Novel Picornavirus Detected in Wild Deer: Identification, Genomic Characterisation, and Prevalence in Australia.
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ABSTRACT:
SUBMITTER: Huaman JL
PROVIDER: S-EPMC8706930 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundEnterocytozoon bieneusi is reported to be a common microsporidian of humans and animals in various countries. However, E. bieneusi has yet to be recorded in animals in Australia. Here, we undertook the first molecular epidemiological investigation of E. bieneusi in three species of deer (Cervus elaphus, Dama dama and Rusa unicolor) that live in the catchment areas that supply the city of Melbourne with drinking water.MethodsGenomic DNA was extracted from a total of 610 individual faecal samples from wild deer, including sambar deer (Rusa unicolor) (n = 516), red deer (Cervus elaphus) (n = 77) and fallow deer (Dama dama) (n = 17) from nine catchment areas, and then tested using a nested PCR-based sequencing approach employing internal transcribed spacer (ITS) of nuclear ribosomal DNA as the genetic marker.ResultsEnterocytozoon bieneusi was detected in 25 of all 610 (4.1%) samples exclusively in samples from sambar deer. The analysis of ITS sequence data revealed three known (D, J and Type IV) and two new (MWC_d1 and MWC_d2) genotypes of E. bieneusi. Although the significance of the latter two new genotypes is presently unknown, phylogenetic analysis of ITS sequence data sets showed that they cluster with genotypes D and Type IV, which have been recorded previously in humans. These findings suggest that sambar deer in the water catchments harbour zoonotic genotypes of E. bieneusi.ConclusionsFurther insight into the epidemiology of E. bieneusi in wildlife, water and the environment in Australia will be important to have an informed position on the public health significance of microsporidiosis caused by this microbe.
| S-EPMC5751821 | biostudies-literature
Project description:Endogenous retroviruses (ERVs) are the remnants of past retroviral infections that once invaded the host's germline and were vertically transmitted. ERV sequences have been reported in mammals, but their distribution and diversity in cervids are unclear. Using next-generation sequencing, we identified a nearly complete genome of an endogenous betaretrovirus in fallow deer (Dama dama). Further genomic analysis showed that this provirus, tentatively named cervid endogenous betaretrovirus 1 (CERV β1), has typical betaretroviral genome features (gag-pro-pol-env) and the betaretrovirus-specific dUTPase domain. In addition, CERV β1 pol sequences were detected by PCR in the six non-native deer species with wild populations in Australia. Phylogenetic analyses demonstrated that CERV β1 sequences from subfamily Cervinae clustered as sister taxa to ERV-like sequences in species of subfamily Muntiacinae. These findings, therefore, suggest that CERV β1 endogenisation occurred after the split of these two subfamilies (between 3.3 and 5 million years ago). Our results provide important insights into the evolution of betaretroviruses in cervids.
| S-EPMC8877266 | biostudies-literature
Project description:Bluetongue virus (BTV), transmitted by midges (Culicoides sp), is distributed worldwide and causes disease in ruminants. In particular, BT can be a debilitating disease in sheep causing serious trade and socio-economic consequences at both local and global levels. Across Australia, a sentinel cattle herd surveillance program monitors the BTV activity. Prior to 2014, BTV-1, -2, -3, -7, -9, -15, -16, -20, -21 and -23 had been isolated in Australia, but no bluetongue disease has occurred in a commercial Australian flock. We routinely use a combination of serology, virus isolation, RT-PCR and next generation and conventional nucleotide sequencing technologies to detect and phylogenetically characterize incursions of novel BTV strains into Australia. Screening of Northern Territory virus isolates in 2015 revealed BTV-5, a serotype new to Australia. We derived the complete genome of this isolate and determined its phylogenetic relationship with exotic BTV-5 isolates. Gene segments 2, 6, 7 and 10 exhibited a close relationship with the South African prototype isolate RSArrrr/5. This was the first Australian isolation of a Western topotype of segment 10. Serological surveillance data highlighted the antigenic cross-reactivity between BTV-5 and BTV-9. Phylogenetic investigation of segments 2 and 6 of these serotypes confirmed their unconventional relationships within the BTV serogroup. Our results further highlighted a need for a revision of the current serologically based system for BTV strain differentiation and importantly, implied a potential for genome segments of pathogenic Western BTV strains to rapidly enter Southeast Asia. This emphasized a need for continued high-level surveillance of vectors and viruses at strategic locations in the north of Australia The expansion of routine characterization and classification of BTV to a whole genome approach is recommended, to better monitor the presence and level of establishment of novel Western topotype segments within the Australian episystem.
| S-EPMC6556758 | biostudies-literature
Project description:While picornaviruses are known to infect different animals, their existence in the domestic cat was unknown. We describe the discovery of a novel feline picornavirus (FePV) from stray cats in Hong Kong. From samples from 662 cats, FePV was detected in fecal samples from 14 cats and urine samples from 2 cats by reverse transcription-PCR (RT-PCR). Analysis of five FePV genomes revealed a distinct phylogenetic position and genomic features, with low sequence homologies to known picornaviruses especially in leader and 2A proteins. Among the viruses that belong to the closely related bat picornavirus groups 1 to 3 and the genus Sapelovirus, G+C content and sequence analysis of P1, P2, and P3 regions showed that FePV is most closely related to bat picornavirus group 3. However, FePV possessed other distinct features, including a putative type IV internal ribosome entry site/segment (IRES) instead of type I IRES in bat picornavirus group 3, protein cleavage sites, and H-D-C catalytic triad in 3C(pro) different from those in sapeloviruses and bat picornaviruses, and the shortest leader protein among known picornaviruses. These results suggest that FePV may belong to a new genus in the family Picornaviridae. Western blot analysis using recombinant FePV VP1 polypeptide showed a high seroprevalence of 33.6% for IgG among the plasma samples from 232 cats tested. IgM was also detected in three cats positive for FePV in fecal samples, supporting recent infection in these cats. Further studies are important to understand the pathogenicity, epidemiology, and genetic evolution of FePV in these common pet animals.
| S-EPMC3255865 | biostudies-literature
Project description:BackgroundHepatitis E virus (HEV) is one of the major causes of acute viral hepatitis worldwide. In Europe, food-borne zoonotic transmission of HEV genotype 3 has been associated with domestic pigs and wild boar. Controversial data are available on the circulation of the virus in animals that are used for human consumption, and to date, no gold standard has yet been defined for the diagnosis of HEV-associated hepatitis. To investigate the current HEV infection status in Lithuanian pigs and wild ungulates, the presence of viral RNA was analyzed by nested reverse transcription polymerase chain reaction (RT-nPCR) in randomly selected samples, and the viral RNA was subsequently genotyped.ResultsIn total, 32.98 and 22.55% of the domestic pig samples were HEV-positive using RT-nPCR targeting the ORF1 and ORF2 fragments, respectively. Among ungulates, 25.94% of the wild boar samples, 22.58% of the roe deer samples, 6.67% of the red deer samples and 7.69% of the moose samples were positive for HEV RNA using primers targeting the ORF1 fragment. Using primers targeting the ORF2 fragment of the HEV genome, viral RNA was only detected in 17.03% of the wild boar samples and 12.90% of the roe deer samples. Phylogenetic analysis based on a 348-nucleotide-long region of the HEV ORF2 showed that all obtained sequences detected in Lithuanian domestic pigs and wildlife belonged to genotype 3. In this study, the sequences identified from pigs, wild boars and roe deer clustered within the 3i subtype reference sequences from the GenBank database. The sequences obtained from pig farms located in two different counties of Lithuania were of the HEV 3f subtype. The wild boar sequences clustered within subtypes 3i and 3h, clearly indicating that wild boars can harbor additional subtypes of HEV. For the first time, the ORF2 nucleotide sequences obtained from roe deer proved that HEV subtype 3i can be found in a novel host.ConclusionThe results of the viral prevalence and phylogenetic analyses clearly demonstrated viral infection in Lithuanian pigs and wild ungulates, thus highlighting a significant concern for zoonotic virus transmission through both the food chain and direct contact with animals. Unexpected HEV genotype 3 subtype diversity in Lithuania and neighboring countries revealed that further studies are necessary to understand the mode of HEV transmission between animals and humans in the Baltic States region.
| S-EPMC5824565 | biostudies-literature
Project description:BackgroundTo date, little has been documented about microorganisms harboured within Australian native ticks or their pathogenic potential. Recently, a Borrelia sp. related to the Relapsing Fever (RF) group was identified in a single tick removed from a wild echidna (Tachyglossus aculeatus). The present study investigated the presence of Borrelia in 97 Bothriocroton concolor ticks parasitizing echidnas in Queensland, New South Wales, and Victoria, Australia, using nested PCR with Borrelia-specific primers targeting the 16S rRNA (16S) and flaB genes.ResultsBorrelia-specific PCR assays confirmed the presence of a novel Borrelia sp. related to the RF and reptile-associated (REP) spirochaetes in 38 (39 %) B. concolor ticks. This novel Borrelia sp. was identified in 41 % of the B. concolor ticks in Queensland and New South Wales, but not in any ticks from Victoria. The resulting flaB sequences (407 bp) were 88 and 86 % similar to the flaB sequences from Borrelia turcica and Borrelia hermsii, respectively. Of the ticks confirmed as Borrelia-positive following the flaB assay, 28 were positive with the 16S assay. Phylogenetic analysis of the 16S sequences (1097 bp) suggests that these sequences belong to a novel Borrelia sp., which forms a unique monophyletic clade that is similar to, but distinct from, RF Borrelia spp. and REP-associated Borrelia spp.ConclusionsWe conclude that the novel Borrelia sp. identified in this study does not belong to the Borrelia burgdorferi (sensu lato) complex, and that the phylogenetic analysis of the partial 16S gene sequences suggests it forms a unique monophyletic cluster in the genus Borrelia, potentially forming a fourth major group in this genus associated with monotremes in Australia. However, a thorough molecular characterisation will be required to confirm the phylogenetic position of this unique Borrelia sp. The zoonotic potential and pathogenic consequences of this novel Borrelia sp. are unknown at the current time.
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Project description:A respiratory disease syndrome has been observed in large numbers of wild shingleback lizards (Tiliqua rugosa) admitted to wildlife care facilities in the Perth metropolitan region of Western Australia. Mortality rates are reportedly high without supportive treatment and care. Here we used next generation sequencing techniques to screen affected and unaffected individuals admitted to Kanyana Wildlife Rehabilitation Centre in Perth between April and December 2015, with the resultant discovery of a novel nidovirus significantly associated with cases of respiratory disease according to a case definition based on clinical signs. Interestingly this virus was also found in 12% of apparently healthy individuals, which may reflect testing during the incubation period or a carrier status, or it may be that this agent is not causative in the disease process. This is the first report of a nidovirus in lizards globally. In addition to detection of this virus, characterisation of a 23,832 nt segment of the viral genome revealed the presence of characteristic nidoviral genomic elements providing phylogenetic support for the inclusion of this virus in a novel genus alongside Ball Python nidovirus, within the Torovirinae sub-family of the Coronaviridae. This study highlights the importance of next generation sequencing technologies to detect and describe emerging infectious diseases in wildlife species, as well as the importance of rehabilitation centres to enhance early detection mechanisms through passive and targeted health surveillance. Further development of diagnostic tools from these findings will aid in detection and control of this agent across Australia, and potentially in wild lizard populations globally.
| S-EPMC5102451 | biostudies-literature
Project description:Listeria monocytogenes is a major human and animal foodborne pathogen. However, data from environmental reservoirs remain scarce. Here, we used whole-genome sequencing to characterize Listeria species isolates recovered over 1 year from wild animals in their natural habitats in Spain. Three different Listeria spp. (L. monocytogenes [n = 19], Listeria ivanovii subsp. londoniensis [n = 4], and Listeria innocua [n = 3]) were detected in 23 animal tonsils (9 deer, 14 wild boars) and 2 feeding troughs. No Listeria species was detected in feces. L. monocytogenes was detected in tonsils of 44.4% (8 out of 18) of deer and 40.7% (11 out of 27) of wild boars. L. monocytogenes isolates belonged to 3 different core genome multilocus sequence typing (cgMLST) types (CTs) of 3 distinct sublineages (SL1, SL387, and SL155) from lineages I and II. While cgMLST type L1-SL1-ST1-CT5279 (IVb; clonal complex 1 [CC1]) occurred only in one animal, types L1-SL387-ST388-CT5239 (IVb; CC388) and L2-SL155-ST155-CT1170 (IIa; CC155) were retrieved from multiple animals. In addition, L1-SL387-ST388-CT5239 (IVb; CC388) isolates were collected 1 year apart, revealing their long-term occurrence within the animal population and/or environmental reservoir. The presence of identical L. monocytogenes strains in deer and wild boars suggests contamination from a common food or environmental source, although interhost transmission cannot be excluded. Pathogenicity islands LIPI-1, LIPI-3, and LIPI-4 were present in 100%, 5%, and 79% of the L. monocytogenes isolates, respectively, and all L. monocytogenes lineage II isolates (n = 3) carried SSI-1 stress islands. This study highlights the need for monitoring L. monocytogenes environmental contamination and the importance of tonsils as a possible L. monocytogenes intrahost reservoir.IMPORTANCE Listeria monocytogenes is a foodborne bacterial pathogen responsible for listeriosis. Whole-genome sequencing has been extensively used in public health and food industries to characterize circulating Listeria isolates, but genomic data on isolates occurring in natural environments and wild animals are still scarce. Here, we show that wild animals carry pathogenic Listeria and that the same genotypes can be found at different time points in different host species. This work highlights the need of Listeria species monitoring of environmental contamination and the importance of tonsils as a possible L. monocytogenes intrahost reservoir.
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Project description:We identified novel viruses in feces from cattle with diarrhea collected in 2009 in Hokkaido Prefecture, Japan, by using a metagenomics approach and determined the (near) complete sequences of the virus. Sequence analyses revealed that they had a standard picornavirus genome organization, i.e. 5' untranslated region (UTR) - L- P1 (VP4- VP3- VP2- VP1) - P2 (2A- 2B- 2C) - P3 (3A- 3B- 3C-3D) - 3'UTR- poly(A). They are closely related to other unclassified Chinese picornaviruses; bat picornaviruses group 1-3, feline picornavirus, and canine picornavirus, sharing 45.4-51.4% (P1), 38.0-44.9% (P2), and 49.6-53.3% (P3) amino acid identities, respectively. The phylogenetic analyses and detailed genome characterization showed that they, together with the unclassified Chinese picornaviruses, grouped as a cluster for the P1, 2C, 3CD and VP1 coding regions. These viruses had conserved features (e.g. predicted protein cleavage sites, presence of a leader protein, 2A, 2C, 3C, and 3D functional domains), suggesting they have a common ancestor. Reverse-transcription-PCR assays, using specific primers designed from the 5'UTR sequence of these viruses, showed that 23.0% (20/87) of fecal samples from cattle with diarrhea were positive, indicating the prevalence of these picornavirus in the Japanese cattle population in Hokkaido Prefecture. However, further studies are needed to investigate the pathogenic potential and etiological role of these viruses in cattle.
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Project description:PCR diagnostics detected 100% prevalence of Helicobacter in 425 wild house mice (Mus musculus) from across central Europe. Of seven species identified, the five most frequent were Helicobacter rodentium (78%), H. typhlonius (53%), H. hepaticus (41%), H. bilis (30%), and H. muridarum (1%). Double infections were more common (42%) than single (30%) and triple (21%) infections. Wild house mice could be considered potential reservoirs of Helicobacter strains for both humans and other vertebrates.
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