Cited by 47Zoonotic diseases and public healthAnimal Virus Infections StudiesVirology and Viral Diseases

Red fox viromes in urban and rural landscapes

Open access
Campbell, Sarah J, Ashley, Wilbur, Gil-Fernandez, Margarita, Newsome, Thomas M, Di Giallonardo, Francesca, Ortiz-Baez, Ayda Susana, Mahar, Jackie E, Towerton, Alison L +4 more·2020·Virus Evolution

Abstract

The Red fox (Vulpes vulpes) has established large populations in Australia’s urban and rural areas since its introduction following European settlement. The cryptic and highly adaptable nature of foxes allows them to invade cities and live among humans whilst remaining largely unnoticed. Urban living and access to anthropogenic food resources also influence fox ecology. Urban foxes grow larger, live at higher densities, and are more social than their rural counterparts. These ecological changes in urban red foxes are likely to impact the pathogens that they harbour, and foxes could pose a disease risk to humans and other species that share these urban spaces. To investigate this possibility, we used a meta-transcriptomic approach to characterise the virome of urban and rural foxes across the Greater Sydney region in Australia. Urban and rural foxes differed significantly in virome composition, with rural foxes harbouring a greater abundance of viruses compared to their urban counterparts. We identified ten potentially novel vertebrate-associated viruses in both urban and rural foxes, some of which are related to viruses associated with disease in domestic species and humans. These included members of the Astroviridae, Picobirnaviridae, Hepeviridae, and Picornaviridae as well as rabbit haemorrhagic disease virus-2. This study sheds light on the viruses carried by urban and rural foxes and emphasises the need for greater genomic surveillance of foxes and other invasive species at the human–wildlife interface.

AI snapshot

Written from the paper’s full text.

TL;DR

Using meta-transcriptomics of 29 red foxes across Greater Sydney, this study characterized urban and rural fox viromes and found significant compositional differences, with rural foxes having greater viral abundance and urban foxes slightly higher viral diversity. It identified ten potentially novel vertebrate-associated viruses, including rabbit haemorrhagic disease virus-2 and viruses related to those found in domestic pets and humans.

Key findings

  • Urban, rural, and ectoparasite viromes differed significantly (ANOSIM R = 1, P = 0.0167). Rural foxes had higher total viral abundance (2.03 ± 3.31%, n = 3) than urban foxes (0.03 ± 0.04%, n = 2), while urban foxes had slightly higher diversity (21 vs 19 viral families).
  • Ten potentially novel vertebrate-associated viruses were identified across Astroviridae, Picobirnaviridae, Hepeviridae, Picornaviridae, and Caliciviridae. Examples include vixey virus (97.65% amino acid identity to canine kobuvirus), vulpix virus (96.11% to feline astrovirus), charmer virus (80.27% to wolf picobirnavirus), and RHDV2 (99.62% to rabbit RHDV2).
  • Females harboured higher viral diversity (25 families) than males (13 families) and higher total viral abundance (1.97 ± 3.36%, n = 3 vs 0.12 ± 0.17%, n = 2). Vertebrate-associated viral transcripts made up 98.23% of rural male and 97.84% of rural female viral reads, versus 2.41% in urban males and 0.39% in urban females.
  • Picornaviridae dominated rural viromes (77.33–98.97% of the virome). Indicator species analysis associated Picornaviridae with rural samples (stat = 0.978, P = 0.0496) and Nodaviridae with urban samples (stat = 0.998, P = 0.0498).

Methods

  • Fresh red fox carcasses were collected from the Greater Sydney region: 29 foxes total (13 males, 16 females; 25 adults, 4 juveniles). Liver, faecal, and ectoparasite samples were pooled by land use, sex, and sample type into nine representative libraries and sequenced on a NextSeq 500 with 2 × 75 bp output.
  • Meta-transcriptomic reads were assembled de novo with Trinity, assigned taxonomically using BLASTn and Diamond (BLASTX), and viral transcript abundance was estimated with RSEM.
  • Virome diversity and composition were compared using nMDS and ANOSIM based on Bray–Curtis dissimilarity, with indicator species analysis; phylogenetic relationships of vertebrate-associated viruses were inferred from RdRp sequences using MAFFT, trimAl, and PhyML with 1,000 bootstrap replicates.

Limitations

  • Stated: the small sample size and pooling mean individual animals may have inflated abundance or diversity estimates (e.g., the rural female pool contained >5% viruses); a representative urban-to-rural land-use gradient was not possible; fresh rural samples were difficult to obtain because poison baiting is the principal control method; some virus transcripts may result from reagent contamination; and the study cannot definitively show that the viruses cause disease or spill-over.
  • Evident from the text: only nine pooled libraries were analysed, so individual-level prevalence and statistical power are limited, and habitat/sex effects are confounded by pooling and uneven pool sizes (3–13 foxes per pool). No vertebrate-associated viruses were detected in the ectoparasite pool, so the role of fleas or ticks in fox virome composition was not assessed.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1093/ve/veaa065

Cites

73 of 73 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

33 of 56 cited sources checked · 19 supported · 0 flagged · accuracy not yet measured

  • Premisecitation

    High-density living and increased contact can increase pathogen transmission rates among hosts.

    “High-density living and increased contact can increase pathogen transmission rates among hosts (Nunn et al. 2015).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Nunn et al. 2015 source
  • Premisecitation

    Urban animals often habituate to humans.

    “In addition, as urban animals often habituate to humans (Bateman and Fleming 2012), we might predict an increase in fox–human interactions with the potential for diseased transmission between the two species.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Bateman and Fleming 2012 source
  • Premisecitation

    Urbanisation influences pathogen exposure and prevalence in wildlife.

    “Urbanisation influences pathogen exposure and prevalence in wildlife.”
    Quote in the paperSubstantial claim2 of 3 sources checked
    • cites Riley, Foley, and Chomel 2004 source
    • cites Vieira et al. 2013 source

      The Results report that urban residence was associated with higher seropositivity to three tick-borne pathogens, and the Discussion reports higher overall seroprevalence in urban than rural dogs. The study concerns domestic dogs, not wildlife, and compares locations rather than demonstrating an effect of urbanisation itself. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
    • cites Gibbs et al. 2006 source
  • Findingown data

    The hepevirus detected in this study was phylogenetically distinct from the fox hepatitis E virus previously detected.

    “In contrast, the hepevirus detected here was phylogenetically distinct from the fox hepatitis E virus previously detected (Bodewes et al. 2013) and instead was more closely related to hepeviruses detected in freshwater mussels and a house mouse.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Bodewes et al. 2013 source
  • Findingcitation

    The picobirnavirus-related transcript found here is similar to picobirnaviruses described as potentially zoonotic in humans with gastroenteritis.

    “It is also similar to picobirnaviruses described as potentially zoonotic in humans with gastroenteritis (Yinda et al. 2019).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Yinda et al. 2019 source
  • Classified as probably not a substantial claim. 44
  • May combine two claims. 23
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Red foxes are broadly distributed across natural and forested landscapes as well as highly urbanised, human-dominated areas.

    “They are broadly distributed across natural and forested landscapes as well as highly urbanised, human dominated areas (Saunders, Gentle, and Dickman 2010; Bateman and Fleming 2012).”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites Saunders, Gentle, and Dickman 2010 source
    • cites Bateman and Fleming 2012 source

      The “History of carnivore urban adaptation” section describes red foxes as occupying habitats from arctic tundra and deserts to metropolitan centres, supporting their broad distribution across natural and highly urbanised areas. The passages in our copy do not specifically establish their distribution in forested landscapes. (LLM, conf=0.83)

      Experimental — accuracy not yet measured
  • May combine two claims.

    Premisecitation

    Urban living and access to anthropogenic food resources influence fox ecology.

    “Urban living and access to anthropogenic food resources also influence fox ecology.”
    Quote in the paperSubstantial claim1 of 3 sources checked
    • cites Contesse et al. 2004 source
    • cites Bateman and Fleming 2012 source
    • cites Stepkovitch 2017

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Urban environments may enhance conspecific tolerance and social behaviours in foxes.

    “Thus, urban environments may enhance conspecific tolerance and social behaviours in foxes (Macdonald 1979, 1983; Marks and Bloomfield 1999; Dorning and Harris 2019).”
    Quote in the paperNot a substantial claim1 of 3 sources checked
    • cites Macdonald 1979, 1983

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

    • cites Marks and Bloomfield 1999 source
    • cites Dorning and Harris 2019 source

      The Discussion reports social interactions among foxes at provisioned food patches in an urban area and concludes that patchy resources facilitated sociality. It does not establish that urban environments, rather than patchy resources, enhance tolerance or social behaviour; it notes that similar interactions may occur in other habitats. No page number is available in our copy. (LLM, conf=0.82)

      Experimental — accuracy not yet measured
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Domestic mammals tend to hold central positions in mammal viral transmission networks.

    “Domestic mammals tend to hold central positions in mammal viral transmission networks (Wells et al. 2020).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Wells et al. 2020 source
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The prevalence of parvovirus increases with proximity to urban areas in grey foxes in the USA.

    “For example, the prevalence of parvovirus increases with proximity to urban areas in grey foxes (Urocyon cinereoargenteus) in the USA (Riley, Foley, and Chomel 2004), and dogs in urban areas in Brazil harbour more tick-borne pathogens than rural dogs (Vieira et al. 2013).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Riley, Foley, and Chomel 2004 source
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Confirmed zoonotic cases of hepatitis E include transmission to humans from domestic pigs, cats, and wild rodents.

    “Confirmed zoonotic cases include transmission to humans from domestic pigs, cats, and wild rodents (Meng 2010; Dremsek et al. 2012).”
    Quote in the paperNot a substantial claim2 of 2 sources checked
    • cites Meng 2010 source

      Section 4.3 reports human hepatitis E cases linked to pig products and reported transmission from a pet pig and a pet cat to their owners. It says only that rodents may play a role in HEV transmission; it does not report a confirmed rodent-to-human case. (LLM, conf=0.91)

      Experimental — accuracy not yet measured
    • cites Dremsek et al. 2012 source

      The paper’s summary links human hepatitis E cases to zoonotic transmission from domestic pigs, supporting that part of the claim. It does not mention cats as a source, and its rat-HEV findings are preliminary: it says the role of rat HEV in human disease still needs assessment, not that rodent-to-human transmission is confirmed. The indexed passages have no page labels. (LLM, conf=0.90)

      Experimental — accuracy not yet measured
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Picobirnaviruses are found in humans and other mammals and are thought to be linked with gastroenteritis, but their role in disease remains unclear.

    “Picobirnaviruses are found in humans and other mammals and are thought to be linked with gastroenteritis, however their role in disease remains unclear (Malik et al. 2014; Conceição-Neto et al. 2016).”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites Malik et al. 2014 source
    • cites Conceição-Neto et al. 2016 source
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Some human astroviruses are more closely related to those in animals than to each other, suggesting that these viruses periodically emerge from zoonotic origins.

    “Some human astroviruses are more closely related to those in animals than to each other, suggesting that these viruses periodically emerge from zoonotic origins (Kapoor et al. 2009).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Kapoor et al. 2009 source
  • May combine two claims.

    Premisecitation

    RNA viruses are in general characterised by lower host specificity than DNA viruses, reflecting an increased occurrence of cross-species transmission.

    “Although this may in part be due to the reliance on transcript-based viral detection, RNA viruses are in general characterised by lower host specificity than DNA viruses, reflecting an increased occurrence of cross-species transmission (Geoghegan, Duchêne, and Holmes 2017; Wells et al. 2020).”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites Geoghegan, Duchêne, and Holmes 2017 source
    • cites Wells et al. 2020 source
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Eukaryotic parasites are already known to infect human hosts following the wildlife-domestic pet-human transmission network.

    “Indeed, eukaryotic parasites are already known to infect human hosts following the wildlife–domestic pet–human transmission network (Wells et al. 2018).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Wells et al. 2018 source

      The Roles of domestic animal hosts section (p. 23) reports that humans and dogs share many helminth parasites with wildlife, supporting the claim that these parasites infect human hosts at this interface. But the paper does not establish transmission along a wildlife–pet–human route: it says its analysis cannot determine the direction of host shifts (p. 24). (LLM, conf=0.88)

      Experimental — accuracy not yet measured
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    This is the second time that RHDV2 has been found in non-rabbit hosts.

    “This is the second time that RHDV2 has been found in non-rabbit hosts (Chong et al. 2019), presumably through rabbit consumption in this case.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Chong et al. 2019 source

      The Results section reports PCR-confirmed RHDV2 in Tasmanian devil fecal samples, supporting detection in a non-rabbit animal. Our copy does not establish that the citing paper’s finding was the second such detection. The Discussion also cautions that the virus may have come from the devils’ diet rather than replicating in them; page numbers are unavailable in our copy. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    There is evidence that picobirnaviruses may actually be bacteriophage rather than eukaryote-associated viruses.

    “There is, however, evidence that picobirnaviruses may actually be bacteriophage rather than eukaryote-associated viruses (Krishnamurthy and Wang 2018), such that the virology of these viruses is currently unclear.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Krishnamurthy and Wang 2018 source
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    RHDV2 began circulating in Australia in 2015.

    “A novel variant of the disease, RHDV2, began circulating in Australia in 2015 and is presumed to be an incursion from Europe where it first emerged in 2010 (Hall et al. 2015).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Hall et al. 2015 source
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Dogs in urban areas in Brazil harbour more tick-borne pathogens than rural dogs.

    “For example, the prevalence of parvovirus increases with proximity to urban areas in grey foxes (Urocyon cinereoargenteus) in the USA (Riley, Foley, and Chomel 2004), and dogs in urban areas in Brazil harbour more tick-borne pathogens than rural dogs (Vieira et al. 2013).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Vieira et al. 2013 source

      The Discussion reports that 91.2% of sampled urban dogs were seropositive for at least one tick-borne disease agent and were 13.7 times more likely to be seropositive than rural dogs. But the study sampled dogs in one region of Paraná and measured antibodies, so it does not establish that urban dogs across Brazil harbour more pathogens. (LLM, conf=0.87)

      Experimental — accuracy not yet measured
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Kobuviruses have been isolated from dogs and other mammals with diarrhoeic symptoms.

    “Whilst we cannot assume that these viruses cause disease, kobuviruses have been isolated from dogs and other mammals with diarrhoeic symptoms (Reuter, Boros, and Pankovics 2011; Di Martino et al. 2013).”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites Reuter, Boros, and Pankovics 2011 source
    • cites Di Martino et al. 2013 source
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Astroviruses have a broad host range and are frequently detected in the faeces of mammals, birds, and humans with gastroenteritis.

    “Astroviruses have a broad host range (Donato and Vijaykrishna 2017) and are frequently detected in the faeces of mammals, birds, and humans with gastroenteritis (Finkbeiner et al. 2009; De Benedictis et al. 2011).”
    Quote in the paperNot a substantial claim3 of 3 sources checked
    • cites Donato and Vijaykrishna 2017 source
    • cites Finkbeiner et al. 2009 source

      The cited paper supports detection in humans: its Abstract reports astrovirus VA1 in fecal samples from a gastroenteritis outbreak and describes human astroviruses associated with diarrhea. It also notes that astroviruses infect a variety of species, but does not establish that they are frequently detected in the feces of mammals and birds with gastroenteritis. The sentence attributes the separate broad-host-range clause to Donato and Vijaykrishna, not to this paper. (LLM, conf=0.84)

      Experimental — accuracy not yet measured
    • cites De Benedictis et al. 2011 source

      The Introduction describes astroviruses in many mammalian and avian hosts, and the avian astrovirus section reports frequent detection in turkeys with diarrhea. But the Abstract and Conclusions say the association with enteric disease is not well documented in many animal hosts. The source therefore does not support the unqualified claim that astroviruses are frequently detected in the faeces of mammals, birds, and humans with gastroenteritis. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Hepeviridae cause hepatitis E in mammals and have been isolated from various domestic and wild animals including foxes in the Netherlands.

    “We discovered viral transcripts with some sequence similarity to the Hepeviridae that cause hepatitis E in mammals, which has already been isolated from various domestic and wild animals including foxes in the Netherlands (Meng 2010; Bodewes et al. 2013).”
    Quote in the paperNot a substantial claim2 of 2 sources checked
    • cites Meng 2010 source

      The Introduction and §4.3 describe HEV in humans and several domestic and wild animals. Section 4.3 distinguishes confirmed viral recovery from antibody detection, however, and the paper does not report isolation from foxes in the Netherlands. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
    • cites Bodewes et al. 2013 source

      The paper reports hepatitis E viruses in domestic animals and identifies hepevirus sequences in feces from red foxes collected in the Netherlands (Abstract and study description; page not supplied). It did not isolate a virus or establish that the foxes were infected: it says the sequences might have come from their prey. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Sapeloviruses cause encephalitis in domestic pigs.

    “Additionally, the fox picornaviruses found here are closely related to sapeloviruses that cause encephalitis in domestic pigs (Lan et al. 2011; Schock et al. 2014; Arruda et al. 2017).”
    Quote in the paperNot a substantial claim1 of 3 sources checked
    • cites Lan et al. 2011 source
    • cites Schock et al. 2014 source
    • cites Arruda et al. 2017 source

      The Introduction reports that porcine sapelovirus was detected in pigs with neurologic disease and severe polioencephalomyelitis. The Diagnostics section says the virus was associated with the lesions but explicitly notes that disease causation has not been established. Thus the paper supports an association in domestic pigs, not the unqualified claim that sapeloviruses cause encephalitis. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    RHDV2 is presumed to be an incursion from Europe, where it first emerged in 2010.

    “A novel variant of the disease, RHDV2, began circulating in Australia in 2015 and is presumed to be an incursion from Europe where it first emerged in 2010 (Hall et al. 2015).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Hall et al. 2015 source
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    A combination of biological and ecological differences, such as hormones, diet, and environment, could contribute to variation in male and female viromes.

    “Alternatively, a combination of biological and ecological differences, such as hormones, diet, and environment, could contribute to variation in male and female viromes (Vemuri et al. 2019).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Vemuri et al. 2019 source

      The sections on sex hormones in rodent models and on diet, GIT transit and adiposity (pages not provided) link hormones and diet to sex differences in gut microbiota. But the review says discussion of interactions involving viruses is beyond its scope; it does not establish that hormones, diet and environment contribute to variation in male and female viromes. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Australian lace monitors consuming human refuse experience improved body condition and reduced blood parasite infection compared to those that do not subsist on anthropogenic food waste.

    “Australian lace monitors (Varanus varius) consuming human refuse experience improved body condition and reduced blood parasite infection compared to those that do not subsist on anthropogenic food waste (Jessop et al. 2012).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Jessop et al. 2012 source
  • May combine two claims.

    Findingown data

    Liver samples were dominated by eukaryotic transcripts (92.90-99.43%), largely comprising fox RNA.

    “BLAST analyses revealed that the faecal samples were dominated by bacteria (51.17–84.61%), whilst the liver samples were dominated by eukaryotic transcripts (92.90–99.43%), largely comprising fox RNA.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    Meta-transcriptomic sequencing of nine representative pooled samples resulted in 44-57 million paired reads per pool (593,406,706 reads in total).

    “Meta-transcriptomic sequencing of nine representative pooled samples resulted in 44–57 million paired reads per pool (593,406,706 reads in total).”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Ectoparasites differed substantially to liver and faecal samples with 50.97 per cent of reads classed as 'unmatched'.

    “The ectoparasites (fleas and ticks) differed substantially to the liver and faecal samples with 50.97 per cent of reads classed as ‘unmatched’ meaning they did not share sequence similarity to any known sequence.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    Vixey virus had a relative abundance of 0.007 per cent.

    “The longer sequence, tentatively named vixey virus, shared highest amino acid identity with canine kobuvirus from a domestic dog (97.65%) and had a relative abundance of 0.007 per cent (Table 2).”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Overall, twenty-one viral families were identified in transcripts from urban foxes and nineteen from rural foxes.

    “Overall, twenty-one viral families were identified in transcripts from urban foxes and nineteen from rural foxes.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    Charmer virus had a relative abundance of 0.0001 per cent.

    “The sequence, tentatively named charmer virus, shared an 80.27 per cent amino acid identity with a picobirnavirus found in wolves and had a relative abundance of 0.0001 per cent (Table 2).”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    Vulpix virus had a relative abundance of 0.046 per cent.

    “Notably, the sequence shared a 96.11 per cent amino acid identity with feline astrovirus D1 and had a relative abundance of 0.046 per cent (Table 2).”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Phylogenetic analysis of the RdRp encoding region placed swiper virus in proximity to both house mouse hepevirus and elicom virus-1, with these viruses forming a distinct monophyletic group.

    “Whilst its closest genetic relative is not from a vertebrate host suggesting it may be a diet-associated contaminant, phylogenetic analysis of the RdRp encoding region placed this hepevirus in proximity to both house mouse hepevirus and elicom virus-1, with these viruses forming a distinct monophyletic group (Fig. 4).”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    A much larger percentage of the viral transcripts identified were vertebrate associated in rural foxes (male: 98.23% and female: 97.84%) compared to urban foxes (male: 2.41% and female: 0.39%), although this percentage was higher in males in both groups.

    “A much larger percentage of the viral transcripts identified were vertebrate associated in rural foxes (male: 98.23% and female: 97.84%) compared to urban foxes (male: 2.41% and female: 0.39%), although this percentage was higher in males in both groups.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    Wilde virus-3 had a relative abundance of 0.0004 per cent.

    “Three sequences, tentatively named wilde virus-1, 2, and 3, all shared between 73 and 89 per cent amino acid identity with canine picornavirus and had relative abundances of 5.66 per cent, 0.00058 per cent, and 0.0004 per cent, respectively (Table 2).”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    Wilde virus-2 had a relative abundance of 0.00058 per cent.

    “Three sequences, tentatively named wilde virus-1, 2, and 3, all shared between 73 and 89 per cent amino acid identity with canine picornavirus and had relative abundances of 5.66 per cent, 0.00058 per cent, and 0.0004 per cent, respectively (Table 2).”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Tod virus-1 and tod virus-2 both shared 98 per cent amino acid identity with canine picodicistrovirus.

    “Two of the sequences, tentatively named tod virus-1 and tod virus-2, both shared 98 per cent amino acid identity with canine picodicistrovirus (Table 2).”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Premisecitation

    Foxes interact with human refuse, consume food scraps, eat from pet bowls and wildlife feeding stations, and defaecate nearby, increasing the potential for pathogen transfer.

    “Foxes interact with human refuse, including compost and rubbish bins, and consume food scraps from surfaces such as outdoor barbeques and furniture, eat from pet bowls and wildlife feeding stations, and defaecate nearby, increasing the potential for pathogen transfer (Contesse et al. 2004).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Contesse et al. 2004 source
  • May combine two claims.

    Interpretationnone given

    The remainder of viral reads comprised mostly invertebrate-, plant-, and fungi-associated virus transcripts, which were most likely acquired from the foxes' diet.

    “The remainder comprised mostly invertebrate-, plant-, and fungi-associated virus transcripts, which were most likely acquired from the foxes’ diet.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Foxes killed by poison baits were excluded.

    “Foxes killed by poison baits were excluded.”
    Quote in the paperNot a substantial claim
  • Classified as probably not a substantial claim.

    Study design and conductreasoning

    Samples were taken as soon as possible after death to minimise degradation of RNA.

    “To minimise degradation of RNA, samples were taken as soon as possible after death (03:19:00 ± 02:59:00 h post-mortem, n = 27).”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given

    One carcase had been frozen for approximately 1 week and one carcase had been dead for an unknown amount of time.

    “One carcase had been frozen for approximately 1 week and one carcase had been dead for an unknown amount of time.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Urban foxes live at higher densities than rural counterparts.

    “Urban areas support surprisingly high densities of foxes. For example, there are up to sixteen individuals per km2 in Melbourne (Marks and Bloomfield 1999), compared to just 0.2 individuals per km2 in rural areas (Saunders, Gentle, and Dickman 2010).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Marks and Bloomfield 1999 source
    • cites Saunders, Gentle, and Dickman 2010 source
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Interpretationown data

    Swiper virus's closest genetic relative is not from a vertebrate host, suggesting it may be a diet-associated contaminant.

    “Whilst its closest genetic relative is not from a vertebrate host suggesting it may be a diet-associated contaminant, phylogenetic analysis of the RdRp encoding region placed this hepevirus in proximity to both house mouse hepevirus and elicom virus-1, with these viruses forming a distinct monophyletic group (Fig. 4).”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationreasoning

    The divergent phylogenetic position of the hepevirus detected here could mean that it results from dietary consumption.

    “Hence, although we have classed the virus as vertebrate associated, its divergent phylogenetic position could in fact mean that it results from dietary consumption.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    Due to the small sample size, differences may be due to some individual animals contributing more to overall abundance or diversity in their respective pool than others.

    “However, due to the small sample size, differences may be due to some individual animals contributing more to overall abundance or diversity in their respective pool than others.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductown data

    Whilst virome composition was compared among a relatively small number of samples, this is balanced by the fact that each sample comprises the viromes of multiple individual foxes (n = 3-13 foxes per pool; Table 1).

    “Whilst virome composition was compared among a relatively small number of samples, this is balanced by the fact that each sample comprises the viromes of multiple individual foxes (n = 3–13 foxes per pool; Table 1).”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Interpretationreasoning

    The RHDV2 virus in fox faeces is simply a gut contaminant with no active RHDV2 replication in the fox host.

    “It is likely, then, that Sydney foxes consume diseased rabbits and the virus is simply a gut contaminant with no active RHDV2 replication in the fox host.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    RHDV2 has become the dominant strain circulating in Australia's wild rabbits.

    “RHDV2 has become the dominant strain circulating in Australia’s wild rabbits (Mahar et al. 2018).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Mahar et al. 2018 source
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The prevalence of West Nile virus in wild birds in the USA increases with proximity to urban areas and human population density.

    “In addition, the prevalence of West Nile virus in wild birds in the USA increases with proximity to urban areas and human population density (Gibbs et al. 2006).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Gibbs et al. 2006 source
  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Study design and conductnone given

    Some virus transcripts found here may be the result of contamination by reagents.

    “In this context, it is important to note that some virus transcripts found here may be the result of contamination by reagents.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationnone given

    The RHDV2 in the fox samples was presumably acquired through rabbit consumption.

    “This is the second time that RHDV2 has been found in non-rabbit hosts (Chong et al. 2019), presumably through rabbit consumption in this case.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Antibodies against RHDV have been detected in red foxes in Germany, with no evidence of illness or viral replication.

    “Although it is worth noting that antibodies against RHDV have been detected in red foxes in Germany, there was no evidence of illness or viral replication (Frölich, Klima, and Dedek 1998).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Frölich, Klima, and Dedek 1998 source
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Males may be more likely to be involved in aggressive encounters with conspecifics than females.

    “However, our understanding of red fox sociality in Australia is limited (Newsome 1995) and males may be more likely to be involved in aggressive encounters with conspecifics than females (White and Harris 1994).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites White and Harris 1994 source
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationnone given

    Differences in overall abundance and diversity of viruses present in foxes may be a reflection of differences in diet and environment.

    “Whilst differences in overall abundance and diversity of viruses present in foxes may be a reflection of differences in diet and environment, we found rural foxes to have a much higher abundance of vertebrate-associated viruses than urban.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing), S4 (based).

    Interpretationnone given

    Multiple co-occurring factors could simultaneously affect viral infection in Sydney's foxes.

    “Multiple co-occurring factors could simultaneously affect viral infection in Sydney’s foxes.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Premisecitation

    Foxes in urban Sydney grow larger and are heavier than foxes in rural areas.

    “Foxes in urban Sydney grow larger and are heavier than foxes in rural areas (Stepkovitch et al. 2019), and there may be an advantage to consuming anthropogenic food sources for overall condition and pathogen resistance.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Stepkovitch et al. 2019 source
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationown data

    The difference in viromes between male and female foxes may indicate different ecologies and behaviours in male and female foxes.

    “This difference in viromes may indicate different ecologies and behaviours in male and female foxes.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationcitation

    Greater sociality in females may increase viral transmission opportunities.

    “Whilst other studies looking at sex differences and immunity suggest that females typically display stronger immune responses and reduced pathogen load compared to males (Klein 2000), greater sociality in females (Macdonald 1979, 1983) may increase viral transmission opportunities.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Macdonald 1979 source
    • cites Macdonald 1983 source
  • May combine two claims.

    Premisecitation

    Kit foxes in urban areas in California show less nutritional stress, increased body condition, and improved immune function compared to foxes in a nearby nature reserve.

    “Kit foxes (Vulpes macrotis) in urban areas in California show less nutritional stress, increased body condition, and improved immune function when compared to foxes in a nearby nature reserve (Cypher and Frost 1999).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Cypher and Frost 1999 source
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Females typically display stronger immune responses and reduced pathogen load compared to males.

    “Whilst other studies looking at sex differences and immunity suggest that females typically display stronger immune responses and reduced pathogen load compared to males (Klein 2000), greater sociality in females (Macdonald 1979, 1983) may increase viral transmission opportunities.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Klein 2000 source
57 of 57
  • The paper relies on this without support.

    It is unknown whether urban and rural foxes have different viral compositions.

    “Although red foxes are known to harbour a diversity of viruses (Bodewes et al. 2013; Lojkić et al. 2016), it is unknown whether urban and rural foxes have different viral compositions.”
  • The paper relies on this without support.

    Viruses detected in fox faecal samples are associated with the foxes rather than being transient dietary or environmental contaminants.

    “We show that Sydney’s red foxes, in both urban and rural environments, harbour a wide diversity of viruses, some of which are genetically similar to those that infect domestic pets and humans.”
    “All vertebrate-associated viruses found here were RNA viruses.”
  • The paper relies on this without support.

    Genetic similarity between viruses found in foxes and viruses infecting humans or domestic animals indicates potential for cross-species transmission or zoonotic potential.

    “The close genetic similarity of the viruses found here to viruses frequently found in common domestic pets such as cats and dogs suggests that cross-species transmission between foxes and domestic species may have occurred.”
    “Our findings indicate that foxes may be reservoirs for viral pathogens with zoonotic potential.”
  • The paper relies on this without support.

    The RHDV2 sequence detected in urban male samples, despite being too short for phylogenetic analysis, is correctly identified as RHDV2.

    “The viral sequence in the urban male samples was too short to enable phylogenetic analysis.”
    “One of the most striking observations was the identification of RHDV2 (a positive-sense single-stranded RNA virus) in rural female and urban male faecal samples.”
4 of 4

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Wilde virus-2 location conflicts with Table 2

    Minor

    The paragraph introduces Wilde viruses 1, 2, and 3 as sequences from rural samples, whereas Table 2 places Wilde virus-2 in an urban male faecal sample.

  • Wilde virus-3 identity falls outside the stated range

    Minor

    The text says all three Wilde viruses have 73-89 per cent amino acid identity with canine picornavirus, but Table 2 gives Wilde virus-3 an identity of 96.22 per cent.

  • Juvenile sample count differs between methods sections

    Minor

    The sample-collection section classifies four foxes as juveniles, but the RNA-extraction section says only two juveniles were sampled.

  • Sequencing total conflicts with the per-pool range

    Minor

    Nine pools with 44-57 million paired reads each would contain 396-513 million read pairs, not 593,406,706 reads. Counting individual reads instead would give at least 792 million.

4 of 4

Cites

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Sorted by citations

Authors
Campbell, S. J., Ashley, W., Gil-Fernandez, M., Newsome, T. M., Di Giallonardo, F., Ortiz-Baez, A. S., Mahar, J. E., Towerton, A. L., Gillings, M., Holmes, E. C., Carthey, A. J. R., & Geoghegan, J. L.
Affiliations
  • Macquarie University (AU)
  • Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
  • The University of Sydney (AU)
  • The Kirby Institute, University of New South Wales, Sydney, New South Wales 2052, Australia
  • Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
  • Government of New South Wales (AU)
  • New Zealand Institute for Public Health and Forensic Science (NZ)
Corresponding author
Geoghegan, Jemma L
Venue
Virus Evolution
Published
2020-07-01
Volume
6
Issue
2
Pages
veaa065-veaa065
ISSN
2057-1577 (ISSN-L)
OpenAlex
W3080280624
Cited by
47
References
73
Citations by year
2026: 3 · 2025: 12 · 2024: 9 · 2023: 10 · 2022: 10 · 2021: 3
FWCI
4.31
Type
journal article
Language
en
Open access
Locations
  • Virus Evolution (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • Greater Sydney Local Land Services
  • ARC Australian Laureate Fellowship (FL170100022)
Topics
  • Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Zoonotic diseases and public health
  • Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
  • Health Sciences › Medicine › Epidemiology › Virology and Viral Diseases
Keywords
red fox, virome, urban foxes, invasive species, human-wildlife interface, zoonotic risk, Astroviridae, Hepeviridae, picornavirus, viral genomic surveillance, Greater Sydney

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-28.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-28.

Cited sources are checked by gpt-6-sol.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

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