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Sacristán C, Ewbank AC, Duarte-Benvenuto A, Sacristán I, Zamana-Ramblas R, Costa-Silva S, Lanes Ribeiro V, Bertozzi CP, Del Rio do Valle R, Castilho PV, Colosio AC, Marcondes MCC, Lailson-Brito J, de Freitas Azevedo A, Carvalho VL, Pessi CF, Cremer M, Esperón F, Catão-Dias JL. Survey of selected viral agents (herpesvirus, adenovirus and hepatitis E virus) in liver and lung samples of cetaceans, Brazil. Sci Rep 2024; 14:2689. [PMID: 38302481 PMCID: PMC10834590 DOI: 10.1038/s41598-023-45315-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/18/2023] [Indexed: 02/03/2024] Open
Abstract
Hepatic and pulmonary lesions are common in cetaceans, despite their poorly understood viral etiology. Herpesviruses (HV), adenoviruses (AdV) and hepatitis E virus (HEV) are emerging agents in cetaceans, associated with liver and/or pulmonary damage in mammals. We isolated and molecularly tested DNA for HV and AdV (n = 218 individuals; 187 liver and 108 lung samples) and RNA for HEV (n = 147 animals; 147 liver samples) from six cetacean families. All animals stranded or were bycaught in Brazil between 2001 and 2021. Positive-animals were analyzed by histopathology. Statistical analyses assessed if the prevalence of viral infection could be associated with the variables: species, family, habitat, region, sex, and age group. All samples were negative for AdV and HEV. Overall, 8.7% (19/218) of the cetaceans were HV-positive (4.8% [9/187] liver and 11.1% [12/108] lung), without HV-associated lesions. HV-prevalence was statistically significant higher in Pontoporiidae (19.2%, 10/52) when compared to Delphinidae (4.1%, 5/121), and in southeastern (17.1%, 13/76)-the most industrialized Brazilian region-when compared to the northeastern region (2.4%, 3/126). This study broadens the herpesvirus host range in cetaceans, including its description in pygmy sperm whales (Kogia breviceps) and humpback whales (Megaptera novaeangliae). Further studies must elucidate herpesvirus drivers in cetaceans.
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Affiliation(s)
- C Sacristán
- Centro de Investigación en Sanidad Animal (CISA-INIA), CSIC, Carretera Algete-El Casar de Talamanca, Km. 8,1, 28130, Valdeolmos, Madrid, Spain.
- School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, Brazil.
| | - A C Ewbank
- School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - A Duarte-Benvenuto
- School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - I Sacristán
- Centro de Investigación en Sanidad Animal (CISA-INIA), CSIC, Carretera Algete-El Casar de Talamanca, Km. 8,1, 28130, Valdeolmos, Madrid, Spain
| | - R Zamana-Ramblas
- School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - S Costa-Silva
- School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, Brazil
| | | | - C P Bertozzi
- São Paulo State University - UNESP, São Vicente, SP, Brazil
| | - R Del Rio do Valle
- Instituto Ecoema de Estudo e Conservação do Meio Ambiente, Peruíbe, SP, Brasil
| | - P V Castilho
- Universidade do Estado de Santa Catarina-UDESC, Laguna, SC, Brazil
| | - A C Colosio
- Instituto Baleia Jubarte, Caravelas, BA, Brazil
| | | | - J Lailson-Brito
- Laboratório de Mamíferos Aquáticos e Bioindicadores 'Profa Izabel M. G. do N. Gurgel' (MAQUA), Faculdade de Oceanografia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - A de Freitas Azevedo
- Laboratório de Mamíferos Aquáticos e Bioindicadores 'Profa Izabel M. G. do N. Gurgel' (MAQUA), Faculdade de Oceanografia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - V L Carvalho
- Associação de Pesquisa e Preservação de Ecossistemas Aquáticos, Caucaia, CE, Brazil
| | - C F Pessi
- Instituto de Pesquisas Cananéia (IpeC), Cananéia, SP, Brazil
| | - M Cremer
- Laboratório de Ecologia e Conservação de Tetrápodes Marinhos e Costeiros - TETRAMAR, Universidade da Região de Joinville - UNIVILLE, São Francisco Do Sul, SC, Brazil
| | - F Esperón
- Universidad Europea, Villaviciosa de Odon, Spain
| | - J L Catão-Dias
- School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, Brazil
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Kaiserman J, O’Hara BA, Haley SA, Atwood WJ. An Elusive Target: Inhibitors of JC Polyomavirus Infection and Their Development as Therapeutics for the Treatment of Progressive Multifocal Leukoencephalopathy. Int J Mol Sci 2023; 24:8580. [PMID: 37239927 PMCID: PMC10218015 DOI: 10.3390/ijms24108580] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Progressive multifocal leukoencephalopathy (PML) is a rare demyelinating disease caused by infection with JC Polyomavirus (JCPyV). Despite the identification of the disease and isolation of the causative pathogen over fifty years ago, no antiviral treatments or prophylactic vaccines exist. Disease onset is usually associated with immunosuppression, and current treatment guidelines are limited to restoring immune function. This review summarizes the drugs and small molecules that have been shown to inhibit JCPyV infection and spread. Paying attention to historical developments in the field, we discuss key steps of the virus lifecycle and antivirals known to inhibit each event. We review current obstacles in PML drug discovery, including the difficulties associated with compound penetrance into the central nervous system. We also summarize recent findings in our laboratory regarding the potent anti-JCPyV activity of a novel compound that antagonizes the virus-induced signaling events necessary to establish a productive infection. Understanding the current panel of antiviral compounds will help center the field for future drug discovery efforts.
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Affiliation(s)
| | | | | | - Walter J. Atwood
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
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Sandybayev N, Beloussov V, Strochkov V, Solomadin M, Granica J, Yegorov S. Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome. Microorganisms 2022; 10:microorganisms10122327. [PMID: 36557580 PMCID: PMC9785614 DOI: 10.3390/microorganisms10122327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
The COVID-19 pandemic and heightened perception of the risk of emerging viral infections have boosted the efforts to better understand the virome or complete repertoire of viruses in health and disease, with a focus on infectious respiratory diseases. Next-generation sequencing (NGS) is widely used to study microorganisms, allowing the elucidation of bacteria and viruses inhabiting different body systems and identifying new pathogens. However, NGS studies suffer from a lack of standardization, in particular, due to various methodological approaches and no single format for processing the results. Here, we review the main methodological approaches and key stages for studies of the human virome, with an emphasis on virome changes during acute respiratory viral infection, with applications for clinical diagnostics and epidemiologic analyses.
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Affiliation(s)
- Nurlan Sandybayev
- Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
- Correspondence: ; Tel.: +7-778312-2058
| | - Vyacheslav Beloussov
- Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
- Molecular Genetics Laboratory TreeGene, Almaty 050009, Kazakhstan
| | - Vitaliy Strochkov
- Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
| | - Maxim Solomadin
- School of Pharmacy, Karaganda Medical University, Karaganda 100000, Kazakhstan
| | - Joanna Granica
- Molecular Genetics Laboratory TreeGene, Almaty 050009, Kazakhstan
| | - Sergey Yegorov
- Michael G. DeGroote Institute for Infectious Disease Research, Faculty of Health Sciences, McMaster University, Hamilton, ON L8S 4LB, Canada
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Smith K, Fielding R, Schiavone K, Hall KR, Reid VS, Boyea D, Smith EL, Schmidlin K, Fontenele RS, Kraberger S, Varsani A. Circular DNA viruses identified in short-finned pilot whale and orca tissue samples. Virology 2021; 559:156-164. [PMID: 33892449 DOI: 10.1016/j.virol.2021.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 12/15/2022]
Abstract
Members of the Delphinidae family are widely distributed across the world's oceans. We used a viral metagenomic approach to identify viruses in orca (Orcinus orca) and short-finned pilot whale (Globicephala macrorhynchus) muscle, kidney, and liver samples from deceased animals. From orca tissue samples (muscle, kidney, and liver), we identified a novel polyomavirus (Polyomaviridae), three cressdnaviruses, and two genomoviruses (Genomoviridae). In the short-finned pilot whale we were able to identify one genomovirus in a kidney sample. The presence of unclassified cressdnavirus within two samples (muscle and kidney) of the same animal supports the possibility these viruses might be widespread within the animal. The orca polyomavirus identified here is the first of its species and is not closely related to the only other dolphin polyomavirus previously discovered. The identification and verification of these viruses expands the current knowledge of viruses that are associated with the Delphinidae family.
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Affiliation(s)
- Kendal Smith
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Russell Fielding
- HTC Honors College, Coastal Carolina University, Conway, SC, 29528, USA.
| | - Kelsie Schiavone
- Department of Earth and Environmental Systems, The University of the South, Sewanee, TN, 37383, USA
| | - Katharine R Hall
- Department of Earth and Environmental Systems, The University of the South, Sewanee, TN, 37383, USA
| | - Vincent S Reid
- Barrouallie Whaler's Project, Saint Vincent and the Grenadines
| | | | - Emma L Smith
- Department of Chemical & Biological Sciences, University of the West Indies-Cave Hill, Barbados
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA; Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, 7700, Cape Town, South Africa.
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Cho M, Kim H, Son HS. Codon usage patterns of LT-Ag genes in polyomaviruses from different host species. Virol J 2019; 16:137. [PMID: 31727090 PMCID: PMC6854729 DOI: 10.1186/s12985-019-1245-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/17/2019] [Indexed: 11/10/2022] Open
Abstract
Background Polyomaviruses (PyVs) have a wide range of hosts, from humans to fish, and their effects on hosts vary. The differences in the infection characteristics of PyV with respect to the host are assumed to be influenced by the biochemical function of the LT-Ag protein, which is related to the cytopathic effect and tumorigenesis mechanism via interaction with the host protein. Methods We carried out a comparative analysis of codon usage patterns of large T-antigens (LT-Ags) of PyVs isolated from various host species and their functional domains and sequence motifs. Parity rule 2 (PR2) and neutrality analysis were applied to evaluate the effects of mutation and selection pressure on codon usage bias. To investigate evolutionary relationships among PyVs, we carried out a phylogenetic analysis, and a correspondence analysis of relative synonymous codon usage (RSCU) values was performed. Results Nucleotide composition analysis using LT-Ag gene sequences showed that the GC and GC3 values of avian PyVs were higher than those of mammalian PyVs. The effective number of codon (ENC) analysis showed host-specific ENC distribution characteristics in both the LT-Ag gene and the coding sequences of its domain regions. In the avian and fish PyVs, the codon diversity was significant, whereas the mammalian PyVs tended to exhibit conservative and host-specific evolution of codon usage bias. The results of our PR2 and neutrality analysis revealed mutation bias or highly variable GC contents by showing a narrow GC12 distribution and wide GC3 distribution in all sequences. Furthermore, the calculated RSCU values revealed differences in the codon usage preference of the LT-AG gene according to the host group. A similar tendency was observed in the two functional domains used in the analysis. Conclusions Our study showed that specific domains or sequence motifs of various PyV LT-Ags have evolved so that each virus protein interacts with host cell targets. They have also adapted to thrive in specific host species and cell types. Functional domains of LT-Ag, which are known to interact with host proteins involved in cell proliferation and gene expression regulation, may provide important information, as they are significantly related to the host specificity of PyVs.
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Affiliation(s)
- Myeongji Cho
- Laboratory of Computational Biology & Bioinformatics, Institute of Public Health and Environment, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Hayeon Kim
- Department of Biomedical Laboratory Science, Kyungdong University, 815 Gyeonhwon-ro, Munmak, Wonju, Gangwondo, 24695, South Korea
| | - Hyeon S Son
- Laboratory of Computational Biology & Bioinformatics, Institute of Public Health and Environment, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea. .,SNU Bioinformatics Institute, Interdisciplinary Graduate Program in Bioinformatics, College of Natural Science, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea.
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Novel Polyomaviruses in Mammals from Multiple Orders and Reassessment of Polyomavirus Evolution and Taxonomy. Viruses 2019; 11:v11100930. [PMID: 31658738 PMCID: PMC6833039 DOI: 10.3390/v11100930] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/04/2019] [Accepted: 10/07/2019] [Indexed: 12/14/2022] Open
Abstract
As the phylogenetic organization of mammalian polyomaviruses is complex and currently incompletely resolved, we aimed at a deeper insight into their evolution by identifying polyomaviruses in host orders and families that have either rarely or not been studied. Sixteen unknown and two known polyomaviruses were identified in animals that belong to 5 orders, 16 genera, and 16 species. From 11 novel polyomaviruses, full genomes could be determined. Splice sites were predicted for large and small T antigen (LTAg, STAg) coding sequences (CDS) and examined experimentally in transfected cell culture. In addition, splice sites of seven published polyomaviruses were analyzed. Based on these data, LTAg and STAg annotations were corrected for 10/86 and 74/86 published polyomaviruses, respectively. For 25 polyomaviruses, a spliced middle T CDS was observed or predicted. Splice sites that likely indicate expression of additional, alternative T antigens, were experimentally detected for six polyomaviruses. In contrast to all other mammalian polyomaviruses, three closely related cetartiodactyl polyomaviruses display two introns within their LTAg CDS. In addition, the VP2 of Glis glis (edible dormouse) polyomavirus 1 was observed to be encoded by a spliced transcript, a unique experimental finding within the Polyomaviridae family. Co-phylogenetic analyses based on LTAg CDS revealed a measurable signal of codivergence when considering all mammalian polyomaviruses, most likely driven by relatively recent codivergence events. Lineage duplication was the only other process whose influence on polyomavirus evolution was unambiguous. Finally, our analyses suggest that an update of the taxonomy of the family is required, including the creation of novel genera of mammalian and non-mammalian polyomaviruses.
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Díaz-Delgado J, Fernández A, Sierra E, Sacchini S, Andrada M, Vela AI, Quesada-Canales Ó, Paz Y, Zucca D, Groch K, Arbelo M. Pathologic findings and causes of death of stranded cetaceans in the Canary Islands (2006-2012). PLoS One 2018; 13:e0204444. [PMID: 30289951 PMCID: PMC6173391 DOI: 10.1371/journal.pone.0204444] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 09/07/2018] [Indexed: 12/11/2022] Open
Abstract
This study describes the pathologic findings and most probable causes of death (CD) of 224 cetaceans stranded along the coastline of the Canary Islands (Spain) over a 7-year period, 2006-2012. Most probable CD, grouped as pathologic categories (PCs), was identified in 208/224 (92.8%) examined animals. Within natural PCs, those associated with good nutritional status represented 70/208 (33.6%), whereas, those associated with significant loss of nutritional status represented 49/208 (23.5%). Fatal intra- and interspecific traumatic interactions were 37/208 (17.8%). Vessel collisions included 24/208 (11.5%). Neonatal/perinatal pathology involved 13/208 (6.2%). Fatal interaction with fishing activities comprised 10/208 (4.8%). Within anthropogenic PCs, foreign body-associated pathology represented 5/208 (2.4%). A CD could not be determined in 16/208 (7.7%) cases. Natural PCs were dominated by infectious and parasitic disease processes. Herein, our results suggest that between 2006 and 2012, in the Canary Islands, direct human activity appeared responsible for 19% of cetaceans deaths, while natural pathologies accounted for 81%. These results, integrating novel findings and published reports, aid in delineating baseline knowledge on cetacean pathology and may be of value to rehabilitators, caregivers, diagnosticians and future conservation policies.
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Affiliation(s)
- Josué Díaz-Delgado
- Veterinary Histology and Pathology, Institute of Animal Health and Food Hygiene (IUSA), University of Las Palmas of Gran Canaria, Las Palmas of Gran Canaria, Spain
- Wildlife Comparative Pathology Laboratory, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Antonio Fernández
- Veterinary Histology and Pathology, Institute of Animal Health and Food Hygiene (IUSA), University of Las Palmas of Gran Canaria, Las Palmas of Gran Canaria, Spain
| | - Eva Sierra
- Veterinary Histology and Pathology, Institute of Animal Health and Food Hygiene (IUSA), University of Las Palmas of Gran Canaria, Las Palmas of Gran Canaria, Spain
| | - Simona Sacchini
- Veterinary Histology and Pathology, Institute of Animal Health and Food Hygiene (IUSA), University of Las Palmas of Gran Canaria, Las Palmas of Gran Canaria, Spain
| | - Marisa Andrada
- Veterinary Histology and Pathology, Institute of Animal Health and Food Hygiene (IUSA), University of Las Palmas of Gran Canaria, Las Palmas of Gran Canaria, Spain
| | - Ana Isabel Vela
- Department of Animal Health, Veterinary College, Complutense University, Madrid, Spain
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET). Complutense University, Madrid, Spain
| | - Óscar Quesada-Canales
- Veterinary Histology and Pathology, Institute of Animal Health and Food Hygiene (IUSA), University of Las Palmas of Gran Canaria, Las Palmas of Gran Canaria, Spain
| | - Yania Paz
- Veterinary Histology and Pathology, Institute of Animal Health and Food Hygiene (IUSA), University of Las Palmas of Gran Canaria, Las Palmas of Gran Canaria, Spain
| | - Daniele Zucca
- Veterinary Histology and Pathology, Institute of Animal Health and Food Hygiene (IUSA), University of Las Palmas of Gran Canaria, Las Palmas of Gran Canaria, Spain
| | - Kátia Groch
- Wildlife Comparative Pathology Laboratory, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Manuel Arbelo
- Veterinary Histology and Pathology, Institute of Animal Health and Food Hygiene (IUSA), University of Las Palmas of Gran Canaria, Las Palmas of Gran Canaria, Spain
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Cerezo A, Quesada-Canales O, Sierra E, Díaz-Delgado J, Fernández A, Henningson J, Arbelo M. Pyogranulomatous obliterative laryngotracheitis by Rhizopus arrhizus (syn. R. oryzae) in a free-ranging Atlantic spotted dolphin Stenella frontalis. DISEASES OF AQUATIC ORGANISMS 2018; 130:153-158. [PMID: 30198490 DOI: 10.3354/dao03268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We report the gross and microscopic findings and molecular identification of fungal hyphate infection in a juvenile female Atlantic spotted dolphin Stenella frontalis found dead off Arguineguin, Gran Canaria (Canary Islands, Spain). On necropsy examination, the animal had a large cranial intrathoracic mass and multiple variably-sized nodules throughout the larynx and trachea that obliterated the lumen. Microscopically, the masses were composed of abundant pyogranulomatous inflammation with numerous fungal hyphae. These were pauciseptate (coenocytic) and had non-parallel walls, non-dichotomous irregular to right angle branching, and bulbous dilations. PCR analysis from these inflammatory foci yielded Rhizopus arrhizus (syn. R. oryzae). This fungal pathogen is often ascribed to opportunistic infections in immunosuppressed humans and animals. In the present case, a potential cause for immunosuppression was not identified; PCR analysis for cetacean morbillivirus was negative. Herein, we report the first confirmed case of R. arrhizus infection in a free-living Atlantic cetacean. These findings add to the body of knowledge on fungal disease in cetaceans in general and, in particular, in odontocetes, where respiratory involvement is common.
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Affiliation(s)
- Argiñe Cerezo
- Department of Diagnostic Medicine and Pathobiology, Kansas State Veterinary Diagnostic Laboratory, 1800 Denison Avenue, Manhattan, KS 66506, USA
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Biology, evolution, and medical importance of polyomaviruses: An update. INFECTION GENETICS AND EVOLUTION 2017. [DOI: 10.1016/j.meegid.2017.06.011] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Kumar A, Murthy S, Kapoor A. Evolution of selective-sequencing approaches for virus discovery and virome analysis. Virus Res 2017; 239:172-179. [PMID: 28583442 PMCID: PMC5819613 DOI: 10.1016/j.virusres.2017.06.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/28/2016] [Accepted: 06/02/2017] [Indexed: 12/11/2022]
Abstract
Description of virus enrichment techniques for metagenomics based virome analysis. Usefulness of recently developed virome capture sequencing techniques. Perspective on negative and positive selection approaches for virome analysis.
Recent advances in sequencing technologies have transformed the field of virus discovery and virome analysis. Once mostly confined to the traditional Sanger sequencing based individual virus discovery, is now entirely replaced by high throughput sequencing (HTS) based virus metagenomics that can be used to characterize the nature and composition of entire viromes. To better harness the potential of HTS for the study of viromes, sample preparation methodologies use different approaches to exclude amplification of non-viral components that can overshadow low-titer viruses. These virus-sequence enrichment approaches mostly focus on the sample preparation methods, like enzymatic digestion of non-viral nucleic acids and size exclusion of non-viral constituents by column filtration, ultrafiltration or density gradient centrifugation. However, recently a new approach of virus-sequence enrichment called virome-capture sequencing, focused on the amplification or HTS library preparation stage, was developed to increase the ability of virome characterization. This new approach has the potential to further transform the field of virus discovery and virome analysis, but its technical complexity and sequence-dependence warrants further improvements. In this review we discuss the different methods, their applications and evolution, for selective sequencing based virome analysis and also propose refinements needed to harness the full potential of HTS for virome analysis.
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Affiliation(s)
- Arvind Kumar
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Satyapramod Murthy
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Amit Kapoor
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA; Department of Pediatrics, College of Medicine and Public Health, Ohio State University, Columbus, OH 43210, USA.
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Varsani A, Frankfurter G, Stainton D, Male MF, Kraberger S, Burns JM. Identification of a polyomavirus in Weddell seal (Leptonychotes weddellii) from the Ross Sea (Antarctica). Arch Virol 2017; 162:1403-1407. [PMID: 28124141 DOI: 10.1007/s00705-017-3239-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 12/23/2016] [Indexed: 11/25/2022]
Abstract
Viruses are ubiquitous in nature, however, very few have been identified that are associated with Antarctic animals. Here we report the identification of a polyomavirus in the kidney tissue of a deceased Weddell seal from the Ross Sea, Antarctica. The circular genome (5186 nt) has typical features of polyomaviruses with a small and larger T-antigen open reading frames (ORFs) and three ORFs encoding VP1, VP2 and VP3 capsid proteins. The genome of the Weddell seal polyomavirus (WsPyV) shares 85.4% genome-wide pairwise identity with a polyomavirus identified in a California sea lion. To our knowledge WsPyV is the first viral genome identified in Antarctic pinnipeds and the third polyomavirus to be identified from an Antarctic animal, the other two being from Adélie penguin (Pygoscelis adeliae) and a sharp-spined notothen (Trematomus pennellii), both sampled in the Ross sea. The GenBank accession number: KX533457.
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Affiliation(s)
- Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA.
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand.
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, 7001, South Africa.
| | - Greg Frankfurter
- Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Daisy Stainton
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Maketalena F Male
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Simona Kraberger
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Jennifer M Burns
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK, 99508, USA.
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COINFECTION OF CALIFORNIA SEA LION ADENOVIRUS 1 AND A NOVEL POLYOMAVIRUS IN A HAWAIIAN MONK SEAL (NEOMONACHUS SCHAUINSLANDI). J Zoo Wildl Med 2016; 47:427-37. [PMID: 27468013 DOI: 10.1638/2014-0252.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The Hawaiian monk seal (Neomonachus schauinslandi) is an endangered species. Here, we present a clinical case of a 26-yr-old male Hawaiian monk seal (HMS) kept in an aquarium with a history of intermittent anorexia and evidence of renal disease. Histologic examination revealed eosinophilic intranuclear inclusions in the liver. Conventional nested PCR protocols were used to test for viruses, and it tested positive for adenovirus and polyomavirus, and negative for herpesvirus. The adenovirus partial polymerase gene is 100% homologous to that of California sea lion adenovirus 1 (CSLAdV-1). CSLAdV-1 causes viral hepatitis in CSL, and has recently been reported in different species of otariids in an aquarium in Japan ( Otaria flavescens and Arctocephalus pusillus ) and a sequence from Spain has been submitted in NCBI as Otaria flavescens adenovirus-1. The polyomavirus in this animal is a novel virus, and is the first polyomavirus discovered in Hawaiian monk seals. This new virus is designated Hawaiian monk seal polyomavirus (HMSPyV-1), and is 83% homologous to California sea lion Polyomavirus-1 (CSLPyV-1). This is the first report of viral coinfection in a HMS and clinical significance in this case remains unclear but may be associated with advanced age.
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Frey KG, Bishop-Lilly KA. Next-Generation Sequencing for Pathogen Detection and Identification. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Anthony SJ, Garner MM, Palminteri L, Navarrete-Macias I, Sanchez-Leon MD, Briese T, Daszak P, Lipkin WI. West Nile virus in the British Virgin Islands. ECOHEALTH 2014; 11:255-257. [PMID: 24504904 DOI: 10.1007/s10393-014-0910-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 12/30/2013] [Accepted: 01/10/2014] [Indexed: 06/03/2023]
Abstract
West Nile virus (WNV) first emerged in the US in 1999 and has since spread across the Americas. Here, we report the continued expansion of WNV to the British Virgin Islands following its emergence in a flock of free-roaming flamingos. Histologic review of a single chick revealed lesions consistent with WNV infection, subsequently confirmed with PCR, immunohistochemistry and in situ hybridization. Full genome analysis revealed 99% sequence homology to strains circulating in the US over the past decade. This study highlights the need for rapid necropsy of wild bird carcasses to fully understand the impact of WNV on wild populations.
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Affiliation(s)
- S J Anthony
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY, USA,
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Yamaguchi H, Kobayashi S, Maruyama J, Sasaki M, Takada A, Kimura T, Sawa H, Orba Y. Role of the C-terminal region of vervet monkey polyomavirus 1 VP1 in virion formation. J Vet Med Sci 2014; 76:637-44. [PMID: 24419975 PMCID: PMC4073331 DOI: 10.1292/jvms.13-0568] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Recently, we detected novel vervet monkey polyomavirus 1 (VmPyV) in a vervet monkey.
Among amino acid sequences of major capsid protein VP1s of other polyomaviruses, VmPyV VP1
is the longest with additional amino acid residues in the C-terminal region. To examine
the role of VmPyV VP1 in virion formation, we generated virus-like particles (VLPs) of
VmPyV VP1, because VLP is a useful tool for the investigation of the morphological
characters of polyomavirus virions. After the full-length VmPyV VP1 was subcloned into a
mammalian expression plasmid, the plasmid was transfected into human embryonic kidney 293T
(HEK293T) cells. Thereafter, VmPyV VLPs were purified from the cell lysates of the
transfected cells via sucrose gradient sedimentation. Electron microscopic analyses
revealed that VmPyV VP1 forms VLPs with a diameter of approximately 50 nm that are
exclusively localized in cell nuclei. Furthermore, we generated VLPs consisting of the
deletion mutant VmPyV VP1 (ΔC VP1) lacking the C-terminal 116 amino acid residues and
compared its VLP formation efficiency and morphology to those of VLPs from wild-type VmPyV
VP1 (WT VP1). WT and ΔC VP1 VLPs were similar in size, but the number of ΔC VP1 VLPs was
much lower than that of WT VP1 VLPs in VP1-expressing HEK293T cells. These results suggest
that the length of VP1 is unrelated to virion morphology; however, the C-terminal region
of VmPyV VP1 affects the efficiency of its VLP formation.
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Affiliation(s)
- Hiroki Yamaguchi
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan
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Bennett MD, Gillett A. Butcherbird polyomavirus isolated from a grey butcherbird (Cracticus torquatus) in Queensland, Australia. Vet Microbiol 2014; 168:302-11. [DOI: 10.1016/j.vetmic.2013.11.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 11/11/2013] [Accepted: 11/13/2013] [Indexed: 10/26/2022]
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Bogich TL, Anthony SJ, Nichols JD. Surveillance theory applied to virus detection: a case for targeted discovery. Future Virol 2013. [DOI: 10.2217/fvl.13.105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Virus detection and mathematical modeling have gone through rapid developments in the past decade. Both offer new insights into the epidemiology of infectious disease and characterization of future risk; however, modeling has not yet been applied to designing the best surveillance strategies for viral and pathogen discovery. We review recent developments and propose methods to integrate viral and pathogen discovery and mathematical modeling through optimal surveillance theory, arguing for a more targeted approach to novel virus detection guided by the principles of adaptive management and structured decision-making.
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Affiliation(s)
- Tiffany L Bogich
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
- Princeton University, Dept of Ecology & Evolutionary Biology, Princeton, NJ, USA
| | - Simon J Anthony
- Center for Infection & Immunity, Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY, USA
- EcoHealth Alliance, 17th Floor, 460 West 34th Street, New York, NY, USA
| | - James D Nichols
- US Geological Survey, Patuxent Wildlife Research Center, Laurel, MD, USA
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