Red fox viromes in urban and rural landscapes

Making sense of the virome in light of evolution and ecology

Understanding the patterns and drivers of viral prevalence and abundance is of key importance for understanding pathogen emergence. Over the last decade, metagenomic sequencing has exponentially expanded our knowledge of the diversity and evolution of viruses associated with all domains of life. However, as most of these 'virome' studies are primarily descriptive, our understanding of the predictors of virus prevalence, abundance and diversity, and their variation in space and time, remains limited. For example, we do not yet understand the relative importance of ecological predictors (e.g. seasonality and habitat) versus evolutionary predictors (e.g. host and virus phylogenies) in driving virus prevalence and diversity. Few studies are set up to reveal the factors that predict the virome composition of individual hosts, populations or species. In addition, most studies of virus ecology represent a snapshot of single species viromes at a single point in time and space. Fortunately, recent studies have begun to use metagenomic data to directly test hypotheses about the evolutionary and ecological factors which drive virus prevalence, sharing and diversity. By synthesizing evidence across studies, we present some over-arching ecological and evolutionary patterns in virome composition, and illustrate the need for additional work to quantify the drivers of virus prevalence and diversity.

Urbanisation and Host Relatedness Shape Virome Composition in a Widespread, Generalist Carnivore

Urban wildlife species have the potential to serve as links in disease transmission between wildlife, humans and domestic animals at the wildland-urban interface (WUI), contributing to both sustained cross-species transmission of pathogens and the emergence of diseases in susceptible populations. However, the relative roles of host and environmental factors in shaping the composition of pathogen communities in urban wildlife is understudied. In this study, we integrated DNA and RNA virome data with host genomic and GPS datasets to investigate factors shaping virome composition in bobcats (Lynx rufus ) at the WUI in the Tucson Mountains, Arizona, USA. Using a hybrid-capture approach for 31 scats and 17 buccal swabs, we identified multiple viruses that could affect carnivore health at the WUI, including canine parvovirus, feline astrovirus, Felis catus papillomaviruses 2 and 3 and Lyon-IARC polyomavirus. Models of virome composition and distribution of viral taxa indicated contributions of host genetic relatedness and factors relating to urbanisation (such as percentages of urban land cover, road and building densities and distances to roads). Genetic associations with virome compositions were particularly influenced by females. While females exhibit significant isolation by distance, partial Mantel tests revealed a significant correlation between beta diversity and host genetic distance in females only. To our knowledge, this study represents the first assessment of factors shaping virome composition in a wild felid. Our finding of known feline and canine pathogens in bobcats underscores the potential of the WUI to facilitate cross-species transmission between wild and domestic animals.

Metatranscriptomic identification of novel RNA viruses from raccoon dog (Nyctereutes procyonoides) feces in Japan

The raccoon dog (Nyctereutes procyonoides), classified in the order Carnivora within the family Canidae, is native to East Asia and widely distributed throughout Japan due to its adaptability to various environments. Despite the close relationship between raccoon dogs and other animals, viruses infecting raccoon dogs have not been thoroughly investigated in Japan. In this study, we performed metatranscriptomic analyses using fecal samples collected from latrines of wild raccoon dogs in two locations on mainland Japan. Nearly complete viral genomes were identified, including viruses belonging to the genus Kobuvirus (CaKoV), an unclassified canine sapelovirus within the subfamily Ensavirinae (CaSaV), the Genius Mamastrovirus (CaAstV), unclassified hepe-astro-like virus (bastrovirus-like) (Bast-like V), and an unclassified dicistrovirus (DiciV) within the family Dicistroviridae. Phylogenetic analyses revealed that raccoon dog CaKoV, CaSaV, and CaAstV are related to canine strains but form independent clusters specific to raccoon dogs, suggesting they have evolved within this host population. Bast-like V, detected for the first time in raccoon dogs, showed high sequence identity with viruses previously identified in Chinese shrews. The shared insectivorous nature of these hosts and in silico host range predictions suggest that Bast-like Vs may originate from arthropod viruses. Although DiciV is likely of dietary origin due to its arthropod hosts, the large number of sequence reads detected and the phylogenetic clustering of raccoon dog DiciVs with mammalian DiciVs indicate the need to assess their potential infectivity in mammals and the risk of spillover. These findings suggest that raccoon dogs harbor endemic viruses within the canine population and may act as potential vectors for viruses with unknown infectivity in mammals but with spillover risk.

Urbanization enhances body condition, but not innate immune defences, in a common waterbird

There is a growing body of evidence that urbanization can affect body condition and immune function in wild birds, although these effects may be complex and taxa-specific. Here, we assessed the effects of urbanization on body condition (size-corrected body mass and haemoglobin concentration) and innate immune defences (haemolysis-haemagglutination assay, haptoglobin concentration and bacterial killing assay) in 136 Eurasian coots (Fulica atra) from three urban and three non-urban populations across Poland. We also quantified the heterophil to lymphocyte ratio to control for the potential effect of physiological stress on immune defences. We found that urban coots showed significantly better condition than non-urban ones. At the same time, we found no relationship between any immune defence and urbanization or condition. Thus, our study offers no support for condition-dependent immune function. Our analyses also revealed significant differences between male and female coots in both condition and immune defences; however, we found no evidence for sex-specific responses to urbanization. In conclusion, our study provides correlative evidence that urban habitat enhances condition, but not immune defences in the Eurasian coot.

Demographic and zoological drivers of infectome diversity in companion cats with ascites

Cats (Felidae) have become an integral part of many households. However, our understanding of the full spectrum of pathogens affecting cats (referred to as the infectome) is limited, mainly due to the inadequacy of commonly used diagnostic tools in capturing the complete diversity of potential pathogens and the prevalence of pathogen co-infections. In this study, we employed a meta-transcriptomic approach to simultaneously characterize the infectome contributing to different disease syndromes and to investigate spatial, demographic, and ecological factors influencing pathogen diversity and community composition in a cohort of 27 hospitalized cats and seven stray cats. We identified 15 species of pathogens, with Candidatus Rickettsia tarasevichiae and Tritrichomonas foetus representing potential spillover risks. Importantly, although most cases of ascites hyperplasia were explained by coinfection with multiple pathogens, we identified the potential novel clinical outcomes of M. aubagnense infection among cats. We demonstrated that the increase in infectome diversity can be explained by a variety of predictors including age growth, temperature increase, and a higher proportion of females, with age growth presenting the strongest effect. Fine-scale analysis indicated that a higher diversity of infectomes were harbored in young cats rather than adult ones. Our results demonstrated that most feline diseases are better explained by the presence of virus-bacteria or virus-virus coinfection. This study serves as a timely endorsement for clinical diagnosis by vets to consider the cause of a disease based on a panel of cryptical co-infecting pathogens rather than on individual infectious agents.

IMPORTANCE

Frequent studies reported the risks of cats as an intermediate host of zoonotic pathogens (e.g., SARS-CoV-2). Cats have a physically close interaction with their owners through activities like petting, kissing, and being licked on the cheek and hands. However, there are still limited studies that systematically investigate the infectome structure of cats. In this study, we employed a meta-transcriptomics approach to characterize 15 species of pathogens in cats, with Candidatus Rickettsia tarasevichiae first characterizing infection in diseased cats. Most feline diseases were better explained by the presence of virus-bacteria or virus-virus coinfection. The increase in infectome diversity could be influenced by a variety of predictors including age growth, temperature increase, and a higher proportion of females. A higher diversity of pathogens was harbored in young cats rather than adults. Importantly, we showed the value of linking the modern influx of meta-transcriptomics with comparative ecology and demography and of utilizing it to affirm that ecological and demographic variations impact the total infectome.

Rabbit hemorrhagic disease virus 2, 2010-2023: a review of global detections and affected species

Rabbit hemorrhagic disease virus 2/genotype GI.2 (RHDV2/GI.2; Caliciviridae, Lagovirus) causes a highly contagious disease with hepatic necrosis and disseminated intravascular coagulation in several Leporidae species. RHDV2 was first detected in European rabbits (Oryctolagus cuniculus) in France in 2010 and has since spread widely. We gather here data on viral detections reported in various countries and affected species, and discuss pathology, genetic differences, and novel diagnostic aspects. RHDV2 has been detected almost globally, with cases reported in Europe, Africa, Oceania, Asia, and North America as of 2023. Since 2020, large scale outbreaks have occurred in the United States and Mexico and, at the same time, cases have been reported for the first time in previously unaffected countries, such as China, Japan, Singapore, and South Africa, among others. Detections have been notified in domestic and wild European rabbits, hares and jackrabbits (Lepus spp.), several species of cottontail and brush rabbits (Sylvilagus spp.), pygmy rabbits (Brachylagus idahoensis), and red rock rabbits (Pronolagus spp.). RHDV2 has also been detected in a few non-lagomorph species. Detection of RHDV2 causing RHD in Sylvilagus spp. and Leporidae species other than those in the genera Oryctolagus and Lepus is very novel. The global spread of this fast-evolving RNA virus into previously unexploited geographic areas increases the likelihood of host range expansion as new species are exposed; animals may also be infected by nonpathogenic caliciviruses that are disseminated by almost all species, and with which genetic recombination may occur.

Exploring Canine Picornavirus Diversity in the USA Using Wastewater Surveillance: From High-Throughput Genomic Sequencing to Immuno-Informatics and Capsid Structure Modeling

The SARS-CoV-2 pandemic resulted in a scale-up of viral genomic surveillance globally. However, the wet lab constraints (economic, infrastructural, and personnel) of translating novel virus variant sequence information to meaningful immunological and structural insights that are valuable for the development of broadly acting countermeasures (especially for emerging and re-emerging viruses) remain a challenge in many resource-limited settings. Here, we describe a workflow that couples wastewater surveillance, high-throughput sequencing, phylogenetics, immuno-informatics, and virus capsid structure modeling for the genotype-to-serotype characterization of uncultivated picornavirus sequences identified in wastewater. Specifically, we analyzed canine picornaviruses (CanPVs), which are uncultivated and yet-to-be-assigned members of the family Picornaviridae that cause systemic infections in canines. We analyzed 118 archived (stored at -20 °C) wastewater (WW) samples representing a population of ~700,000 persons in southwest USA between October 2019 to March 2020 and October 2020 to March 2021. Samples were pooled into 12 two-liter volumes by month, partitioned (into filter-trapped solids [FTSs] and filtrates) using 450 nm membrane filters, and subsequently concentrated to 2 mL (1000×) using 10,000 Da MW cutoff centrifugal filters. The 24 concentrates were subjected to RNA extraction, CanPV complete capsid single-contig RT-PCR, Illumina sequencing, phylogenetics, immuno-informatics, and structure prediction. We detected CanPVs in 58.3% (14/24) of the samples generated 13,824,046 trimmed Illumina reads and 27 CanPV contigs. Phylogenetic and pairwise identity analyses showed eight CanPV genotypes (intragenotype divergence <14%) belonging to four clusters, with intracluster divergence of <20%. Similarity analysis, immuno-informatics, and virus protomer and capsid structure prediction suggested that the four clusters were likely distinct serological types, with predicted cluster-distinguishing B-cell epitopes clustered in the northern and southern rims of the canyon surrounding the 5-fold axis of symmetry. Our approach allows forgenotype-to-serotype characterization of uncultivated picornavirus sequences by coupling phylogenetics, immuno-informatics, and virus capsid structure prediction. This consequently bypasses a major wet lab-associated bottleneck, thereby allowing resource-limited settings to leapfrog from wastewater-sourced genomic data to valuable immunological insights necessary for the development of prophylaxis and other mitigation measures.

Entourage: all-in-one sequence analysis software for genome assembly, virus detection, virus discovery, and intrasample variation profiling

BACKGROUND

Pan-virus detection, and virome investigation in general, can be challenging, mainly due to the lack of universally conserved genetic elements in viruses. Metagenomic next-generation sequencing can offer a promising solution to this problem by providing an unbiased overview of the microbial community, enabling detection of any viruses without prior target selection. However, a major challenge in utilising metagenomic next-generation sequencing for virome investigation is that data analysis can be highly complex, involving numerous data processing steps.

RESULTS

Here, we present Entourage to address this challenge. Entourage enables short-read sequence assembly, viral sequence search with or without reference virus targets using contig-based approaches, and intrasample sequence variation quantification. Several workflows are implemented in Entourage to facilitate end-to-end virus sequence detection analysis through a single command line, from read cleaning, sequence assembly, to virus sequence searching. The results generated are comprehensive, allowing for thorough quality control, reliability assessment, and interpretation. We illustrate Entourage's utility as a streamlined workflow for virus detection by employing it to comprehensively search for target virus sequences and beyond in raw sequence read data generated from HeLa cell culture samples spiked with viruses. Furthermore, we showcase its flexibility and performance on a real-world dataset by analysing a preassembled Tara Oceans dataset. Overall, our results show that Entourage performs well even with low virus sequencing depth in single digits, and it can be used to discover novel viruses effectively. Additionally, by using sequence data generated from a patient with chronic SARS-CoV-2 infection, we demonstrate Entourage's capability to quantify virus intrasample genetic variations, and generate publication-quality figures illustrating the results.

CONCLUSIONS

Entourage is an all-in-one, versatile, and streamlined bioinformatics software for virome investigation, developed with a focus on ease of use. Entourage is available at https://codeberg.org/CENMIG/Entourage under the MIT license.

Direct detection of canine picornavirus complete coding sequence in wastewater using long-range reverse-transcriptase polymerase chain reaction and long-read sequencing

We describe four complete coding sequence (cCDS) of canine picornavirus from wastewater in Arizona, USA detected by coupling cCDS single-contig (∼7.5 kb) reverse-transcriptase polymerase chain reaction (RT-PCR) and low-cost long-read high-throughput sequencing. For viruses of medical/veterinary importance, this workflow expands possibilities of wastewater based genomic epidemiology for exploring virus evolutionary dynamics especially in low-resource settings.

European Wild Carnivores and Antibiotic Resistant Bacteria: A Review

Antibiotic resistance is a global concern that affects not only human health but also the health of wildlife and the environment. Wildlife can serve as reservoirs for antibiotic-resistant bacteria, and antibiotics in veterinary medicine and agriculture can contribute to the development of resistance in these populations. Several European carnivore species, such as wolves, foxes, otters, and bears, can be exposed to antibiotics by consuming contaminated food, water, or other resources in their habitats. These animals can also be indirectly exposed to antibiotics through interactions with domestic animals and human activities in their environment. Antibiotic resistance in wildlife can harm ecosystem health and also impact human health indirectly through various pathways, including zoonotic disease transmission. Moreover, the spread of resistant bacteria in wildlife can complicate conservation efforts, as it can threaten already endangered species. This review aims to describe the presence of antibiotic-resistant bacteria in wild carnivores in Europe.

From roads to biobanks: Roadkill animals as a valuable source of genetic data

To protect biodiversity we must understand its structure and composition including the bacteria and microparasites associated with wildlife, which may pose risks to human health. However, acquiring this knowledge often presents challenges, particularly in areas of high biodiversity where there are many undescribed and poorly studied species and funding resources can be limited. A solution to fill this knowledge gap is sampling roadkill (animals that die on roads as a result of collisions with circulating vehicles). These specimens can help characterize local wildlife and their associated parasites with fewer ethical and logistical challenges compared to traditional specimen collection. Here we test this approach by analyzing 817 tissue samples obtained from 590 roadkill vertebrate specimens (Amphibia, Reptilia, Aves and Mammalia) collected in roads within the Tropical Andes of Ecuador. First, we tested if the quantity and quality of recovered DNA varied across roadkill specimens collected at different times since death, exploring if decomposition affected the potential to identify vertebrate species and associated microorganisms. Second, we compared DNA stability across taxa and tissues to identify potential limitations and offer recommendations for future work. Finally, we illustrate how these samples can aid in taxonomic identification and parasite detection. Our study shows that sampling roadkill can help study biodiversity. DNA was recovered and amplified (allowing species identification and parasite detection) from roadkill even 120 hours after death, although risk of degradation increased overtime. DNA was extracted from all vertebrate classes but in smaller quantities and with lower quality from amphibians. We recommend sampling liver if possible as it produced the highest amounts of DNA (muscle produced the lowest). Additional testing of this approach in areas with different environmental and traffic conditions is needed, but our results show that sampling roadkill specimens can help detect and potentially monitor biodiversity and could be a valuable approach to create biobanks and preserve genetic data.

Detection and characterization of novel luchacoviruses, genus Alphacoronavirus, in saliva and feces of meso-carnivores in the northeastern United States

IMPORTANCE

Several coronaviruses (CoVs) have been detected in domesticated, farmed, and wild meso-carnivores, causing a wide range of diseases and infecting diverse species, highlighting their important but understudied role in the epidemiology of these viruses. Assessing the viral diversity hosted in wildlife species is essential to understand their significance in the cross-species transmission of CoVs. Our focus here was on CoV discovery in meso-carnivores in the Northeast United States as a potential "hotspot" area with high density of humans and urban wildlife. This study identifies novel alphacoronaviruses circulating in multiple free-ranging wild and domestic species in this area and explores their potential epidemiological importance based on regions of the Spike gene, which are relevant for virus-host interactions.

Detection and characterization of novel luchacoviruses, genus Alphacoronavirus, shed in saliva and feces of meso-carnivores in the northeastern United States

Small to mid-sized carnivores, or meso-carnivores, comprise a group of diverse mammals, many of which can adapt to anthropogenically disturbed environments. Wild meso-carnivores living in urban areas may get exposed to or spread pathogens to other species, including stray/feral domestic animals. Several coronaviruses (CoVs) have been detected in domesticated and farmed meso-carnivores, but knowledge of CoVs circulating in free-ranging wild meso-carnivores remains limited. In this study, we analyzed 321 samples collected between 2016 and 2022 from 9 species of free-ranging wild meso-carnivores and stray/feral domestic cats in the northeastern United States. Using a pan-CoV PCR, we screened tissues, feces, and saliva, nasal, and rectal swabs. We detected CoV RNA in fecal and saliva samples of animals in four species: fisher (Pekania pennanti), bobcat (Lynx rufus), red fox (Vulpes vulpes), and domestic cat (Felis catus). Next-generation sequencing revealed that all these viruses belonged to the Luchacovirus subgenus (Alphacoronavirus genus), previously reported only in rodents and lagomorphs (i.e., rabbits). Genetic comparison of the 3'-end of the genome (~12,000bp) revealed that although the viruses detected group with, and have a genetic organization similar to other luchacoviruses, they are genetically distinct from those from rodents and lagomorphs. Genetic characterization of the spike protein revealed that the meso-carnivore luchacoviruses do not have an S1/S2 cleavage motif but do have highly variable structural loops containing cleavage motifs similar to those identified in certain pathogenic CoVs. This study highlights the importance of characterizing the spike protein of CoVs in wild species for further targeted epidemiologic monitoring.

An invasive human commensal and a native marsupial maintain tick populations at the urban fringe

Ticks (Acari: Ixodidae) are major disease vectors globally making it increasingly important to understand how altered vertebrate communities in urban areas shape tick population dynamics. In urban landscapes of Australia, little is known about which native and introduced small mammals maintain tick populations preventing host-targeted tick management and leading to human-wildlife conflict. Here, we determined (1) larval, nymphal, and adult tick burdens on host species and potential drivers, (2) the number of ticks supported by the different host populations, and (3) the proportion of medically significant tick species feeding on the different host species in Northern Sydney. We counted 3551 ticks on 241 mammals at 15 sites and found that long-nosed bandicoots (Perameles nasuta) hosted more ticks of all life stages than other small mammals but introduced black rats (Rattus rattus) were more abundant at most sites (33%-100%) and therefore important in supporting larval and nymphal ticks in our study areas. Black rats and bandicoots hosted a greater proportion of medically significant tick species including Ixodes holocyclus than other hosts. Our results show that an introduced human commensal contributes to maintaining urban tick populations and suggests ticks could be managed by controlling rat populations on urban fringes.

Seasonal dynamics of the wild rodent faecal virome

Viral discovery studies in wild animals often rely on cross-sectional surveys at a single time point. As a result, our understanding of the temporal stability of wild animal viromes remains poorly resolved. While studies of single host-virus systems indicate that host and environmental factors influence seasonal virus transmission dynamics, comparable insights for whole viral communities in multiple hosts are lacking. Utilizing noninvasive faecal samples from a long-term wild rodent study, we characterized viral communities of three common European rodent species (Apodemus sylvaticus, A. flavicollis and Myodes glareolus) living in temperate woodland over a single year. Our findings indicate that a substantial fraction of the rodent virome is seasonally transient and associated with vertebrate or bacteria hosts. Further analyses of one of the most common virus families, Picornaviridae, show pronounced temporal changes in viral richness and evenness, which were associated with concurrent and up to ~3-month lags in host density, ambient temperature, rainfall and humidity, suggesting complex feedbacks from the host and environmental factors on virus transmission and shedding in seasonal habitats. Overall, this study emphasizes the importance of understanding the seasonal dynamics of wild animal viromes in order to better predict and mitigate zoonotic risks.

Viruses of Freshwater Mussels during Mass Mortality Events in Oregon and Washington, USA

Freshwater mussels (Unionida) are globally imperiled, in part due to largely unexplained mass mortality events (MMEs). While recent studies have begun to investigate the possibility that mussel MMEs in the Eastern USA may be caused by infectious diseases, mussels in the Western USA have received relatively little attention in this regard. We conducted a two-year epidemiologic investigation of the role of viruses in ongoing MMEs of the Western pearlshell (Margaritifera falcata) and the Western ridged mussel (Gonidea angulata) in the Chehalis River and Columbia River watersheds in the Western USA. We characterized viromes of mussel hemolymph from 5 locations in 2018 and 2020 using metagenomic methods and identified 557 viruses based on assembled contiguous sequences, most of which are novel. We also characterized the distribution and diversity of a previously identified mussel Gammarhabdovirus related to pathogenic finfish viruses. Overall, we found few consistent associations between viruses and mussel health status. Variation in mussel viromes was most strongly driven by location, with little influence from date, species, or health status, though these variables together only explained ~1/3 of variation in virome composition. Our results demonstrate that Western freshwater mussels host remarkably diverse viromes, but no single virus or combination of viruses appears to be associated with morbidity or mortality during MMEs. Our findings have implications for the conservation of imperiled freshwater mussels, including efforts to enhance natural populations through captive propagation.

A One-Year Retrospective Analysis of Viral and Parasitological Agents in Wildlife Animals Admitted to a First Aid Hospital

This study aimed to provide information on the presence and frequency of viral and parasitic agents in wildlife presented to a Veterinary Teaching Hospital in 2020-2021. Serum and faecal samples were collected from 50 rescued animals (roe deer, fallow deer, foxes, badgers, pine martens, and porcupines) and examined by serological, molecular, and parasitological techniques. Transtracheal wash (TTW) was also collected post-mortem from roe deer. Overall, the results of the different techniques showed infections with the following viral and parasitic agents: Bovine Viral Diarrhea Virus, Small Ruminant Lentiviruses, Kobuvirus, Astrovirus, Canine Adenovirus 1, Bopivirus, gastrointestinal strongyles, Capillaria, Ancylostomatidae, Toxocara canis, Trichuris vulpis, Hymenolepis, Strongyloides, Eimeria, Isospora, Dictyocaulus, Angiostrongylus vasorum, Crenosoma, Dirofilaria immitis, Neospora caninum, Giardia duodenalis, and Cryptosporidium. Sequencing (Tpi locus) identified G. duodenalis sub-assemblages AI and BIV in one roe deer and one porcupine, respectively. Adult lungworms collected from the TTW were identified as Dictyocaulus capreolus (COX1 gene). This is the first molecular identification of G. duodenalis sub-assemblage AI and D. capreolus in roe deer in Italy. These results show a wide presence of pathogens in wild populations and provide an overview of environmental health surveillance.

Diversity of viral communities in faecal samples of farmed red foxes

Emerging and existing viruses from various human and animal samples have been studied and analyzed using viral metagenomics, which has proven to be an effective technique. Foxes, as a kind of significant economic animal, are widely raised in China. Viruses carried by foxes may potentially infect humans or other animals. There are currently very few studies of faecal virome in farmed foxes. Using viral metagenomics, we evaluated the faecal virome of twenty-four foxes collected from the same farm in Jilin Province, China. Some sequences more closely related to the families Parvoviridae, Picornaviridae, Smacoviridae, Anelloviridae, and Herpesviridae were detected in the faecal sample. The main animal viruses that infect farmed red foxes were parvovirus and picornavirus. Five smacovirus strains were found and provided evidence for genetic diversity in the genus Smacoviridae. In addition, some viruses infecting avian species or rats were detected in this study. The study helped us better understand faecal virome in farmed red foxes and assisted in the surveillance and prevention of viral diseases in these animals.

Elimination of Foreign Sequences in Eukaryotic Viral Reference Genomes Improves the Accuracy of Virome Analysis

Widespread in public databases, foreign contaminant sequences pose a substantial obstacle in genomic analyses. Such contamination in viral genome databases is also notorious but more complicated and often causes questionable results in various applications, particularly in virome-based virus detection. Here, we conducted comprehensive screening and identification of the foreign sequences hidden in the largest eukaryotic viral genome collections of GenBank and UniProt using a scrutiny pipeline, which enables us to rigorously detect those problematic viral sequences (PVSs) with origins in hosts, vectors, and laboratory components. As a result, a total of 766 nucleotide PVSs and 276 amino acid PVSs with lengths up to 6,605 bp were determined, which were widely distributed in 39 families with many involving highly public health-concerning viruses, such as hepatitis C virus, Crimean-Congo hemorrhagic fever virus, and filovirus. The majority of these PVSs are genomic fragments of hosts including humans and bacteria. However, they cannot simply be regarded as foreign contaminants, since parts of them are results of natural occurrence or artificial engineering of viruses. Nevertheless, they severely disturb such sequence-based analyses as genome annotation, taxonomic assignment, and virome profiling. Therefore, we provide a clean version of the eukaryotic viral reference data set by the removal of these PVSs, which allows more accurate virome analysis with less time consumed than with other comprehensive databases. IMPORTANCE High-throughput sequencing-based viromics highly depends on reference databases, but foreign contamination is widespread in public databases and often leads to confusing and even wrong conclusions in genomic analysis and viromic profiling. To address this issue, we systematically detected and identified the contamination in the largest viral sequence collections of GenBank and UniProt based on a stringent scrutiny pipeline. We found hundreds of PVSs that are related to hosts, vectors, and laboratory components. By the removal of them, the resulting data set greatly improves the accuracy and efficiency of eukaryotic virome profiling. These results refresh our knowledge of the type and origin of PVSs and also have warning implications for viromic analysis. Viromic practitioners should be aware of these problems caused by PVSs and need to realize that a careful review of bioinformatic results is necessary for a reliable conclusion.

Novel Virus Identification through Metagenomics: A Systematic Review

Metagenomic Next Generation Sequencing (mNGS) allows the evaluation of complex microbial communities, avoiding isolation and cultivation of each microbial species, and does not require prior knowledge of the microbial sequences present in the sample. Applications of mNGS include virome characterization, new virus discovery and full-length viral genome reconstruction, either from virus preparations enriched in culture or directly from clinical and environmental specimens. Here, we systematically reviewed studies that describe novel virus identification through mNGS from samples of different origin (plant, animal and environment). Without imposing time limits to the search, 379 publications were identified that met the search parameters. Sample types, geographical origin, enrichment and nucleic acid extraction methods, sequencing platforms, bioinformatic analytical steps and identified viral families were described. The review highlights mNGS as a feasible method for novel virus discovery from samples of different origins, describes which kind of heterogeneous experimental and analytical protocols are currently used and provides useful information such as the different commercial kits used for the purification of nucleic acids and bioinformatics analytical pipelines.

Impact of sample clarification by size exclusion on virus detection and diversity in wastewater-based epidemiology

The use of wastewater-based epidemiology (WBE) for early detection of virus circulation and response during the SARS-CoV-2 pandemic increased interest in and use of virus concentration protocols that are quick, scalable, and efficient. One such protocol involves sample clarification by size fractionation using either low-speed centrifugation to produce a clarified supernatant or membrane filtration to produce an initial filtrate depleted of solids, eukaryotes and bacterial present in wastewater (WW), followed by concentration of virus particles by ultrafiltration of the above. While this approach has been successful in identifying viruses from WW, it assumes that majority of the viruses of interest should be present in the fraction obtained by ultrafiltration of the initial filtrate, with negligible loss of viral particles and viral diversity. We used WW samples collected in a population of ~700,000 in southwest USA between October 2019 and March 2021, targeting three non-enveloped viruses (enteroviruses [EV], canine picornaviruses [CanPV], and human adenovirus 41 [Ad41]), to evaluate whether size fractionation of WW prior to ultrafiltration leads to appreciable differences in the virus presence and diversity determined. We showed that virus presence or absence in WW samples in both portions (filter trapped solids [FTS] and filtrate) are not consistent with each other. We also found that in cases where virus was detected in both fractions, virus diversity (or types) captured either in FTS or filtrate were not consistent with each other. Hence, preferring one fraction of WW over the other can undermine the capacity of WBE to function as an early warning system and negatively impact the accurate representation of virus presence and diversity in a population.

Novel viral and microbial species in a translocated Toutouwai (Petroica longipes) population from Aotearoa/New Zealand

BACKGROUND

Translocation is a common tool in wildlife management and its implementation has resulted in many conservation successes. During translocations, any associated infectious agents are moved with their wildlife hosts. Accordingly, translocations can present a risk of infectious disease emergence, although they also provide an opportunity to restore natural infectious communities ('infectome') and mitigate the long-term risks of reduced natural resistance.

METHODS

We used metatranscriptomic sequencing to characterise the cloacal infectome of 41 toutouwai (North Island robin, Petroica longipes) that were translocated to establish a new population within the North Island of New Zealand. We also screened for pathogenic bacteria, fungi and parasites.

RESULTS

Although we did not detect any known avian diseases, which is a positive outcome for the translocated toutouwai population, we identified a number of novel viruses of interest, including a novel avian hepatovirus, as well as a divergent calici-like virus and four hepe-like viruses of which the host species is unknown. We also revealed a novel spirochete bacterium and a coccidian eukaryotic parasite.

CONCLUSIONS

The presumably non-pathogenic viruses and microbial species identified here support the idea that most microorganisms likely do not cause disease in their hosts, and that translocations could serve to help restore and maintain native infectious communities. We advise greater surveillance of infectious communities of both native and non-native wildlife before and after translocations to better understand the impact, positive or negative, that such movements may have on both host and infectome ecology.

Canine picornaviruses detected in wastewater in Arizona, USA 2019 and 2021

Virus surveillance by wastewater-based epidemiology (WBE) in two Arizona municipalities in Maricopa County, USA (~700,000 people), revealed the presence of six canine picornavirus (CanPV) variants: five in 2019 and one in 2021. Phylogenetic analysis suggests these viruses might be from domestic dog breeds living within or around the area. Phylogenetic and pairwise identity analyses suggest over 15 years of likely enzootic circulation of multiple lineages of CanPV in the USA and possibly globally. Considering <10 CanPV sequences are publicly available in GenBank as of June 2, 2022, the results provided here constitute an increase of current knowledge on CanPV diversity and highlight the need for increased surveillance.

Human Land-Use Impacts Viral Diversity and Abundance in a New Zealand River

Although water-borne viruses have important implications for the health of humans and other animals, little is known about the impact of human land use on viral diversity and evolution in water systems such as rivers. We used metatranscriptomic sequencing to compare the diversity and abundance of viruses at sampling sites along a single river in New Zealand that differed in human land-use impacts, ranging from pristine to urban. From this, we identified 504 putative virus species, of which 97 per cent were novel. Many of the novel viruses were highly divergent and likely included a new subfamily within the Parvoviridae. We identified at least sixty-three virus species that may infect vertebrates—most likely fish and water birds—from the Astroviridae, Birnaviridae, Parvoviridae, and Picornaviridae. No putative human viruses were detected. Importantly, we observed differences in the composition of viral communities at sites impacted by human land use (farming and urban) compared to native forest sites (pristine). At the viral species level, the urban sites had higher diversity (327 virus species) than the farming (n = 150) and pristine sites (n = 119), and more viruses were shared between the urban and farming sites (n = 76) than between the pristine and farming or urban sites (n = 24). The two farming sites had a lower viral abundance across all host types, while the pristine sites had a higher abundance of viruses associated with animals, plants, and fungi. We also identified viruses linked to agriculture and human impact at the river sampling sites in farming and urban areas that were not present at the native forest sites. Although based on a small sample size, our study suggests that human land use can impact viral communities in rivers, such that further work is needed to reduce the impact of intensive farming and urbanisation on water systems.

Rabbit Haemorrhagic Disease Virus 2 (RHDV2; GI.2) in Ireland Focusing on Wild Irish Hares (Lepus timidus hibernicus): An Overview of the First Outbreaks and Contextual Review

Rabbit haemorrhagic disease virus 2 (RHDV2; GI.2) is a pathogenic lagovirus that emerged in 2010, and which now has a global distribution. Outbreaks have been associated with local population declines in several lagomorph species, due to rabbit haemorrhagic disease (RHD)-associated mortality raising concerns for its potential negative impact on threatened or vulnerable wild populations. The Irish hare (Lepus timidus hibernicus) is endemic to Ireland, and is of conservation interest. The first cases of RHDV2 in Ireland were reported in domestic rabbits (Oryctolagus cuniculus) in 2016, soon followed by the first known case in a wild rabbit also in 2016, from a population reported to be experiencing high fatalities. During summer 2019, outbreaks in wild rabbits were confirmed in several locations throughout Ireland. Six cases of RHDV2 in wild hares were confirmed between July and November 2019, at four locations. Overall, 27 cases in wildlife were confirmed in 2019 on the island of Ireland, with a predominantly southern distribution. Passive surveillance suggests that the Irish hare is susceptible to lethal RHDV2 infection, and that spillover infection to hares is geographically widespread in eastern areas of Ireland at least, but there is a paucity of data on epidemiology and population impacts. A literature review on RHD impact in closely related Lepus species suggests that intraspecific transmission, spillover transmission, and variable mortality occur in hares, but there is variability in reported resistance to severe disease and mortality amongst species. Several key questions on the impact of the pathogen in Irish hares remain. Surveillance activities throughout the island of Ireland will be important in understanding the spread of infection in this novel host.

Secrets of the Astute Red Fox (Vulpes vulpes, Linnaeus, 1758): An Inside-Ecosystem Secret Agent Serving One Health

An ecosystem’s health is based on a delicate balance between human, nonhuman animal, and environmental health. Any factor that leads to an imbalance in one of the components results in disease. There are several bioindicators that allow us to evaluate the status of ecosystems. The red fox (Vulpes vulpes, Linnaeus, 1758) has the widest world distribution among mammals. It is highly adaptable, lives in rural and urban areas, and has a greatly diverse diet. Being susceptible to environmental pollution and zoonotic agents, red foxes may act as sentinels to detect environmental contaminants, climatic changes and to prevent and control outbreaks of emerging or re-emerging zoonosis. This paper aims to compile the latest information that is related to the red fox as a sentinel of human, animal, and environmental health.

The Influence of Habitat on Viral Diversity in Neotropical Rodent Hosts

Rodents are important reservoirs of numerous viruses, some of which have significant impacts on public health. Ecosystem disturbances and decreased host species richness have been associated with the emergence of zoonotic diseases. In this study, we aimed at (a) characterizing the viral diversity in seven neotropical rodent species living in four types of habitats and (b) exploring how the extent of environmental disturbance influences this diversity. Through a metagenomic approach, we identified 77,767 viral sequences from spleen, kidney, and serum samples. These viral sequences were attributed to 27 viral families known to infect vertebrates, invertebrates, plants, and amoeba. Viral diversities were greater in pristine habitats compared with disturbed ones, and lowest in peri-urban areas. High viral richness was observed in savannah areas. Differences in these diversities were explained by rare viruses that were generally more frequent in pristine forest and savannah habitats. Moreover, changes in the ecology and behavior of rodent hosts, in a given habitat, such as modifications to the diet in disturbed vs. pristine forests, are major determinants of viral composition. Lastly, the phylogenetic relationships of four vertebrate-related viral families (Polyomaviridae, Flaviviridae, Togaviridae, and Phenuiviridae) highlighted the wide diversity of these viral families, and in some cases, a potential risk of transmission to humans. All these findings provide significant insights into the diversity of rodent viruses in Amazonia, and emphasize that habitats and the host’s dietary ecology may drive viral diversity. Linking viral richness and abundance to the ecology of their hosts and their responses to habitat disturbance could be the starting point for a better understanding of viral emergence and for future management of ecosystems.

The canid pest ejector challenge: controlling urban foxes while keeping domestic dogs safe

Abstract ContextIt is widely recognised that red foxes (Vulpes vulpes) are abundant within urban areas; however, it is difficult to apply lethal control measures using poison baits in cities because of concerns about the safety of domestic pets, particularly dogs (Canis familiaris). AimsWe tested canid pest ejectors (CPEs) as a potential method of fox control by measuring visitation and activation behaviour of foxes and other wildlife while assessing non-target risk to domestic dogs. MethodsWe compared eight urban and eight peri-urban sites in Sydney, with half of the sites having restricted access for domestic dogs. We allocated five camera traps and ejectors per site. Through generalised linear mixed models, we compared the probability of ejector activation between foxes and dogs. We also assessed the relationship between dog visitation and distance to habitation and dog restrictions as measures of dog safety. Key resultsBoth species of canids were equally likely to pull the ejector (P=0.26). As expected, dog visitation was significantly lower in sites with dog restrictions (P&lt;0.001). However, it was not related to distance from habitation. Only two non-canid species were recorded pulling the ejector, suggesting high target-specificity for canids. ConclusionsIn sites with dog restrictions, the risk of dog casualties from CPEs is minimal. However, distance from habitation does not increase dog safety, at least within 250m. The ejector is highly specific for canids. ImplicationsWe provide specific recommendations for the design of a potential fox control program using CPEs in urban and peri-urban areas. The ejector may be a safe method for fox control in cities when deployed at places without domestic dogs.