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Sarkar SN, Harioudh MK, Shao L, Perez J, Ghosh A. The Many Faces of Oligoadenylate Synthetases. J Interferon Cytokine Res 2023; 43:487-494. [PMID: 37751211 PMCID: PMC10654648 DOI: 10.1089/jir.2023.0098] [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: 07/17/2023] [Accepted: 08/13/2023] [Indexed: 09/27/2023] Open
Abstract
2'-5' Oligoadenylate synthetases (OAS) are interferon-stimulated genes that are most well-known to protect hosts from viral infections. They are evolutionarily related to an ancient family of Nucleotidyltransferases, which are primarily involved in pathogen-sensing and innate immune response. Classical function of OAS proteins involves double-stranded RNA-stimulated polymerization of adenosine triphosphate in 2'-5' oligoadenylates (2-5A), which can activate the latent RNase (RNase L) to degrade RNA. However, accumulated evidence over the years have suggested alternative mode of antiviral function of several OAS family proteins. Furthermore, recent studies have connected some OAS proteins with wider function beyond viral infection. Here, we review some of the canonical and noncanonical functions of OAS proteins and their mechanisms.
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Affiliation(s)
- Saumendra N. Sarkar
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Munesh K. Harioudh
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Lulu Shao
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Joseph Perez
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Arundhati Ghosh
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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2
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Moniruzzaman M, Erazo Garcia MP, Farzad R, Ha AD, Jivaji A, Karki S, Sheyn U, Stanton J, Minch B, Stephens D, Hancks DC, Rodrigues RAL, Abrahao JS, Vardi A, Aylward FO. Virologs, viral mimicry, and virocell metabolism: the expanding scale of cellular functions encoded in the complex genomes of giant viruses. FEMS Microbiol Rev 2023; 47:fuad053. [PMID: 37740576 PMCID: PMC10583209 DOI: 10.1093/femsre/fuad053] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/29/2023] [Accepted: 09/21/2023] [Indexed: 09/24/2023] Open
Abstract
The phylum Nucleocytoviricota includes the largest and most complex viruses known. These "giant viruses" have a long evolutionary history that dates back to the early diversification of eukaryotes, and over time they have evolved elaborate strategies for manipulating the physiology of their hosts during infection. One of the most captivating of these mechanisms involves the use of genes acquired from the host-referred to here as viral homologs or "virologs"-as a means of promoting viral propagation. The best-known examples of these are involved in mimicry, in which viral machinery "imitates" immunomodulatory elements in the vertebrate defense system. But recent findings have highlighted a vast and rapidly expanding array of other virologs that include many genes not typically found in viruses, such as those involved in translation, central carbon metabolism, cytoskeletal structure, nutrient transport, vesicular trafficking, and light harvesting. Unraveling the roles of virologs during infection as well as the evolutionary pathways through which complex functional repertoires are acquired by viruses are important frontiers at the forefront of giant virus research.
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Affiliation(s)
- Mohammad Moniruzzaman
- Rosenstiel School of Marine Atmospheric, and Earth Science, University of Miami, Coral Gables, FL 33149, United States
| | - Maria Paula Erazo Garcia
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Roxanna Farzad
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Anh D Ha
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Abdeali Jivaji
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Sangita Karki
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Uri Sheyn
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Joshua Stanton
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Benjamin Minch
- Rosenstiel School of Marine Atmospheric, and Earth Science, University of Miami, Coral Gables, FL 33149, United States
| | - Danae Stephens
- Rosenstiel School of Marine Atmospheric, and Earth Science, University of Miami, Coral Gables, FL 33149, United States
| | - Dustin C Hancks
- Department of Immunology, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX, United States
| | - Rodrigo A L Rodrigues
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Jonatas S Abrahao
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
- Center for Emerging, Zoonotic, and Arthropod-Borne Infectious Disease, Virginia Tech, Blacksburg, VA 24061, United States
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3
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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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Cruciani D, Crotti S, Paoloni D, La Morgia V, Felici A, Papa P, Cosseddu GM, Moscati L, Gobbi P. Health Status of the Eastern Grey Squirrel ( Sciurus carolinensis) Population in Umbria: Results of the LIFE Project 'U-SAVEREDS'. Animals (Basel) 2022; 12:ani12202741. [PMID: 36290127 PMCID: PMC9597752 DOI: 10.3390/ani12202741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/09/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022] Open
Abstract
Simple Summary Invasive alien species are non-native species introduced deliberately or unintentionally beyond their past or present natural distribution, and their introduction and spread threatens local biological diversity. The Eastern grey squirrel is native to North America and was introduced to the British Islands, Italy, and South Africa. Around the year 2000, a new population of grey squirrels was recorded in Perugia, central Italy, where the species populated an area of approximately 50 km2, both in woodland and urban areas. The Eastern grey squirrel represents a huge threat to the conservation of the native Eurasian red squirrel when the two species coexist. Moreover, given their confident behaviour with humans, the non-native squirrels can negatively impact public health. The U-SAVEREDS Project was set up for Eurasian red squirrel conservation in Umbria through the eradication of the alien species and it also provided information on the health status of the Eastern grey squirrel to identify any infectious agents. The recovery of zoonotic pathogens allowed to assess the Eastern grey squirrel’s impact on human and domestic and wild animals’ health, provide helpful feedback for the management and eradication procedures, and raise public awareness through environmental education. Abstract The introduction of the Eastern grey squirrel (Sciurus carolinensis) in Europe is one of the best-known cases of invasive alien species (IAS) colonisation, that poses a severe risk to the conservation of biodiversity. In 2003, it was released in a private wildlife park near the city of Perugia (Italy), where it is replacing the native Eurasian red squirrel (Sciurus vulgaris). The LIFE13 BIO/IT/000204 Project (U-SAVEREDS) was set up for the Sciurus vulgaris conservation in Umbria through an eradication campaign of grey squirrels. One hundred and fifty-four animals were analysed for bacteriological, mycological, virological, and serological investigations (C4 action). Sanitary screening showed that Sciurus carolinensis is a dermatophyte carrier, and therefore, it could cause public health issues for humans, considering its confident behaviour. Moreover, it has been marginally responsible for the spreading of Candida albicans, Coxiella burnetii, and Borrelia lusitaniae. Health status evaluation conducted on the Sciurus carolinensis population indicated that it is necessary to raise awareness of its impacts on biodiversity and human health. Moreover, the health status and behaviours of the IAS must be considered when control or eradication campaigns are planned.
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Affiliation(s)
- Deborah Cruciani
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati” (IZSUM), Via G. Salvemini 1, 06126 Perugia, Italy
- Correspondence:
| | - Silvia Crotti
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati” (IZSUM), Via G. Salvemini 1, 06126 Perugia, Italy
| | | | - Valentina La Morgia
- Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Via Vitaliano Brancati 48, 00144 Roma, Italy
| | - Andrea Felici
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati” (IZSUM), Via G. Salvemini 1, 06126 Perugia, Italy
| | - Paola Papa
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati” (IZSUM), Via G. Salvemini 1, 06126 Perugia, Italy
| | - Gian Mario Cosseddu
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri” (IZSLT), Via Appia Nuova 1411, 00178 Roma, Italy
- Istituto Zooprofilattico Sperimentale Abruzzo e Molise “G. Caporale” (IZSAM), Campo Boario, 64100 Teramo, Italy
| | - Livia Moscati
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati” (IZSUM), Via G. Salvemini 1, 06126 Perugia, Italy
| | - Paola Gobbi
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati” (IZSUM), Via G. Salvemini 1, 06126 Perugia, Italy
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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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Palmer S, Chappidi S, Pinkham C, Hancks DC. Evolutionary profile for (host and viral) MLKL indicates its activities as a battlefront for extensive counteradaptation. Mol Biol Evol 2021; 38:5405-5422. [PMID: 34436583 PMCID: PMC8662602 DOI: 10.1093/molbev/msab256] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Pathogen infection triggers host innate defenses which may result in the activation of regulated cell death (RCD) pathways such as apoptosis. Given a vital role in immunity, apoptotic effectors are often counteracted by pathogen-encoded antagonists. Mounting evidence indicates that programmed necrosis, which is mediated by the RIPK3/MLKL axis and termed necroptosis, evolved as a countermeasure to pathogen-mediated inhibition of apoptosis. Yet, it is unclear whether components of this emerging RCD pathway display signatures associated with pathogen conflict that are rare in combination but common to key host defense factors, namely, rapid evolution, viral homolog (virolog), and cytokine induction. We leveraged evolutionary sequence analysis that examines rates of amino acid replacement, which revealed: 1) strong and recurrent signatures of positive selection for primate and bat RIPK3 and MLKL, and 2) elevated rates of amino acid substitution on multiple RIPK3/MLKL surfaces suggestive of past antagonism with multiple, distinct pathogen-encoded inhibitors. Furthermore, our phylogenomics analysis across poxvirus genomes illuminated volatile patterns of evolution for a recently described MLKL viral homolog. Specifically, poxviral MLKLs have undergone numerous gene replacements mediated by duplication and deletion events. In addition, MLKL protein expression is stimulated by interferons in human and mouse cells. Thus, MLKL displays all three hallmarks of pivotal immune factors of which only a handful of factors like OAS1 exhibit. These data support the hypothesis that over evolutionary time MLKL functions—which may include execution of necroptosis—have served as a major determinant of infection outcomes despite gene loss in some host genomes.
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Affiliation(s)
- Suzette Palmer
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Sruthi Chappidi
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Chelsea Pinkham
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Dustin C Hancks
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
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Sorouri M, Chang T, Jesudhasan P, Pinkham C, Elde NC, Hancks DC. Signatures of host-pathogen evolutionary conflict reveal MISTR-A conserved MItochondrial STress Response network. PLoS Biol 2020; 18:e3001045. [PMID: 33370271 PMCID: PMC7793259 DOI: 10.1371/journal.pbio.3001045] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 01/08/2021] [Accepted: 12/09/2020] [Indexed: 11/18/2022] Open
Abstract
Host-pathogen conflicts leave genetic signatures in genes that are critical for host defense functions. Using these "molecular scars" as a guide to discover gene functions, we discovered a vertebrate-specific MItochondrial STress Response (MISTR) circuit. MISTR proteins are associated with electron transport chain (ETC) factors and activated by stress signals such as interferon gamma (IFNγ) and hypoxia. Upon stress, ultraconserved microRNAs (miRNAs) down-regulate MISTR1(NDUFA4) followed by replacement with paralogs MItochondrial STress Response AntiViral (MISTRAV) and/or MItochondrial STress Response Hypoxia (MISTRH). While cells lacking MISTR1(NDUFA4) are more sensitive to chemical and viral apoptotic triggers, cells lacking MISTRAV or expressing the squirrelpox virus-encoded vMISTRAV exhibit resistance to the same insults. Rapid evolution signatures across primate genomes for MISTR1(NDUFA4) and MISTRAV indicate recent and ongoing conflicts with pathogens. MISTR homologs are also found in plants, yeasts, a fish virus, and an algal virus indicating ancient origins and suggesting diverse means of altering mitochondrial function under stress. The discovery of MISTR circuitry highlights the use of evolution-guided studies to reveal fundamental biological processes.
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Affiliation(s)
- Mahsa Sorouri
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Institute of Biomedical Studies, Baylor University, Waco, Texas, United States of America
| | - Tyron Chang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Genetics, Development, and Disease PhD Program, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Palmy Jesudhasan
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Chelsea Pinkham
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Nels C. Elde
- Eccles Institute of Human Genetics, The University of Utah Medical School, Utah, United States of America
- * E-mail: (NCE); (DCH)
| | - Dustin C. Hancks
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail: (NCE); (DCH)
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Mead D, Fingland K, Cripps R, Portela Miguez R, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Doulcan J, Quail MA, McCarthy SA, Howe K, Sims Y, Torrance J, Tracey A, Challis R, Durbin R, Blaxter M. The genome sequence of the eastern grey squirrel, Sciurus carolinensis Gmelin, 1788. Wellcome Open Res 2020; 5:27. [PMID: 33215047 PMCID: PMC7653645 DOI: 10.12688/wellcomeopenres.15721.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2020] [Indexed: 12/02/2022] Open
Abstract
We present a genome assembly from an individual male
Sciurus carolinensis (the eastern grey squirrel; Vertebrata; Mammalia; Eutheria; Rodentia; Sciuridae). The genome sequence is 2.82 gigabases in span. The majority of the assembly (92.3%) is scaffolded into 21 chromosomal-level scaffolds, with both X and Y sex chromosomes assembled.
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Affiliation(s)
- Dan Mead
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Kathryn Fingland
- Nottingham Trent University, School of Animal, Rural and Environmental Sciences, Nottingham, NG25 0QF, UK
| | - Rachel Cripps
- Red Squirrel Officer, The Wildlife Trust for Lancashire, Manchester and North Merseyside, The Barn, Berkeley Drive, Bamber Bridge, Preston, PR5 6BY, UK
| | | | - Michelle Smith
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Craig Corton
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Karen Oliver
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Jason Skelton
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Emma Betteridge
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Jale Doulcan
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Michael A Quail
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Shane A McCarthy
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Ying Sims
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - James Torrance
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Richard Challis
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Richard Durbin
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
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Mead D, Fingland K, Cripps R, Portela Miguez R, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Dolucan J, Dudchenko O, Omer AD, Weisz D, Lieberman Aiden E, Fedrigo O, Mountcastle J, Jarvis E, McCarthy SA, Sims Y, Torrance J, Tracey A, Howe K, Challis R, Durbin R, Blaxter M. The genome sequence of the Eurasian red squirrel, Sciurus vulgaris Linnaeus 1758. Wellcome Open Res 2020; 5:18. [PMID: 32587897 PMCID: PMC7309416 DOI: 10.12688/wellcomeopenres.15679.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2020] [Indexed: 01/27/2023] Open
Abstract
We present a genome assembly from an individual male Sciurus vulgaris (the Eurasian red squirrel; Vertebrata; Mammalia; Eutheria; Rodentia; Sciuridae). The genome sequence is 2.88 gigabases in span. The majority of the assembly is scaffolded into 21 chromosomal-level scaffolds, with both X and Y sex chromosomes assembled.
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Affiliation(s)
- Daniel Mead
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Kathryn Fingland
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Nottingham, NG25 0QF, UK
| | - Rachel Cripps
- The Wildlife Trust for Lancashire, Manchester and North Merseyside, Preston, PR5 6BY, UK
| | | | - Michelle Smith
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Craig Corton
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Karen Oliver
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Jason Skelton
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Emma Betteridge
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Jale Dolucan
- Baylor College of Medicine, Houston, TX, 77030, USA
| | | | | | - David Weisz
- Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Olivier Fedrigo
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, 10065, USA
| | - Jacquelyn Mountcastle
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, 10065, USA
| | - Erich Jarvis
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, 10065, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Shane A. McCarthy
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Ying Sims
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - James Torrance
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Richard Challis
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Richard Durbin
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
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10
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Kranzusch PJ. cGAS and CD-NTase enzymes: structure, mechanism, and evolution. Curr Opin Struct Biol 2019; 59:178-187. [PMID: 31593902 PMCID: PMC7127440 DOI: 10.1016/j.sbi.2019.08.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 07/25/2019] [Accepted: 08/25/2019] [Indexed: 01/22/2023]
Abstract
Cyclic GMP-AMP synthase (cGAS) is a signaling enzyme in human cells that controls immune-sensing of cytosolic DNA. The recent discoveries of diverse structural homologs of cGAS in animals and bacteria reveal that cGAS-like signaling is surprisingly ancient and widespread in biology. Together with the Vibrio cholerae protein dinucleotide cyclase in Vibrio (DncV), cGAS and DncV homologs comprise a family of cGAS/DncV-like nucleotidyltransferase (CD-NTase) enzymes that synthesize noncanonical RNA signals including cyclic dinucleotides, cyclic trinucleotides, and linear oligonucleotides. Structural and biochemical breakthroughs provide a framework to understand how CD-NTase signaling allows cells to respond to changing environmental conditions. The CD-NTase family also includes uncharacterized human genes like MB21D2 and Mab21L1, highlighting emerging functions of cGAS-like signaling beyond innate immunity.
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Affiliation(s)
- Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA 02115, USA.
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11
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Koala and Wombat Gammaherpesviruses Encode the First Known Viral NTPDase Homologs and Are Phylogenetically Divergent from All Known Gammaherpesviruses. J Virol 2019; 93:JVI.01404-18. [PMID: 30567986 DOI: 10.1128/jvi.01404-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/12/2018] [Indexed: 11/20/2022] Open
Abstract
There is a large taxonomic gap in our understanding of mammalian herpesvirus genetics and evolution corresponding to those herpesviruses that infect marsupials, which diverged from eutherian mammals approximately 150 million years ago (mya). We compare the genomes of two marsupial gammaherpesviruses, Phascolarctid gammaherpesvirus 1 (PhaHV1) and Vombatid gammaherpesvirus 1 (VoHV1), which infect koalas (Phascolarc tos cinereus) and wombats (Vombatus ursinus), respectively. The core viral genomes were approximately 117 kbp and 110 kbp in length, respectively, sharing 69% pairwise nucleotide sequence identity. Phylogenetic analyses showed that PhaHV1 and VoHV1 formed a separate branch, which may indicate a new gammaherpesvirus genus. The genomes contained 60 predicted open reading frames (ORFs) homologous to those in eutherian herpesviruses and 20 ORFs not yet found in any other herpesvirus. Seven of these ORFs were shared by the two viruses, indicating that they were probably acquired prespeciation, approximately 30 to 40 mya. One of these shared genes encodes a putative nucleoside triphosphate diphosphohydrolase (NTPDase). NTPDases are usually found in mammals and higher-order eukaryotes, with a very small number being found in bacteria. This is the first time that an NTPDase has been identified in any viral genome. Interrogation of public transcriptomic data sets from two koalas identified PhaHV1-specific transcripts in multiple host tissues, including transcripts for the novel NTPDase. PhaHV1 ATPase activity was also demonstrated in vitro, suggesting that the encoded NTPDase is functional during viral infection. In mammals, NTPDases are important in downregulation of the inflammatory and immune responses, but the role of the PhaHV1 NTPDase during viral infection remains to be determined.IMPORTANCE The genome sequences of the koala and wombat gammaherpesviruses show that the viruses form a distinct branch, indicative of a novel genus within the Gammaherpesvirinae Their genomes contain several new ORFs, including ORFs encoding a β-galactoside α-2,6-sialyltransferase that is phylogenetically closest to poxvirus and insect homologs and the first reported viral NTPDase. NTPDases are ubiquitously expressed in mammals and are also present in several parasitic, fungal, and bacterial pathogens. In mammals, these cell surface-localized NTPDases play essential roles in thromboregulation, inflammation, and immune suppression. In this study, we demonstrate that the virus-encoded NTPDase is enzymatically active and is transcribed during natural infection of the host. Understanding how these enzymes benefit viruses can help to inform how they may cause disease or evade host immune defenses.
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12
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Wibbelt G, Tausch SH, Dabrowski PW, Kershaw O, Nitsche A, Schrick L. Berlin Squirrelpox Virus, a New Poxvirus in Red Squirrels, Berlin, Germany. Emerg Infect Dis 2018; 23:1726-1729. [PMID: 28930029 PMCID: PMC5621524 DOI: 10.3201/eid2310.171008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Near Berlin, Germany, several juvenile red squirrels (Sciurus vulgaris) were found with moist, crusty skin lesions. Histology, electron microscopy, and cell culture isolation revealed an orthopoxvirus-like infection. Subsequent PCR and genome analysis identified a new poxvirus (Berlin squirrelpox virus) that could not be assigned to any known poxvirus genera.
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13
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Borisevich SV, Stovba LF, Paveliev DI. POXVIRUS DISEASE OF SQUIRRELS (POXVIRIDAE, CHORDOPOXVIRINAE, SQPV - SQUIRREL POXVIRUS). Vopr Virusol 2018; 63:53-57. [PMID: 36494921 DOI: 10.18821/0507-4088-2018-63-2-53-57] [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: 01/20/2020] [Indexed: 06/17/2023]
Abstract
A new taxon of the subfamily Chordopoxvirinae that may represent a new genus of smallpox viruses is considered in this review. The distribution of gray squirrels (Sciurus carolinensis) throughout the UK during the 20th century and the decrease in the population of red squirrels (Sciurus vulgaris) is one of the most well-documented cases of ecological change of local fauna by the introduced species. The tendency to expand the distribution of the smallpox virus from Great Britain to the Western part of Europe has been noted. The genetic peculiarities of the genome of the poxvirus of squirrels, which determine its biological properties, as well as evolutionary relationships with other poxviruses, are separately described. Determination of the size of the genome by restriction analysis, sequencing of the whole genome, determination of the content of G/C nucleotide pairs, and functional mapping of the majority of genes made it possible to construct a phylogenetic tree. Phylogenetic analysis shows that this is a new representative of the subfamily Chordоpoxvirinae located between the viruses of the molluscum contagiosum and parapoxviruses. Serological and molecular biological methods are used to reveal and identify the causative agent of smallpox. The use of electron microscopy is limited in grey squirrels, due to the absence of organ damage and reproduction of the virus. Identification of the DNA of the causative agent of poxvirus of squirrels based on the use of different types of polymerase chain reaction (nested and in real time) overcomes all these limitations.
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Affiliation(s)
| | - L F Stovba
- 48th Central Scientific Research Institute
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14
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Sarker S, Roberts HK, Tidd N, Ault S, Ladmore G, Peters A, Forwood JK, Helbig K, Raidal SR. Molecular and microscopic characterization of a novel Eastern grey kangaroopox virus genome directly from a clinical sample. Sci Rep 2017; 7:16472. [PMID: 29184134 PMCID: PMC5705601 DOI: 10.1038/s41598-017-16775-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/17/2017] [Indexed: 11/22/2022] Open
Abstract
Poxviruses are large DNA viruses with varying zoonotic potential, and are recognised in a broad range of wildlife. Although poxviruses have been detected in kangaroos, their genetic relationships to poxviruses in other animals and humans is not well understood. Here, we present a novel genome sequence of a marsupial poxvirus, the Eastern grey kangaroopox virus (EKPV-NSW), isolated from a wild eastern grey kangaroo. In the present study, histopathologically confirmed epidermal pox lesions were used to recover the full-length viral genome and perform electron microscopic analysis, with both immature virions and intracellular mature virions detected. Subsequent analysis of the EKPV-NSW genome demonstrated the highest degree of sequence similarity with EKPV-SC strain (91.51%), followed by WKPV-WA (87.93%), and MOCV1 (44.05%). The novel EKPV-NSW complete genome encompasses most of the chordopoxviruses protein coding genes (138) that are required for genome replication and expression, with only three essential protein coding genes being absent. The novel EKPV-NSW is missing 28 predicted genes compared to the recently isolated EKPV-SC, and carries 21 additional unique genes, encoding unknown proteins. Phylogenetic and recombination analyses showed EKPV-NSW to be the distinct available candidate genome of chordopoxviruses.
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Affiliation(s)
- Subir Sarker
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, VIC 3086, Australia.
| | - Hayley K Roberts
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, VIC 3086, Australia
| | - Naomie Tidd
- Veterinary Diagnostic Laboratory, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Shayne Ault
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
- Lake Road Veterinary Clinic, 327 Lake Albert Road, Kooringal, NSW 2650, Australia
| | - Georgia Ladmore
- Lake Road Veterinary Clinic, 327 Lake Albert Road, Kooringal, NSW 2650, Australia
| | - Andrew Peters
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Karla Helbig
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, VIC 3086, Australia
| | - Shane R Raidal
- Veterinary Diagnostic Laboratory, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
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15
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Farré D, Martínez-Vicente P, Engel P, Angulo A. Immunoglobulin superfamily members encoded by viruses and their multiple roles in immune evasion. Eur J Immunol 2017; 47:780-796. [PMID: 28383780 DOI: 10.1002/eji.201746984] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/11/2017] [Accepted: 03/29/2017] [Indexed: 12/31/2022]
Abstract
Pathogens have developed a plethora of strategies to undermine host immune defenses in order to guarantee their survival. For large DNA viruses, these immune evasion mechanisms frequently rely on the expression of genes acquired from host genomes. Horizontally transferred genes include members of the immunoglobulin superfamily, whose products constitute the most diverse group of proteins of vertebrate genomes. Their promiscuous immunoglobulin domains, which comprise the building blocks of these molecules, are involved in a large variety of functions mediated by ligand-binding interactions. The flexible structural nature of the immunoglobulin domains makes them appealing targets for viral capture due to their capacity to generate high functional diversity. Here, we present an up-to-date review of immunoglobulin superfamily gene homologs encoded by herpesviruses, poxviruses, and adenoviruses, that include CD200, CD47, Fc receptors, interleukin-1 receptor 2, interleukin-18 binding protein, CD80, carcinoembryonic antigen-related cell adhesion molecules, and signaling lymphocyte activation molecules. We discuss their distinct structural attributes, binding properties, and functions, shaped by evolutionary pressures to disarm specific immune pathways. We include several novel genes identified from extensive genome database surveys. An understanding of the properties and modes of action of these viral proteins may guide the development of novel immune-modulatory therapeutic tools.
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Affiliation(s)
- Domènec Farré
- Immunology Unit, Department of Biomedical Sciences, Medical School, University of Barcelona, Barcelona, Spain
| | - Pablo Martínez-Vicente
- Immunology Unit, Department of Biomedical Sciences, Medical School, University of Barcelona, Barcelona, Spain
| | - Pablo Engel
- Immunology Unit, Department of Biomedical Sciences, Medical School, University of Barcelona, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Ana Angulo
- Immunology Unit, Department of Biomedical Sciences, Medical School, University of Barcelona, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
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16
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Arriero E, Wanelik KM, Birtles RJ, Bradley JE, Jackson JA, Paterson S, Begon M. From the animal house to the field: Are there consistent individual differences in immunological profile in wild populations of field voles (Microtus agrestis)? PLoS One 2017; 12:e0183450. [PMID: 28817724 PMCID: PMC5560671 DOI: 10.1371/journal.pone.0183450] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 08/06/2017] [Indexed: 12/20/2022] Open
Abstract
Inbred mouse strains, living in simple laboratory environments far removed from nature, have been shown to vary consistently in their immune response. However, wildlife populations are typically outbreeding and face a multiplicity of challenges, parasitological and otherwise. In this study we seek evidence of consistent difference in immunological profile amongst individuals in the wild. We apply a novel method in this context, using longitudinal (repeated capture) data from natural populations of field voles, Microtus agrestis, on a range of life history and infection metrics, and on gene expression levels. We focus on three immune genes, IFN-γ, Gata3, and IL-10, representing respectively the Th1, Th2 and regulatory elements of the immune response. Our results show that there was clear evidence of consistent differences between individuals in their typical level of expression of at least one immune gene, and at most all three immune genes, after other measured sources of variation had been taken into account. Furthermore, individuals that responded to changing circumstances by increasing expression levels of Gata3 had a correlated increase in expression levels of IFN-γ. Our work stresses the importance of acknowledging immunological variation amongst individuals in studies of parasitological and infectious disease risk in wildlife populations.
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Affiliation(s)
- Elena Arriero
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom.,Department of Zoology and Physical Anthropology, University Complutense of Madrid, Madrid, Spain
| | - Klara M Wanelik
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Richard J Birtles
- School of Environment and Life Sciences, University of Salford, Salford, United Kingdom
| | - Janette E Bradley
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Joseph A Jackson
- School of Environment and Life Sciences, University of Salford, Salford, United Kingdom
| | - Steve Paterson
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Mike Begon
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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17
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18
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O'Dea MA, Tu SL, Pang S, De Ridder T, Jackson B, Upton C. Genomic characterization of a novel poxvirus from a flying fox: evidence for a new genus? J Gen Virol 2016; 97:2363-2375. [PMID: 27389615 DOI: 10.1099/jgv.0.000538] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The carcass of an Australian little red flying fox (Pteropus scapulatus) which died following entrapment on a fence was submitted to the laboratory for Australian bat lyssavirus exclusion testing, which was negative. During post-mortem, multiple nodules were noted on the wing membranes, and therefore degenerate PCR primers targeting the poxvirus DNA polymerase gene were used to screen for poxviruses. The poxvirus PCR screen was positive and sequencing of the PCR product demonstrated very low, but significant, similarity with the DNA polymerase gene from members of the Poxviridae family. Next-generation sequencing of DNA extracted from the lesions returned a contig of 132 353 nucleotides (nt), which was further extended to produce a near full-length viral genome of 133 492 nt. Analysis of the genome revealed it to be AT-rich with inverted terminal repeats of at least 1314 nt and to contain 143 predicted genes. The genome contains a surprisingly large number (29) of genes not found in other poxviruses, one of which appears to be a homologue of the mammalian TNF-related apoptosis-inducing ligand (TRAIL) gene. Phylogenetic analysis indicates that the poxvirus described here is not closely related to any other poxvirus isolated from bats or other species, and that it likely should be placed in a new genus.
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Affiliation(s)
- Mark A O'Dea
- School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia
| | - Shin-Lin Tu
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Stanley Pang
- School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia
| | - Thomas De Ridder
- Department of Agriculture and Water Resources, Cairns, Queensland, Australia
| | - Bethany Jackson
- School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia
| | - Chris Upton
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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Ballingall KT, McIntyre A, Lin Z, Timmerman N, Matthysen E, Lurz PW, Melville L, Wallace A, Meredith AL, Romeo C, Wauters LA, Sainsbury AW, McInnes CJ. Limited diversity associated with duplicated class II MHC-DRB genes in the red squirrel population in the United Kingdom compared with continental Europe. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0852-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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20
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Fiegna C, Dagleish M, Coulter L, Milne E, Meredith A, Finlayson J, Di Nardo A, McInnes C. Host-pathogen dynamics of squirrelpox virus infection in red squirrels (Sciurus vulgaris). Vet Microbiol 2016; 182:18-27. [DOI: 10.1016/j.vetmic.2015.10.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/12/2015] [Accepted: 10/13/2015] [Indexed: 11/15/2022]
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21
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Hatcher EL, Wang C, Lefkowitz EJ. Genome variability and gene content in chordopoxviruses: dependence on microsatellites. Viruses 2015; 7:2126-46. [PMID: 25912716 PMCID: PMC4411693 DOI: 10.3390/v7042126] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 03/24/2015] [Accepted: 04/17/2015] [Indexed: 11/20/2022] Open
Abstract
To investigate gene loss in poxviruses belonging to the Chordopoxvirinae subfamily, we assessed the gene content of representative members of the subfamily, and determined whether individual genes present in each genome were intact, truncated, or fragmented. When nonintact genes were identified, the early stop mutations (ESMs) leading to gene truncation or fragmentation were analyzed. Of all the ESMs present in these poxvirus genomes, over 65% co-localized with microsatellites—simple sequence nucleotide repeats. On average, microsatellites comprise 24% of the nucleotide sequence of these poxvirus genomes. These simple repeats have been shown to exhibit high rates of variation, and represent a target for poxvirus protein variation, gene truncation, and reductive evolution.
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Affiliation(s)
- Eneida L Hatcher
- Department of Microbiology, University of Alabama at Birmingham, BBRB 276/11, 845 19th St S, Birmingham, AL 35222, USA.
| | - Chunlin Wang
- Stanford Genome Technology Center, Stanford University, 855 California Ave, Palo Alto, CA 94304, USA.
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, BBRB 276/11, 845 19th St S, Birmingham, AL 35222, USA.
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22
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Affiliation(s)
- Andreas Vilcinskas
- Institute for Phytopathology and Applied Zoology, Justus-Liebig University of Giessen, Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Department of Bioresources, Giessen, Germany
- * E-mail:
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