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Alexander G, Hanns-Joachim R, Stefan K, Eckhard W, Helmut B, Mathias B. Parapoxvirus species revisited by whole genome sequencing: A retrospective analysis of bovine virus isolates. Virus Res 2024; 346:199404. [PMID: 38782262 PMCID: PMC11152744 DOI: 10.1016/j.virusres.2024.199404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/18/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
Parapoxviruses (PPV) of animals are spread worldwide. While the Orf virus (ORFV) species is a molecularly well-characterized prototype pathogen of small ruminants, the genomes of virus species affecting large ruminants, namely Bovine papular stomatitis virus (BPSV) and Pseudocowpox virus (PCPV), are less well known. Using Nanopore sequencing we retrospectively show the whole genome sequences (WGS) of six BPSV, three PCPV isolates and an attenuated ORFV strain, originating from different geographic locations. A phylogenetic tree shows that the de novo assembled genomes belong to PPV species including WGS of reference PPV. Remarkably, Nanopore sequencing allowed the molecular resolution of inverted terminal repeats (ITR) and the hairpin loop within the de novo assembled WGS. Additionally, peculiarities regarding map location of two genes and the heterogeneity of a genomic region were noted. Details for the molecular variability of an interferon response modulatory gene (ORF116) and the PCPV specificity of gene 073.5 are reported. In summary, WGS gained by Nanopore sequencing allowed analysis of complete PPV genomes and confident virus species attribution within a phylogenetic tree avoiding uncertainty of limited gene-based diagnostics. Nanopore-based WGS provides robust comparison of PPV genomes and reliable identity determination of new Poxviruses.
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Affiliation(s)
- Graf Alexander
- Laboratory for Functional Genome Analysis (LAFUGA), Dept. Genomics, Gene Centre, Ludwig-Maximilians-Universität München (LMU), 81377 Munich, Germany
| | - Rziha Hanns-Joachim
- Institute of Immunology, University Hospital Tübingen, Eberhard Karls Universität Tübingen, 72076, Tübingen, Germany
| | - Krebs Stefan
- Laboratory for Functional Genome Analysis (LAFUGA), Dept. Genomics, Gene Centre, Ludwig-Maximilians-Universität München (LMU), 81377 Munich, Germany
| | - Wolf Eckhard
- Laboratory for Functional Genome Analysis (LAFUGA), Dept. Genomics, Gene Centre, Ludwig-Maximilians-Universität München (LMU), 81377 Munich, Germany
| | - Blum Helmut
- Laboratory for Functional Genome Analysis (LAFUGA), Dept. Genomics, Gene Centre, Ludwig-Maximilians-Universität München (LMU), 81377 Munich, Germany
| | - Büttner Mathias
- Institute of Immunology, Faculty of Veterinary Medicine, University of Leipzig, 04103, Leipzig, Germany.
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Pfaff F, Kramer K, King J, Franzke K, Rosenberger T, Höper D, König P, Hoffmann D, Beer M. Detection of Novel Poxvirus from Gray Seal (Halichoerus grypus), Germany. Emerg Infect Dis 2023; 29:1202-1205. [PMID: 37209672 DOI: 10.3201/eid2906.221817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023] Open
Abstract
We detected a novel poxvirus from a gray seal (Halichoerus grypus) from the North Sea, Germany. The juvenile animal showed pox-like lesions and deteriorating overall health condition and was finally euthanized. Histology, electron microscopy, sequencing, and PCR confirmed a previously undescribed poxvirus of the Chordopoxvirinae subfamily, tentatively named Wadden Sea poxvirus.
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Wauters LA, Lurz PWW, Santicchia F, Romeo C, Ferrari N, Martinoli A, Gurnell J. Interactions between native and invasive species: A systematic review of the red squirrel-gray squirrel paradigm. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1083008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
The eastern gray squirrel (Sciurus carolinensis) has been labeled as one of the 100 worst invasive alien species by the IUCN. In Europe, the species has been introduced to Britain, Ireland and Italy, and its subsequent spread has resulted in wide-scale extinction of native Eurasian red squirrels (Sciurus vulgaris) from the areas colonized by the gray squirrel. This replacement of a native by an alien competitor is one of the best documented cases of the devastating effects of biological invasions on native fauna. To understand how this replacement occurs, we present a systematic review of the literature on competition and interactions between red and gray squirrels. We describe the patterns of red and gray squirrel distribution in those parts of Europe where gray squirrels occur and summarize the evidence on the different processes and mechanisms determining the outcome of competition between the native and alien species including the influence of predators and pathogens. Some of the drivers behind the demise of the red squirrel have been intensively studied and documented in the past 30 years, but recent field studies and mathematical models revealed that the mechanisms underlying the red-gray paradigm are more complex than previously thought and affected by landscape-level processes. Therefore, we consider habitat type and multi-species interactions, including host-parasite and predator-prey relationships, to determine the outcome of the interaction between the two species and to better address gray squirrel control efforts.
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A Peek into the Bacterial Microbiome of the Eurasian Red Squirrel ( Sciurus vulgaris). Animals (Basel) 2022; 12:ani12050666. [PMID: 35268234 PMCID: PMC8909207 DOI: 10.3390/ani12050666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 11/18/2022] Open
Abstract
Sciurus vulgaris (the Eurasian red squirrel) is native to Europe and Asia, but due to habitat destruction or fragmentation, interspecific competition, and infectious diseases, especially in European island areas the species finds itself at the brink of extinction. The repopulation of such bare habitats requires healthy squirrel specimens, either translocated from other wild habitats or reintroduced to the wilderness following captive breeding. Captivity, nonetheless, has shown an immense capacity to reshape the structure of wild species’ microbiota, adapting it to the less diverse diet and fewer environmental challenges. Therefore, assessing the differences between “wild” and “captive” microbiota in this species could elucidate if special living conditions are needed in order to augment the survival rate of specimens reintroduced into the wild. Furthermore, the microflora profile of the normal flora of healthy red squirrels raised in captivity could support clinicians in addressing infectious diseases episodes and also raise awareness on the zoonotic risk. Hence, this study aimed at documenting the bacterial species carried by S. vulgaris, disclosing overall similarities and variability patterns of the microbiota identified in individuals from two different living environments. We anticipated that the bacterial community would be less diverse in individuals raised in captivity, owing to their restrictive diet and to unchanging conditions in the enclosure. We also hypothesized that there would be a higher prevalence of zoonotic microorganisms in the captive animals, due to the proximity of humans and of other domestic species. To test this, samples (n = 100) were taken from five body regions of 20 red squirrels, both free-ranging and bred in captivity, processed by classical microbiology techniques, and further identified by biochemical assay (VITEK®2 Compact System). A relatively poor bacterial community, comprising 62 bacterial strains belonging to 18 species and 8 different genera, was identified. Most of these microorganisms were reported for the first time in S. vulgaris. With no discrimination between living environments, the highest prevalence (p < 0.001), was registered in Staphylococcus sciuri (60%; 12/20), followed by Escherichia coli (45%; 9/20) and Bacillus cereus (35%; 7/20). The results suggest unremarkable differences in diversity and richness of the resident aerobic microbiota of S. vulgaris, in relation to the living environment.
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DIAGNOSING AND CATEGORIZING LEPROSY IN LIVE EURASIAN RED SQUIRRELS ( SCIURUS VULGARIS) FOR MANAGEMENT, SURVEILLANCE, AND TRANSLOCATION PURPOSES. J Zoo Wildl Med 2021; 52:648-659. [PMID: 34130408 DOI: 10.1638/2020-0066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2021] [Indexed: 11/21/2022] Open
Abstract
The presence of Mycobacterium lepromatosis and Mycobacterium leprae in Eurasian red squirrel (Sciurus vulgaris, ERS) carcasses throughout the British Isles, and leprosy as a disease, have recently been reported using histological and molecular diagnostic methods. In 2016, the first longitudinal study of ERS affected by leprosy was initiated. One of the main challenges was the reliable diagnosis of leprosy in live ERS, which is important for (a) welfare and case management and (b) surveillance or pretranslocation screening efforts. We explored diagnostic methods ranging from detailed clinical assessment and informative categorization of observed lesions, thermal imaging, serology (antiphenolic glycolipid-I antibody [αPGL-I] detection) to molecular methods (polymerase chain reaction [PCR]). For PCR the ear was established as the optimal sampling site. Based on the experiences from this 2-yr study we propose an objective categorization system for clinical lesions and a diagnostic framework for the combination of the diagnostic tools we found to be effective in live ERS: clinical assessment, αPGL-I serology, and PCR. Thermal imaging did not offer additional information for leprosy diagnostics in ERS. We propose an amended definition of leprosy lesions in ERS as "skin areas of local hair loss, in which a firm-rubbery, glossy swelling develops, that may ulcerate" and standardized terminology for describing ERS leprosy status. The information presented forms the basis of a consistent, reliable diagnostic and reporting system for leprosy cases in ERS.
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Hodo CL, Mauldin MR, Light JE, Wilkins K, Tang S, Nakazawa Y, Emerson GL, Ritter JM, Mansell JL, Hamer SA. Novel Poxvirus in Proliferative Lesions of Wild Rodents in East Central Texas, USA. Emerg Infect Dis 2019; 24:1069-1072. [PMID: 29774837 PMCID: PMC6004845 DOI: 10.3201/eid2406.172057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Northern pygmy mice from 2 localities in East Central Texas, USA, had proliferative epidermal lesions on the tail and feet. Electron microscopy of lesion tissue revealed poxvirus. Phylogenetic analyses indicated the virus differed 35% from its closest relatives, the Chordopoxvirinae. Future research is needed to determine whether this virus could affect human health.
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Romeo C, McInnes CJ, Dale TD, Shuttleworth C, Bertolino S, Wauters LA, Ferrari N. Disease, invasions and conservation: no evidence of squirrelpox virus in grey squirrels introduced to Italy. Anim Conserv 2018. [DOI: 10.1111/acv.12433] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- C. Romeo
- Department of Veterinary Medicine Università degli Studi di Milano Milan Italy
| | | | - T. D. Dale
- Institute of Integrative Biology University of Liverpool Liverpool UK
| | - C. Shuttleworth
- School of Environment, Natural Resources and Geography Bangor University Bangor Gwynedd UK
| | - S. Bertolino
- Department of Life Sciences and Systems Biology Università degli Studi di Torino Torino Italy
| | - L. A. Wauters
- Department of Theoretical and Applied Sciences Università degli Studi dell'Insubria Varese Italy
| | - N. Ferrari
- Department of Veterinary Medicine Università degli Studi di Milano Milan Italy
- Centro di Ricerca Coordinata Epidemiologia e Sorveglianza Molecolare delle Infezioni Università degli Studi di Milano Milan Italy
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Gelderblom HR, Madeley D. Rapid Viral Diagnosis of Orthopoxviruses by Electron Microscopy: Optional or a Must? Viruses 2018; 10:E142. [PMID: 29565285 PMCID: PMC5923436 DOI: 10.3390/v10040142] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 02/22/2018] [Accepted: 02/22/2018] [Indexed: 12/20/2022] Open
Abstract
Diagnostic electron microscopy (DEM) was an essential component of viral diagnosis until the development of highly sensitive nucleic acid amplification techniques (NAT). The simple negative staining technique of DEM was applied widely to smallpox diagnosis until the world-wide eradication of the human-specific pathogen in 1980. Since then, the threat of smallpox re-emerging through laboratory escape, molecular manipulation, synthetic biology or bioterrorism has not totally disappeared and would be a major problem in an unvaccinated population. Other animal poxviruses may also emerge as human pathogens. With its rapid results (only a few minutes after arrival of the specimen), no requirement for specific reagents and its "open view", DEM remains an important component of virus diagnosis, particularly because it can easily and reliably distinguish smallpox virus or any other member of the orthopoxvirus (OPV) genus from parapoxviruses (PPV) and the far more common and less serious herpesviruses (herpes simplex and varicella zoster). Preparation, enrichment, examination, internal standards and suitable organisations are discussed to make clear its continuing value as a diagnostic technique.
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Affiliation(s)
- Hans R Gelderblom
- (ret) Robert Koch Institute, Centre for Biological Threats and Special Pathogens, ZBS 4: Advanced Light and Electron Microscopy, Seestrasse 10, D-13353 Berlin, Germany.
| | - Dick Madeley
- (ret) University of Newcastle upon Tyne, Burnfoot, Stocksfield, Northumberland, NE43 7TN, UK.
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Erster O, Melamed S, Paran N, Weiss S, Khinich Y, Gelman B, Solomony A, Laskar-Levy O. First Diagnosed Case of Camelpox Virus in Israel. Viruses 2018; 10:v10020078. [PMID: 29438294 PMCID: PMC5850385 DOI: 10.3390/v10020078] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/06/2018] [Accepted: 02/12/2018] [Indexed: 12/21/2022] Open
Abstract
An outbreak of a disease in camels with skin lesions was reported in Israel during 2016. To identify the etiological agent of this illness, we employed a multidisciplinary diagnostic approach. Transmission electron microscopy (TEM) analysis of lesion material revealed the presence of an orthopox-like virus, based on its characteristic brick shape. The virus from the skin lesions successfully infected chorioallantoic membranes and induced cytopathic effect in Vero cells, which were subsequently positively stained by an orthopox-specific antibody. The definite identification of the virus was accomplished by two independent qPCR, one of which was developed in this study, followed by sequencing of several regions of the viral genome. The qPCR and sequencing results confirmed the presence of camelpox virus (CMLV), and indicated that it is different from the previously annotated CMLV sequence available from GenBank. This is the first reported case of CMLV in Israel, and the first description of the isolated CMLV subtype.
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Affiliation(s)
- Oran Erster
- Division of Virology, Kimron Veterinary Institute, P.O. Box 12, Beit Dagan 50250, Israel.
| | - Sharon Melamed
- Department of Infectious Diseases, IIBR P.O. Box 19, Ness Ziona 74100, Israel.
| | - Nir Paran
- Department of Infectious Diseases, IIBR P.O. Box 19, Ness Ziona 74100, Israel.
| | - Shay Weiss
- Department of Infectious Diseases, IIBR P.O. Box 19, Ness Ziona 74100, Israel.
| | - Yevgeny Khinich
- Division of Virology, Kimron Veterinary Institute, P.O. Box 12, Beit Dagan 50250, Israel.
| | - Boris Gelman
- Division of Virology, Kimron Veterinary Institute, P.O. Box 12, Beit Dagan 50250, Israel.
| | - Aharon Solomony
- Negev Veterinary Bureau, Israeli Veterinary Services, Binyamin Ben Asa 1, Be'er Sheba 84102, Israel.
| | - Orly Laskar-Levy
- Department of Infectious Diseases, IIBR P.O. Box 19, Ness Ziona 74100, Israel.
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