Vanderhoeven ◽  
Jessica P. Mosmann ◽  
Adrián Díaz ◽  
Cecilia G. Cuffini
Keyword(s):  
Bird Species ◽  
Farm Animals ◽  
Economic Losses ◽  
Wild Mammals ◽  
Specific Pcr ◽  
Chlamydial Species ◽  
Zoonotic Risk ◽  
Two Samples ◽  
In The Wild ◽  
First Time

Abstract Chlamydias are obligated intracellular Gram-negative bacteria, considered important zoonotic pathogens, broadly present in several bird species and responsible for economic losses in animal production. We analyzed the presence of Chlamydial species with zoonotic risk in farm animals in a highly biodiverse area and with great human circulation, the Argentine, Brazil and Paraguay tri-border area. We surveyed nine farms in an area and nasally swabbed a total of 62 animals. DNA was extracted and specific PCR was performed to identify chlamydial species. We detected Chlamydia spp . in 6.5% (4/62) of the animals tested, positive samples belonged to cattle and none of them showed symptoms of respiratory disease nor had been diagnose with reproductive diseases. Specific nested PCR confirmed two samples belonged to C. pecorum and two to C. psittaci . We report for the first time Chlamydia circulation with zoonotic risk in the region. Surveys in birds and wild mammals could give a better understanding to know what Chlamydial species are circulating in the wild interface. The zoonotic potential should be taking into account as farm workers and the surrounding population could be silent carriers or have respiratory diseases being underdiagnosed, and therefore should be considered in the differential diagnoses.

scholarly journals Raw Sewage Harbors Diverse Viral Populations

mBio ◽  
2011 ◽  
Vol 2 (5) ◽  
Author(s):  
Paul G. Cantalupo ◽  
Byron Calgua ◽  
Guoyan Zhao ◽  
Ayalkibet Hundesa ◽  
Adam D. Wier ◽  
...  
Keyword(s):  
Genetic Material ◽  
Viral Diversity ◽  
Emerging Pathogens ◽  
Viral Genomes ◽  
Untreated Wastewater ◽  
Virus Diversity ◽  
Double Stranded Dna ◽  
Large Numbers ◽  
Ideal System ◽  
Species Specific

ABSTRACTAt this time, about 3,000 different viruses are recognized, but metagenomic studies suggest that these viruses are a small fraction of the viruses that exist in nature. We have explored viral diversity by deep sequencing nucleic acids obtained from virion populations enriched from raw sewage. We identified 234 known viruses, including 17 that infect humans. Plant, insect, and algal viruses as well as bacteriophages were also present. These viruses represented 26 taxonomic families and included viruses with single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), positive-sense ssRNA [ssRNA(+)], and dsRNA genomes. Novel viruses that could be placed in specific taxa represented 51 different families, making untreated wastewater the most diverse viral metagenome (genetic material recovered directly from environmental samples) examined thus far. However, the vast majority of sequence reads bore little or no sequence relation to known viruses and thus could not be placed into specific taxa. These results show that the vast majority of the viruses on Earth have not yet been characterized. Untreated wastewater provides a rich matrix for identifying novel viruses and for studying virus diversity.IMPORTANCEAt this time, virology is focused on the study of a relatively small number of viral species. Specific viruses are studied either because they are easily propagated in the laboratory or because they are associated with disease. The lack of knowledge of the size and characteristics of the viral universe and the diversity of viral genomes is a roadblock to understanding important issues, such as the origin of emerging pathogens and the extent of gene exchange among viruses. Untreated wastewater is an ideal system for assessing viral diversity because virion populations from large numbers of individuals are deposited and because raw sewage itself provides a rich environment for the growth of diverse host species and thus their viruses. These studies suggest that the viral universe is far more vast and diverse than previously suspected.

scholarly journals Hunter-gatherers in context: Mammal community composition in a northern Tanzania landscape used by Hadza foragers and Datoga pastoralists

2020 ◽  
Author(s):  
Brian Wood ◽  
Riccardo S. Millar ◽  
Nicholas Wright ◽  
Joshua Baumgartner ◽  
Hannah Holmquist ◽  
...  
Keyword(s):  
Community Composition ◽  
Camera Traps ◽  
Sub Saharan Africa ◽  
Sampling Effort ◽  
Mammal Species ◽  
Hunter Gatherers ◽  
Wild Mammals ◽  
Northern Tanzania ◽  
Mammal Community ◽  
Species Specific

In many regions of sub Saharan Africa large mammals occur in human-dominated areas, yet their community composition and species-specific densities have rarely been described in areas occupied by traditional hunter-gatherers and pastoralists. Surveys of mammal populations in such areas provide important measures of biodiversity and provide ecological context for understanding hunting practices. Using a sampling grid centered on a Hadza hunter-gatherer camp and covering 36 km² of semi-arid savannah in northern Tanzania, we assessed mammals using camera traps (n = 19 stations) for c. 5 months (2,182 trap nights). In the study area (Tli’ika in the Hadza language), we recorded 36 wild mammal species, resembling a near complete mammal community. Rarefaction curves suggest that sampling effort was sufficient to capture mammal species richness. Species-specific densities were estimated using a random encounter model and site- and species’ body mass- specific estimates of the area sampled at each camera; confidence intervals were estimated using bootstrapping. Point estimates of densities varied by c. four orders of magnitude, from 0.003 ind./km² (African wild dog) to 27.5 ind./km² (Kirk’s dik dik). Densities of livestock (cattle, donkey, sheep and goat) were high, particularly when estimated using directly observed herd sizes. Cumulative biomass density of herbivorous livestock species exceeded that of all wild mammals by a factor of 3.3-38.7. We compare our study’s data to camera trap rates recorded in a fully protected area of northern Tanzania with similar precipitation (Lake Manyara National Park), revealing that abundance indices of most wildlife species in Tli’ika were much lower. We discuss how these data inform studies of Hadza hunting and models of hunter-gatherer foraging ecology and diet.

scholarly journals Uso de la mastofauna silvestre en la comunidad cafetalera de Cumbres de Huicicila, Compostela, Nayarit, México

2019 ◽  
Vol 9 (2) ◽  
pp. 29
Author(s):  
Fátima Carolina Medina-Gutiérrez ◽  
Juan Pablo Ramírez-Silva
Keyword(s):  
Iucn Red List ◽  
Red List ◽  
Camera Traps ◽  
Sampling Effort ◽  
Human Relationship ◽  
Panthera Onca ◽  
Leopardus Pardalis ◽  
Coffee Plantations ◽  
Wild Mammals ◽  
The People

ResumenEl objetivo del presente trabajo fue analizar la percepción y usos de los mamíferos silvestres en un área cafetalera de la comunidad Cumbres de Huicicila, municipio de Compostela, Nayarit. Se utilizaron técnicas etnozoológicas tales como aplicación de encuesta sobre el usos y costumbres que tienen en relación con los mamíferos. Adicionalmente, se usaron cámaras-trampa con un esfuerzo de muestreo de 1,260 días/trampas. En total se obtuvieron 531 videos y 373 registros válidos de mamíferos silvestres de 10 especies pertenecientes a cinco órdenes y siete familias, tres de ellas enlistadas en la NOM-059-SEMARNAT-2010 y la lista roja de la UICN (Panthera onca, Leopardus pardalis y Herpailurus yagouaroundi). A través de las herramientas etnozoológicas se identificaron 15 especies de mamíferos y cinco órdenes. Las personas de la comunidad afirmaron darle algún tipo de uso a los mamíferos que conocen, entre los que destacan el alimenticio, medicinal, tráfico ilegal (venta de especies), cacería e inclusive se mencionaron algunos conflictos de relación depredador-humano. A pesar de lo mencionado, la participación de la comunidad fue positiva. Trabajos de este tipo pueden favorecer la sensibilización hacia la vida silvestre y así, la ejecución de programas de manejo, uso y conservación de mamíferos podría tener éxito y ayudar a la subsistencia de la comunidad.Palabras clave: Cafetales, etnomastozoología, jaguar, mesomamíferos, uso de fauna silvestre.AbstractIn this paper we analyzed the perception and uses of the wild mammals by the population that inhabited in Cumbres de Huicicila community, municipality of Compostela, Nayarit, the information was complemented by the use of camera traps, from which we obtained 531 videos with 373 valid records of wild mammals, with 1,260 days/traps sampling effort . We recorded 10 species belonging to five orders and seven families, three of such (Panthera onca, Leopardus pardalis and Herpailurus yagouaroundi) are listed in NOM-059-2010 and the IUCN red list. The inhabitants of the Cumbres de Huicicila community identify 20 species of mammals, including the 10 species registered by the camera traps, the people of the community know the mammals and are used, they mentioned as food, medicine, illegal trafficking, hunting for leisure and ornaments and even some predatory-human relationship conflicts.Despite them, community participation was positive, we believe that this works can aid to create the awareness of wildlife and thus, the implementation of mammalian management, use and conservation programs could be successful and help the community to increase quality live.Key words: Coffee plantations, ethnozoology, jaguar, medium-sized mammals, use of wildlife.

scholarly journals Species-rich bark and ambrosia beetle fauna (Coleoptera, Curculionidae, Scolytinae) of the Ecuadorian Amazonian Forest Canopy

ZooKeys ◽  
2021 ◽  
Vol 1044 ◽  
pp. 797-813
Author(s):  
Stephanie A. Dole ◽  
Jiri Hulcr ◽  
Anthony I. Cognato
Keyword(s):  
Bark Beetles ◽  
Forest Canopy ◽  
Sampling Effort ◽  
Ecological Groups ◽  
Species Accumulation Curves ◽  
Ambrosia Beetles ◽  
Diversity Assessment ◽  
Α Diversity ◽  
Canopy Fogging ◽  
Diversity Estimates

Canopy fogging was used to sample the diversity of bark and ambrosia beetles (Coleoptera, Curculionidae, Scolytinae) at two western Amazonian rainforest sites in Ecuador. Sampling was conducted by Dr Terry Erwin and assistants from 1994–2006 and yielded 1158 samples containing 2500 scolytine specimens representing more than 400 morphospecies. Here, we analyze a subset of these data representing two ecological groups: true bark beetles (52 morphospecies) and ambrosia beetles (69 morphospecies). A high percentage of these taxa occurred as singletons and doubletons and their species accumulation curves did not reach an asymptote. Diversity estimates placed the total scolytine species richness for this taxon subset present at the two sites between 260 and 323 species. The α-diversity was remarkably high at each site, while the apparently high β-diversity was an artifact of undersampling, as shown by a Monte Carlo resampling analysis. This study demonstrates the utility of canopy fogging for the discovery of new scolytine taxa and for approximate diversity assessment, but a substantially greater sampling effort would be needed for conclusive alpha as well as beta diversity estimates.

scholarly journals Data proliferation, reconciliation, and synthesis in viral ecology

2021 ◽  
Author(s):  
Rory Gibb ◽  
Gregory F. Albery ◽  
Daniel J. Becker ◽  
Liam Brierley ◽  
Ryan Connor ◽  
...  
Keyword(s):  
Best Practice ◽  
Reporting Standards ◽  
Viral Ecology ◽  
Incremental Development ◽  
Structure And Dynamics ◽  
Zoonotic Risk ◽  
Numerous Data ◽  
Association Data ◽  
Synthetic Datasets ◽  
Technological Improvements

AbstractThe fields of viral ecology and evolution have rapidly expanded in the last two decades, driven by technological improvements, and motivated by efforts to discover potentially zoonotic wildlife viruses under the rubric of pandemic prevention. One consequence has been a massive proliferation of host-virus association data, which comprise the backbone of research in viral macroecology and zoonotic risk prediction. These data remain fragmented across numerous data portals and projects, each with their own scope, structure, and reporting standards. Here, we propose that synthesis of host-virus association data is a central challenge to improve our understanding of the global virome and develop foundational theory in viral ecology. To illustrate this, we build an open reconciled mammal-virus database from four key published datasets, applying a standardized taxonomy and metadata. We show that reconciling these datasets provides a substantially richer view of the mammal virome than that offered by any one individual database. We argue for a shift in best practice towards the incremental development and use of synthetic datasets in viral ecology research, both to improve comparability and replicability across studies, and to facilitate future efforts to use machine learning to predict the structure and dynamics of the global virome.

scholarly journals Assemblage of medium and large size mammals in an urban Semideciduous Seasonal Forest fragment in Cerrado biome

2013 ◽  
Vol 13 (2) ◽  
pp. 76-80 ◽  
Author(s):  
Paulo Vitor dos Santos Bernardo ◽  
Fabiano Rodrigues de Melo
Keyword(s):  
Urban Area ◽  
Fragment Size ◽  
Domestic Animals ◽  
Present Species ◽  
Limiting Factor ◽  
Sampling Effort ◽  
Forest Fragment ◽  
Wild Mammals ◽  
Large Size ◽  
Semideciduous Seasonal Forest

Nowadays, the processes of deforestation and loss of habitats represent a major threat to many species of mammals. These processes cause changes in natural landscapes by decreasing area, connectivity, and fragment size, and increasing edge effects and number of fragments. Understanding which and how many species persist in disturbed fragments may indicate the species' minimum requirements and might contribute to their conservation. Here we show how the mammalian fauna of medium and large size (higher than 1 kg) are structured in a semideciduous seasonal forest fragment of 36.5 ha in the urban area of Jataí, Goiás. We performed the sampling with 30 sand track plots (1 x 1 m). We analyzed the relative record frequency and built a collector's curve to demonstrate the sampling effort. With a total effort of 600 track plots × days, we recorded twelve species of mammals with our tracks sampling method, from which only the wild mammals were included in the analyzes (11 species). The estimated species richness reached 13 species (SD (Standard Deviation) = ±1, CI (Confidence Interval) = ±2 (11 – 15 species). The species with the highest relative record frequency was Didelphis albiventris and the species with the lowest was Tamandua tetradactyla. The fragment size must be a limiting factor to the richness and to the occurrence of species, as it may not be sufficient to allow the persistence of a population or an individual. Disturbances that originated from houses, like domestic animals and movement of people, also contributed to the removal and extinction of species. To conserve the species in the fragment, we suggest the prevention of entrance of people and of domestic animals. We also recommend increased connectivity of the fragment with the landscape external to the urban area in order to allow the movement of the currently present species.

scholarly journals Monitoring program for mammals in a protected area of Colombia

2017 ◽  
Vol 22 (1) ◽  
pp. 9
Author(s):  
Germán Jiménez ◽  
Natalia López-Cepeda ◽  
Andrea Delgado ◽  
Ana María Guevara ◽  
Laura Lozano
Keyword(s):  
Activity Patterns ◽  
Monitoring Program ◽  
Camera Traps ◽  
Domestic Dogs ◽  
Sampling Effort ◽  
Wild Mammals ◽  
First Semester ◽  
Independent Events ◽  
Set Up ◽  
The Impact

<p>Between the second semester of 2009 and the first semester of 2011, camera traps were set up in conserved and disturbed habitats in the Otún Quimbaya Flora and Fauna Sanctuary. From a sampling effort of 2,066 camera-days, 673 photographs of 157 independent events were obtained for eight species of wild mammals and a domestic one. Their activity patterns were mainly nocturnal even for those species reported as diurnal. The impact of human interference and exotic species was evident for two species: <em>Tapirus pinchaque</em> and <em>Cerdocyon thous</em>. The former was observed below its altitudinal range with activity patterns mainly crepuscular and nocturnal. The second was observed in the same habitats where domestic dogs were found, with activity patterns mainly crepuscular and nocturnal. These findings suggest that both species have altered their activity patterns. Actions must be focused on decreasing the interaction of these mammals with humans and domestic dogs.</p>

scholarly journals Emergence and Evolution of Novel Reassortant Influenza A Viruses in Canines in Southern China

mBio ◽  
2018 ◽  
Vol 9 (3) ◽  
Author(s):  
Ying Chen ◽  
Nídia S. Trovão ◽  
Guojun Wang ◽  
Weifeng Zhao ◽  
Ping He ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Influenza A ◽  
Southern China ◽  
Influenza Viruses ◽  
Influenza A Viruses ◽  
Potential Threat ◽  
Animal Reservoir ◽  
Human Contact ◽  
Virus Diversity ◽  
Zoonotic Risk

ABSTRACTThe capacity of influenza A viruses (IAVs) to host jump from animal reservoir species to humans presents an ongoing pandemic threat. Birds and swine are considered major reservoirs of viral genetic diversity, whereas equines and canines have historically been restricted to one or two stable IAV lineages with no transmission to humans. Here, by sequencing the complete genomes of 16 IAVs obtained from canines in southern China (Guangxi Zhuang Autonomous Region [Guangxi]) in 2013 to 2015, we demonstrate that the evolution of canine influenza viruses (CIVs) in Asian dogs is increasingly complex, presenting a potential threat to humans. First, two reassortant H1N1 virus genotypes were introduced independently from swine into canines in Guangxi, including one genotype associated with a zoonotic infection. The genomes contain segments from three lineages that circulate in swine in China: North American triple reassortant H3N2, Eurasian avian-like H1N1, and pandemic H1N1. Furthermore, the swine-origin H1N1 viruses have transmitted onward in canines and reassorted with the CIV-H3N2 viruses that circulate endemically in Asian dogs, producing three novel reassortant CIV genotypes (H1N1r, H1N2r, and H3N2r [r stands for reassortant]). CIVs from this study were collected primarily from pet dogs presenting with respiratory symptoms at veterinary clinics, but dogs in Guangxi are also raised for meat, and street dogs roam freely, creating a more complex ecosystem for CIV transmission. Further surveillance is greatly needed to understand the full genetic diversity of CIV in southern China, the nature of viral emergence and persistence in the region’s diverse canine populations, and the zoonotic risk as the viruses continue to evolve.IMPORTANCEMammals have emerged as critically underrecognized sources of influenza virus diversity, including pigs that were the source of the 2009 pandemic and bats and bovines that harbor highly divergent viral lineages. Here, we identify two reassortant IAVs that recently host switched from swine to canines in southern China, including one virus with known zoonotic potential. Three additional genotypes were generated via reassortment events in canine hosts, demonstrating the capacity of dogs to serve as “mixing vessels.” The continued expansion of IAV diversity in canines with high human contact rates requires enhanced surveillance and ongoing evaluation of emerging pandemic threats.

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