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Shaw TM, Maloney SM, Nennig K, Ramuta MD, Norton A, Ibarra R, Kuehnert P, Brinton M, Faaberg K, Kuhn JH, O'Connor DH, Warren CJ, Bailey AL. Ectopic expression of murine CD163 enables cell-culture isolation of lactate dehydrogenase-elevating virus 63 years after its discovery. J Virol 2023; 97:e0093023. [PMID: 37792000 PMCID: PMC10617578 DOI: 10.1128/jvi.00930-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/08/2023] [Indexed: 10/05/2023] Open
Abstract
IMPORTANCE Mouse models of viral infection play an especially large role in virology. In 1960, a mouse virus, lactate dehydrogenase-elevating virus (LDV), was discovered and found to have the peculiar ability to evade clearance by the immune system, enabling it to persistently infect an individual mouse for its entire lifespan without causing overt disease. However, researchers were unable to grow LDV in culture, ultimately resulting in the demise of this system as a model of failed immunity. We solve this problem by identifying the cell-surface molecule CD163 as the critical missing component in cell-culture systems, enabling the growth of LDV in immortalized cell lines for the first time. This advance creates abundant opportunities for further characterizing LDV in order to study both failed immunity and the family of viruses to which LDV belongs, Arteriviridae (aka, arteriviruses).
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Affiliation(s)
- Teressa M Shaw
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
| | - Sara M Maloney
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
| | - Kylie Nennig
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
| | - Mitchell D Ramuta
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
| | - Andrew Norton
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
| | - Rodrigo Ibarra
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
| | - Paul Kuehnert
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
| | - Margo Brinton
- Department of Biology, Georgia State University , Atlanta, Georgia, USA
| | - Kay Faaberg
- Virus and Prion Research Unit, USA Department of Agriculture, National Animal Disease Center , Ames, Iowa, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick , Frederick, Maryland, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
| | - Cody J Warren
- Department of Veterinary Biosciences, The Ohio State University , Columbus, Ohio, USA
| | - Adam L Bailey
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
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Staton M, Cannon E, Sanderson LA, Wegrzyn J, Anderson T, Buehler S, Cobo-Simón I, Faaberg K, Grau E, Guignon V, Gunoskey J, Inderski B, Jung S, Lager K, Main D, Poelchau M, Ramnath R, Richter P, West J, Ficklin S. Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases. Brief Bioinform 2021; 22:6318561. [PMID: 34251419 PMCID: PMC8574961 DOI: 10.1093/bib/bbab238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 12/01/2022] Open
Abstract
Online, open access databases for biological knowledge serve as central repositories for research communities to store, find and analyze integrated, multi-disciplinary datasets. With increasing volumes, complexity and the need to integrate genomic, transcriptomic, metabolomic, proteomic, phenomic and environmental data, community databases face tremendous challenges in ongoing maintenance, expansion and upgrades. A common infrastructure framework using community standards shared by many databases can reduce development burden, provide interoperability, ensure use of common standards and support long-term sustainability. Tripal is a mature, open source platform built to meet this need. With ongoing improvement since its first release in 2009, Tripal provides full functionality for searching, browsing, loading and curating numerous types of data and is a primary technology powering at least 31 publicly available databases spanning plants, animals and human data, primarily storing genomics, genetics and breeding data. Tripal software development is managed by a shared, inclusive governance structure including both project management and advisory teams. Here, we report on the most important and innovative aspects of Tripal after 11 years development, including integration of diverse types of biological data, successful collaborative projects across member databases, and support for implementing FAIR principles.
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Affiliation(s)
| | - Ethalinda Cannon
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA USA
| | | | | | | | | | | | - Kay Faaberg
- USDA-ARS, National Animal Disease Center, Ames, IA, USA
| | - Emily Grau
- University of Connecticut, Storrs, CT USA
| | | | | | | | - Sook Jung
- Washington State University, Pullman, WA USA
| | - Kelly Lager
- USDA-ARS, National Animal Disease Center, Ames, IA, USA
| | - Dorrie Main
- Washington State University, Pullman, WA USA
| | - Monica Poelchau
- USDA-ARS, National Agricultural Library, Beltsville, MD, USA
| | | | | | - Joe West
- University of Tennessee, Knoxville, TN USA
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Durie IA, Dzimianski JV, Daczkowski CM, McGuire J, Faaberg K, Pegan SD. Structural insights into the interaction of papain-like protease 2 from the alphacoronavirus porcine epidemic diarrhea virus and ubiquitin. Acta Crystallogr D Struct Biol 2021; 77:943-953. [PMID: 34196620 PMCID: PMC8251346 DOI: 10.1107/s205979832100509x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/13/2021] [Indexed: 01/02/2023] Open
Abstract
Porcine epidemic diarrhea is a devastating porcine disease that is caused by the alphacoronavirus porcine epidemic diarrhea virus (PEDV). Like other members of the Coronaviridae family, PEDV encodes a multifunctional papain-like protease 2 (PLP2) that has the ability to process the coronavirus viral polyprotein to aid in RNA replication and antagonize the host innate immune response through cleavage of the regulatory proteins ubiquitin (Ub) and/or interferon-stimulated gene product 15 (ISG15) (deubiquitination and deISGylation, respectively). Because Betacoronavirus PLPs have been well characterized, it was sought to determine how PLP2 from the alphacoronavirus PEDV differentiates itself from its related counterparts. PEDV PLP2 was first biochemically characterized, and a 3.1 Å resolution crystal structure of PEDV PLP2 bound to Ub was then solved, providing insight into how Alphacoronavirus PLPs bind to their preferred substrate, Ub. It was found that PEDV PLP2 is a deubiquitinase and readily processes a variety of di-Ub linkages, in comparison with its Betacoronavirus counterparts, which have a narrower range of di-Ub activity but process both Ub and ISG15.
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Affiliation(s)
- Ian A. Durie
- Pharmaceutical and Biomedical Sciences, University of Georgia, 240 West Green Street, Athens, GA 30602, USA
| | - John V. Dzimianski
- Pharmaceutical and Biomedical Sciences, University of Georgia, 240 West Green Street, Athens, GA 30602, USA
| | - Courtney M. Daczkowski
- Pharmaceutical and Biomedical Sciences, University of Georgia, 240 West Green Street, Athens, GA 30602, USA
| | - Jack McGuire
- Pharmaceutical and Biomedical Sciences, University of Georgia, 240 West Green Street, Athens, GA 30602, USA
| | - Kay Faaberg
- Virus and Prion Research Unit, USDA–ARS–National Animal Disease Center, Ames, IA 50010, USA
| | - Scott D. Pegan
- Pharmaceutical and Biomedical Sciences, University of Georgia, 240 West Green Street, Athens, GA 30602, USA
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Shi P, Su Y, Li R, Zhang L, Chen C, Zhang L, Faaberg K, Huang J. Dual Regulation of Host TRAIP Post-translation and Nuclear/Plasma Distribution by Porcine Reproductive and Respiratory Syndrome Virus Non-structural Protein 1α Promotes Viral Proliferation. Front Immunol 2018; 9:3023. [PMID: 30619364 PMCID: PMC6305329 DOI: 10.3389/fimmu.2018.03023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 12/06/2018] [Indexed: 12/11/2022] Open
Abstract
In this study, we show that porcine reproductive and respiratory syndrome virus (PRRSV) non-structural protein 1α (nsp1α) facilitates PRRSV escape from innate immune by modulating nuclear to cytoplasmic translocation and distribution ratio of TRAIP to promote virus proliferation. Mechanistically, TRAIP interacts with PRRSV nsp1α via its K205 site, while NSP1α decreases the SUMOylation and K48 ubiquitination independent of the TRAIP interaction K205 site. Modulation of the dual modification of TRAIP by PRRSV nsp1α results in over-enrichment of TRAIP in the cytoplasm. Enrichment of nsp1α-induced cytoplasmic TRAIP in turn leads to excessive K48 ubiquitination and degradation of serine/threonine-protein kinase (TBK1), thereby antagonizing TBK1-IRF3-IFN signaling. This study proposes a novel mechanism by which PRRSV utilizes host proteins to regulate innate immunity. Findings from this study provides novel perspective to advance our understanding in the pathogenesis of PRRSV.
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Affiliation(s)
- Peidian Shi
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Yanxin Su
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Ruiqiao Li
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Lei Zhang
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Chen Chen
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Lilin Zhang
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Kay Faaberg
- Agricultural Research Service, USDA, National Animal Disease Center, Ames, IA, United States
| | - Jinhai Huang
- School of Life Sciences, Tianjin University, Tianjin, China
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Metwally S, Mohamed F, Faaberg K, Burrage T, Prarat M, Moran K, Bracht A, Mayr G, Berninger M, Koster L, To TL, Nguyen VL, Reising M, Landgraf J, Cox L, Lubroth J, Carrillo C. Pathogenicity and molecular characterization of emerging porcine reproductive and respiratory syndrome virus in Vietnam in 2007. Transbound Emerg Dis 2010; 57:315-29. [PMID: 20629970 DOI: 10.1111/j.1865-1682.2010.01152.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In 2007, Vietnam experienced swine disease outbreaks causing clinical signs similar to the 'porcine high fever disease' that occurred in China during 2006. Analysis of diagnostic samples from the disease outbreaks in Vietnam identified porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV-2). Additionally, Escherichia coli and Streptococcus equi subspecies zooepidemicus were cultured from lung and spleen, and Streptococcus suis from one spleen sample. Genetic characterization of the Vietnamese PRRSV isolates revealed that this virus belongs to the North American genotype (type 2) with a high nucleotide identity to the recently reported Chinese strains. Amino acid sequence in the nsp2 region revealed 95.7-99.4% identity to Chinese strain HUN4, 68-69% identity to strain VR-2332 and 58-59% identity to strain MN184. A partial deletion in the nsp2 gene was detected; however, this deletion did not appear to enhance the virus pathogenicity in the inoculated pigs. Animal inoculation studies were conducted to determine the pathogenicity of PRRSV and to identify other possible agents present in the original specimens. Pigs inoculated with PRRSV alone and their contacts showed persistent fever, and two of five pigs developed cough, neurological signs and swollen joints. Necropsy examination showed mild to moderate bronchopneumonia, enlarged lymph nodes, fibrinous pericarditis and polyarthritis. PRRSV was re-isolated from blood and tissues of the inoculated and contact pigs. Pigs inoculated with lung and spleen tissue homogenates from sick pigs from Vietnam developed high fever, septicaemia, and died acutely within 72 h, while their contact pigs showed no clinical signs throughout the experiment. Streptococcus equi subspecies zooepidemicus was cultured, and PRRSV was re-isolated only from the inoculated pigs. Results suggest that the cause of the swine deaths in Vietnam is a multifactorial syndrome with PRRSV as a major factor.
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Affiliation(s)
- S Metwally
- FAO Reference Center for Vesicular Diseases, USDA, APHIS, Foreign Animal Disease Diagnostic Laboratory, National Veterinary Service Laboratories (NVSL), Plum Island Animal Disease Center (PIADC), Greenport, NY, USA.
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Cho JG, Dee SA, Deen J, Trincado C, Fano E, Jiang Y, Faaberg K, Murtaugh MP, Guedes A, Collins JE, Joo HS. The impact of animal age, bacterial coinfection, and isolate pathogenicity on the shedding of porcine reproductive and respiratory syndrome virus in aerosols from experimentally infected pigs. Can J Vet Res 2006; 70:297-301. [PMID: 17042383 PMCID: PMC1562537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The objective of this study was to evaluate the role of different variables (animal age, bacterial coinfection, and isolate pathogenicity) on the shedding of Porcine reproductive and respiratory syndrome virus (PRRSV) in aerosols. Animals were grouped according to age (2 versus 6 mo) and inoculated with a PRRSV isolate of either low (MN-30100) or high (MN-184) pathogenicity. Selected animals in each group were also inoculated with Mycoplasma hyopneumoniae. The pigs were anesthetized and aerosol samples (1000 breaths/sample) collected on alternating days from 1 to 21 after PRRSV inoculation. The results indicated that animal age (P = 0.09), M. hyopneumoniae coinfection (P = 0.09), and PRRSV isolate pathogenicity (P = 0.15) did not significantly influence the concentration of PRRSV in aerosols. However, inoculation with the PRRSV MN-184 isolate significantly increased the probability of aerosol shedding (P = 0.00005; odds ratio = 3.22). Therefore, the shedding of PRRSV in aerosols may be isolate-dependent.
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Affiliation(s)
| | - Scott A. Dee
- Address all correspondence and reprint requests to Dr. Scott A. Dee; telephone: (612) 625-4786; fax: (612) 625-1210; e-mail:
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Cho JG, Dee SA, Deen J, Guedes A, Trincado C, Fano E, Jiang Y, Faaberg K, Collins JE, Murtaugh MP, Joo HS. Evaluation of the effects of animal age, concurrent bacterial infection, and pathogenicity of porcine reproductive and respiratory syndrome virus on virus concentration in pigs. Am J Vet Res 2006; 67:489-93. [PMID: 16506914 DOI: 10.2460/ajvr.67.3.489] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To evaluate the influences of animal age, bacterial coinfection, and porcine reproductive and respiratory syndrome virus (PRRSV) isolate pathogenicity on virus concentration in pigs. ANIMALS Twenty-one 2-month-old pigs and eighteen 6-month-old pigs. PROCEDURE Pigs were grouped according to age and infected with mildly virulent or virulent isolates of PRRSV. The role of concurrent bacterial infection was assessed by infecting selected pigs with Mycoplasma hyopneumoniae 21 days prior to inoculation with PRRSV. On alternating days, blood and swab specimens of nasal secretions and oropharyngeal secretions were collected. On day 21 after inoculation with PRRSV, selected tissues were harvested. Concentrations of PRRSV were determined by use of quantitative real-time PCR and expressed in units of TCID(50) per milliliter (sera and swab specimens) or TCID(50) per gram (tissue specimens). RESULTS Concentrations of virus were higher in blood and tonsils of pigs infected with virulent PRRSV. Pigs infected with virulent PRRSV and M hyopneumoniae had significantly higher concentrations of viral RNA in lymphoid and tonsillar tissue. Coinfection with M hyopneumoniae resulted in a higher viral load in oropharyngeal swab specimens and blood samples, independent of virulence of the PRRSV isolate. Two-month-old pigs had significantly higher viral loads in lymph nodes, lungs, and tracheal swab specimens than did 6-month-old pigs, independent of virulence of the PRRSV isolate. CONCLUSIONS AND CLINICAL RELEVANCE Multiple factors affect PRRSV concentration in pigs, including pathogenicity of the PRRSV isolate, age, and concurrent infection with M hyopneumoniae.
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Affiliation(s)
- Jenny G Cho
- Swine Disease Eradication Center, College of Veterinary Medicine, University of Minnesota, Saint Paul, 55108, USA
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Dee SA, Torremorell M, Rossow K, Mahlum C, Otake S, Faaberg K. Identification of genetically diverse sequences (ORF 5) of porcine reproductive and respiratory syndrome virus in a swine herd. Can J Vet Res 2001; 65:254-60. [PMID: 11768133 PMCID: PMC1189688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
The ability of genetically diverse strains of porcine reproductive and respiratory syndrome virus (PRRSV) to coexist in a 1750-sow farm was assessed through the case study describing a chronically infected farm, and also by an animal experiment involving the use of swine bioassay. The case study employed a program of monitoring sera from suckling, nursery, and finishing pigs for the presence of PRRSV by polymerase chain reaction (PCR) and virus isolation (VI). The swine bioassay tested homogenates, consisting of lymphoid and pulmonary tissues, collected from 60 breeding animals from the same farm. The open reading frame (ORF) 5 portion of selected positive PRRSV detected from sera or tissues were nucleic acid sequenced and their phylogenies compared. The results indicated the presence of 3 genetically diverse groups, designated PRRSV-A, -B, and -C. Sequence heterology ranged from 5.8 to 11% between groups. Sequence homology ranged from 98.7 to 99.8% within groups. Swine bioassay verified the presence of PRRSV-A in 1 of 60 animals, and no evidence of strains B or C were detected. This paper indicates that based on the evaluation of ORF 5, genetically diverse strains of PRRSV appear to coexist, although the frequency and significance of this observation is not understood.
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Affiliation(s)
- S A Dee
- Department of Clinical and Population Sciences, St. Paul, Minnesota 55108, USA.
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