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Mendoza W, Isaza JP, López L, López-Herrera A, Gutiérrez LA. Bovine Leukemia Virus molecular detection and associated factors among dairy herd workers in Antioquia, Colombia. Acta Trop 2024; 256:107253. [PMID: 38782108 DOI: 10.1016/j.actatropica.2024.107253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/18/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024]
Abstract
The Bovine Leukemia Virus (BLV) affects mainly cattle, is transmitted by exposure to contaminated biological fluids, and generates lymphomas in 5 % of infected animals. The zoonotic potential of BLV has been studied, and it is currently unknown if it circulates in human workers on dairy herds in Antioquia. Objective: To determine the frequency of BLV detection, the genotypes of the virus, and the factors associated with its detection in workers for dairy herds in Antioquia, Colombia. Through a cross-sectional study in 51 dairy herds, 164 adults were recruited. A peripheral blood sample was collected from each participant for molecular detection of the BLV env and tax genes, and associated factors were explored through bivariate and multivariate mixed Poisson model analyses. The analysis showed that 82 % (134/164) of the participants were men, with an average age of 40. Using qPCR, the constitutive gene GAPDH was amplified to evaluate the presence of amplification inhibitors in the DNA samples. Using nested PCR, the amplification of the env viral gene was obtained in 13 % (22/164) of the total samples analyzed, while all the samples tested negative for tax. The amplicons of the env gene were sequenced, and the identity compatible with BLV was verified by BLAST analysis (NCBI). Using molecular phylogeny analysis, based on maximum likelihood and haplotype network analysis, it was identified that BLV genotype 1 is present in the evaluated population. 16 % (26/164) of the participants reported having ever had an accident with surgical material during work with cattle; this variable was associated with BLV positivity even after adjusting for other variables (PRa =2.70, 95 % CI= 1.01- 7.21). Considering that other studies have reported the circulation of BLV genotype 1 in cattle from this same region and the present report in humans from dairy herds, the results suggest a possible zoonotic transmission of BLV genotype 1 in Antioquia, reinforcing the need to continue investigating to determine the potential role of this virus as an etiological agent of disease in livestock farmers in the department.
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Affiliation(s)
- Willington Mendoza
- Grupo Biología de Sistemas, Escuela de Ciencias de la Salud, Facultad de Medicina, Universidad Pontificia Bolivariana. Medellín, Colombia
| | - Juan Pablo Isaza
- Grupo Biología de Sistemas, Escuela de Ciencias de la Salud, Facultad de Medicina, Universidad Pontificia Bolivariana. Medellín, Colombia
| | - Lucelly López
- Grupo de Investigación en Salud Pública, Escuela de Ciencias de la Salud, Facultad de Medicina, Universidad Pontificia Bolivariana. Medellín, Colombia
| | - Albeiro López-Herrera
- Grupo de Investigación Biodiversidad y Genética Molecular (BIOGEM), Universidad Nacional de Colombia Sede Medellín, Colombia
| | - Lina A Gutiérrez
- Grupo Biología de Sistemas, Escuela de Ciencias de la Salud, Facultad de Medicina, Universidad Pontificia Bolivariana. Medellín, Colombia.
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Amato S, Ramsey J, Ahern TP, Rovnak J, Barlow J, Weaver D, Eyasu L, Singh R, Cintolo-Gonzalez J. Exploring the presence of bovine leukemia virus among breast cancer tumors in a rural state. Breast Cancer Res Treat 2023; 202:325-334. [PMID: 37517027 DOI: 10.1007/s10549-023-07061-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 05/31/2023] [Indexed: 08/01/2023]
Abstract
PURPOSE The bovine leukemia virus (BLV) is a deltaretrovirus that causes malignant lymphoma and lymphosarcomas in cattle globally and has high prevalence among large scale U.S. dairy herds. Associations between presence of BLV DNA in human mammary tissue and human breast cancer incidence have been reported. We sought to estimate the prevalence of BLV DNA in breast cancer tissue samples in a rural state with an active dairy industry. METHODS We purified genomic DNA from 56 fresh-frozen breast cancer tissue samples (51 tumor samples, 5 samples representing adjacent normal breast tissue) banked between 2016 and 2019. Using nested PCR assays, multiple BLV tax sequence primers and primers for the long terminal repeat (LTR) were used to detect BLV DNA in tissue samples and known positive control samples, including the permanently infected fetal lamb kidney cell line (FLK-BLV) and blood from BLV positive cattle. RESULTS The median age of patients from which samples were obtained at the time of treatment was 60 (40-93) and all were female. Ninety percent of patients had invasive ductal carcinoma. The majority were poorly differentiated (60%). On PCR assay, none of the tumor samples tested positive for BLV DNA, despite having consistent signals in positive controls. CONCLUSION We did not find BLV DNA in fresh-frozen breast cancer tumors from patients presenting to a hospital in Vermont. Our findings suggest a low prevalence of BLV in our patient population and a need to reevaluate the association between BLV and human breast cancer.
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Affiliation(s)
- Stas Amato
- Department of General Surgery, University of Vermont Medical Center, Burlington, VT, USA
- Department of Surgery, Larner College of Medicine, University of Vermont, 89 Beaumont Ave., B227, Burlington, VT, 05405, USA
| | - Jon Ramsey
- Department of Biochemistry, University of Vermont, Burlington, VT, USA
| | - Thomas P Ahern
- Department of Surgery, Larner College of Medicine, University of Vermont, 89 Beaumont Ave., B227, Burlington, VT, 05405, USA
| | - Joel Rovnak
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - John Barlow
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, USA
| | - Donald Weaver
- Department of Pathology, University of Vermont Medical Center, Burlington, VT, USA
| | - Lud Eyasu
- Department of Surgery, Larner College of Medicine, University of Vermont, 89 Beaumont Ave., B227, Burlington, VT, 05405, USA
| | - Rohit Singh
- Division of Hematology/Oncology, Department of Medicine, University of Vermont Medical Center, Burlington, VT, USA
| | - Jessica Cintolo-Gonzalez
- Department of General Surgery, University of Vermont Medical Center, Burlington, VT, USA.
- Department of Surgery, Larner College of Medicine, University of Vermont, 89 Beaumont Ave., B227, Burlington, VT, 05405, USA.
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de Quadros DL, Ribeiro VA, Rezende MA, Maté YA, Gomes MA, Secchi K, Strottmann DM, Frandoloso R, Kreutz LC. Oncogenic viral DNA related to human breast cancer found on cattle milk and meat. Comp Immunol Microbiol Infect Dis 2023; 101:102053. [PMID: 37672958 DOI: 10.1016/j.cimid.2023.102053] [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: 03/10/2023] [Revised: 08/18/2023] [Accepted: 08/26/2023] [Indexed: 09/08/2023]
Abstract
Bovine leukemia virus (BLV) is a major cause of lymphoma in cattle and has been recently correlated to breast cancer in humans. How and whether BLV might reach humans remains unknown but it could be through cattle-derived milk and meat. Here our aim was to investigate whether BLV DNA could be found in fresh milk and raw meat destined to human consumption and whether anti-BLV antibodies could be detected in human blood at the same geographical region. Milk (n = 36) and meat (n = 54) samples were collected from cows knowingly seropositive or negative to BLV and evaluated by nested PCR targeting BLV tax gene. Human serum samples (n = 900) were tested by ELISA to detect anti-BLV antibodies. BLV DNA was detected in 39 % of the milk samples and in 32 % of meat samples from BLV positive cows. Anti-BLV antibodies were found in 4.1 % of the human serum samples. Our data further supports the hypothesis that BLV might cause a zoonotic infection and indicate that milk and meat from BLV-infected cattle might be considered a potential source of infection to humans.
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Affiliation(s)
- Daniel Lazzari de Quadros
- Universidade de Passo Fundo, Escola de Ciências Agrárias, Inovação e Negócios, Programa de Pós-Graduação em Bioexperimentação, Prédio G3, Campus I, Rodovia BR 285, Km 292, Bairro São José, 99052-900 Passo Fundo, RS, Brazil
| | - Vitoria Agnoletto Ribeiro
- Universidade de Passo Fundo, Escola de Ciências Agrárias, Inovação e Negócios, Programa de Pós-Graduação em Bioexperimentação, Prédio G3, Campus I, Rodovia BR 285, Km 292, Bairro São José, 99052-900 Passo Fundo, RS, Brazil
| | - Mariana Antunes Rezende
- Universidade de Passo Fundo, Escola de Ciências Agrárias, Inovação e Negócios, Programa de Pós-Graduação em Bioexperimentação, Prédio G3, Campus I, Rodovia BR 285, Km 292, Bairro São José, 99052-900 Passo Fundo, RS, Brazil
| | - Yasmin Ampese Maté
- Universidade de Passo Fundo, Escola de Ciências Agrárias, Inovação e Negócios, Programa de Pós-Graduação em Bioexperimentação, Prédio G3, Campus I, Rodovia BR 285, Km 292, Bairro São José, 99052-900 Passo Fundo, RS, Brazil
| | - Márcio Alexandro Gomes
- Universidade de Passo Fundo, Escola de Ciências Agrárias, Inovação e Negócios, Programa de Pós-Graduação em Bioexperimentação, Prédio G3, Campus I, Rodovia BR 285, Km 292, Bairro São José, 99052-900 Passo Fundo, RS, Brazil
| | - Katia Secchi
- Universidade de Passo Fundo, Escola de Ciências Agrárias, Inovação e Negócios, Programa de Pós-Graduação em Bioexperimentação, Prédio G3, Campus I, Rodovia BR 285, Km 292, Bairro São José, 99052-900 Passo Fundo, RS, Brazil
| | - Daisy Maria Strottmann
- Laboratório de Virologia Molecular, Instituto Carlos Chagas (ICC/Fiocruz), Rua Prof. Algacyr Munhoz Mader, 3773, CEP 81350-010 Curitiba, PR, Brazil
| | - Rafael Frandoloso
- Universidade de Passo Fundo, Escola de Ciências Agrárias, Inovação e Negócios, Programa de Pós-Graduação em Bioexperimentação, Prédio G3, Campus I, Rodovia BR 285, Km 292, Bairro São José, 99052-900 Passo Fundo, RS, Brazil
| | - Luiz Carlos Kreutz
- Universidade de Passo Fundo, Escola de Ciências Agrárias, Inovação e Negócios, Programa de Pós-Graduação em Bioexperimentação, Prédio G3, Campus I, Rodovia BR 285, Km 292, Bairro São José, 99052-900 Passo Fundo, RS, Brazil.
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Dos Santos DRL, Silva-Sales M, Fumian TM, Maranhão AG, Malta FC, Ferreira FC, Pimenta MM, Miagostovich MP. Investigation of Human and Animal Viruses in Water Matrices from a Rural Area in Southeastern Region of Brazil and Their Potential Use as Microbial Source-Tracking Markers. FOOD AND ENVIRONMENTAL VIROLOGY 2023; 15:21-31. [PMID: 36629977 DOI: 10.1007/s12560-022-09544-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
This study assessed the sources of contamination of water matrices in a rural area using detection of a host-specific virus (human adenovirus [HAdV], porcine adenovirus [PAdV] and bovine polyomaviruses [BoPyV]) as potential microbial source-tracking tool, and rotavirus A [RVA], given its epidemiological importance in Brazil. From July 2017 to June 2018, 92 samples were collected from eight points (P1-P8) of surface and raw waters in southeastern region of Brazil. Fifty-five (59.8%) were positive for HAdV, 41 (44.5%) for RVA, 10 (10.9%) for PAdV and four (4.3%) for BoPyV. HAdV and RVA were detected at all sites, and over the entire sampling period, PAdV was detected at a porcine breeding area and at Guarda River site, presenting high concentrations up to 2.6 × 109 genome copies per liter [GC/L], and viral concentrations ranging from 9.6 × 101 to 7.1 × 107, while BoPyV (1.5 × 104 GC/L-9.2 × 105 GC/L) was only detected in samples from the bovine breeding areas. The combination of human and animal virus circulation presents a potential impact in the environment due to raw sewage discharge from regional communities, as well as potential hazard to human and animal health.
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Affiliation(s)
- Debora Regina Lopes Dos Santos
- Department of Veterinary Microbiology and Immunology, Universidade Federal Rural Do Rio de Janeiro, Seropédica, Rio de Janeiro, Brazil.
| | - Marcelle Silva-Sales
- Institute of Public Health and Tropical Pathology, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Tulio Machado Fumian
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Adriana Gonçalves Maranhão
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Fábio Correia Malta
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Fernando César Ferreira
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Marcia Maria Pimenta
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Marize Pereira Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
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Bovine Polyomavirus-1 (Epsilonpolyomavirus bovis): An Emerging Fetal Pathogen of Cattle That Causes Renal Lesions Resembling Polyomavirus-Associated Nephropathy of Humans. Viruses 2022; 14:v14092042. [PMID: 36146848 PMCID: PMC9502773 DOI: 10.3390/v14092042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
Abstract
Bovine polyomavirus-1 (BoPyV-1, Epsilonpolyomavirus bovis) is widespread in cattle and has been detected in commercialized beef at supermarkets in the USA and Germany. BoPyV-1 has been questioned as a probable zoonotic agent with documented increase in seropositivity in people exposed to cattle. However, to date, BoPyV-1 has not been causally associated with pathology or disease in any animal species, including humans. Here we describe and illustrate pathological findings in an aborted bovine fetus naturally infected with BoPyV-1, providing evidence of its pathogenicity and probable abortigenic potential. Our results indicate that: (i) BoPyV-1 can cause severe kidney lesions in cattle, including tubulointerstitial nephritis with cytopathic changes and necrosis in tubular epithelial cells, tubular and interstitial inflammation, and interstitial fibroplasia; (ii) lesions are at least partly attributable to active viral replication in renal tubular epithelial cells, which have abundant intranuclear viral inclusions; (iii) BoPyV-1 large T (LT) antigen, resulting from early viral gene expression, can be detected in infected renal tubular epithelial cells using a monoclonal antibody raised against Simian Virus-40 polyomavirus LT antigen; and (iv) there is productive BoPyV-1 replication and virion assembly in the nuclei of renal tubular epithelial cells, as demonstrated by the ultrastructural observation of abundant arrays of viral particles with typical polyomavirus morphology. Altogether, these lesions resemble the “cytopathic-inflammatory pathology pattern” proposed in the pathogenesis of Human polyomavirus-1-associated nephropathy in immunocompromised people and kidney allograft recipients. Additionally, we sequenced the complete genome of the BoPyV-1 infecting the fetus, which represents the first whole genome of a BoPyV-1 from the Southern Hemisphere. Lastly, the BoPyV-1 strain infecting this fetus was isolated, causing a cytopathic effect in Madin–Darby bovine kidney cells. We conclude that BoPyV-1 is pathogenic to the bovine fetus under natural circumstances. Further insights into the epidemiology, biology, clinical relevance, and zoonotic potential of BoPyV-1 are needed.
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Cammarata RV, Barrios ME, Díaz SM, García López G, Fortunato MS, Torres C, Blanco Fernández MD, Mbayed VA. Assessment of Microbiological Quality of Fresh Vegetables and Oysters Produced in Buenos Aires Province, Argentina. FOOD AND ENVIRONMENTAL VIROLOGY 2021; 13:507-519. [PMID: 34449055 DOI: 10.1007/s12560-021-09496-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
Fresh vegetables and shellfish are prone to microbial contamination through irrigation or breeding with sewage-polluted waters, as well as by infected food handlers. In this work, we studied the presence of human and bovine polyomaviruses and human norovirus in fresh lettuces, strawberries and oysters produced in Buenos Aires province, Argentina. In oysters, we also investigated F-specific RNA bacteriophages, indicator Escherichia coli (E. coli) and pathogen bacteria of concern (Salmonella spp., Vibrio spp.). Within vegetables, we found viral contamination of human origin given the presence of human-associated polyomaviruses -MCPyV, HPyV6, JCPyV, and SV40- in lettuce and strawberry samples (16 and 10%, respectively), probably coming from irrigation waters and food handling. Among oysters, human (MCPyV, 4.2%) and bovine (BPyV1, 8.4%) polyomaviruses were detected even with low counts of E. coli. Bacteriophages (n = 3) and Salmonella spp. (n = 1) were also found, while Vibrio spp. was not detected. These results may indicate that the contamination in oysters comes from human and animal excreta, probably present in breeding waters. Norovirus was not detected in any food sample. To our knowledge, this is the first description of SV40 in lettuces and MCPyV and BPyV1 in oysters. The detection of different viral contaminants encourages further studies to evaluate the need for including viral indicators in microbiological standards. The identification of possible sources and routes of contamination using viral markers during routine microbiological controls, such as the polyomaviruses used in this work, would be useful to focus attention on the most hazardous stages of the food production chain.
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Affiliation(s)
- Robertina Viviana Cammarata
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Junín 956, 1113, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, 1425, Buenos Aires, Argentina
| | - Melina Elizabeth Barrios
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Junín 956, 1113, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, 1425, Buenos Aires, Argentina
| | - Sofía Micaela Díaz
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Junín 956, 1113, Buenos Aires, Argentina
- Agencia Nacional de Promoción Científica y Tecnológica, Ministerio de Ciencia y Tecnología, Godoy Cruz 2370, 1425, Buenos Aires, Argentina
| | - Guadalupe García López
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica. Cátedra de Salud Pública e Higiene Ambiental, Junín 956, 1113, Buenos Aires, Argentina
| | - María Susana Fortunato
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica. Cátedra de Salud Pública e Higiene Ambiental, Junín 956, 1113, Buenos Aires, Argentina
| | - Carolina Torres
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Junín 956, 1113, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, 1425, Buenos Aires, Argentina
| | - María Dolores Blanco Fernández
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Junín 956, 1113, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, 1425, Buenos Aires, Argentina
| | - Viviana Andrea Mbayed
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Junín 956, 1113, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, 1425, Buenos Aires, Argentina.
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Bovine Polyomavirus 2 is a Probable Cause of Non-Suppurative Encephalitis in Cattle. Pathogens 2020; 9:pathogens9080620. [PMID: 32751201 PMCID: PMC7459705 DOI: 10.3390/pathogens9080620] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/26/2020] [Accepted: 07/27/2020] [Indexed: 12/22/2022] Open
Abstract
Tissues from two cows with neurological signs that were admitted to the Vetsuisse Faculty under suspicion of rabies and bovine spongiform encephalopathy (BSE), respectively, were further analyzed for this case report. After histopathological examination and exclusion of BSE and rabies, the animals were diagnosed with etiologically unresolved disseminated non-suppurative encephalitis. Using next-generation sequencing, we detected the full genome of bovine polyomavirus 2 (BoPyV2) in brain samples from both animals. This virus has been identified in beef samples in three independent studies conducted in the United States and Germany, but has not been linked to any disease. Analysis of the two new BoPyV2 genome sequences revealed close phylogenetic relationships to one another and to BoPyV2 isolates detected in beef samples. In situ hybridization demonstrated the presence of viral nucleic acid in all investigated brain areas and in areas with signs of inflammation in both animals. Thus, we provide the first evidence that BoPyV2 is a probable cause of non-suppurative encephalitis in cattle, and encourage further molecular and serological testing to elucidate the disease's epidemiology, as well as experimental transmission studies to prove causality between the infection and disease.
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Fishman JA. Prevention of infection in xenotransplantation: Designated pathogen‐free swine in the safety equation. Xenotransplantation 2020; 27:e12595. [DOI: 10.1111/xen.12595] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/06/2020] [Accepted: 02/18/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Jay A. Fishman
- MGH Transplant Center Transplantation Infectious Disease and Compromised Host Program Infectious Disease Division Massachusetts General Hospital Boston MA USA
- Harvard Medical School Boston MA USA
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Tisza MJ, Pastrana DV, Welch NL, Stewart B, Peretti A, Starrett GJ, Pang YYS, Krishnamurthy SR, Pesavento PA, McDermott DH, Murphy PM, Whited JL, Miller B, Brenchley J, Rosshart SP, Rehermann B, Doorbar J, Ta'ala BA, Pletnikova O, Troncoso JC, Resnick SM, Bolduc B, Sullivan MB, Varsani A, Segall AM, Buck CB. Discovery of several thousand highly diverse circular DNA viruses. eLife 2020; 9:51971. [PMID: 32014111 PMCID: PMC7000223 DOI: 10.7554/elife.51971] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/06/2020] [Indexed: 12/18/2022] Open
Abstract
Although millions of distinct virus species likely exist, only approximately 9000 are catalogued in GenBank's RefSeq database. We selectively enriched for the genomes of circular DNA viruses in over 70 animal samples, ranging from nematodes to human tissue specimens. A bioinformatics pipeline, Cenote-Taker, was developed to automatically annotate over 2500 complete genomes in a GenBank-compliant format. The new genomes belong to dozens of established and emerging viral families. Some appear to be the result of previously undescribed recombination events between ssDNA and ssRNA viruses. In addition, hundreds of circular DNA elements that do not encode any discernable similarities to previously characterized sequences were identified. To characterize these ‘dark matter’ sequences, we used an artificial neural network to identify candidate viral capsid proteins, several of which formed virus-like particles when expressed in culture. These data further the understanding of viral sequence diversity and allow for high throughput documentation of the virosphere. When scientists hunt for new DNA sequences, sometimes they get a lot more than they bargained for. Such is the case in metagenomic surveys, which analyze not just DNA of a particular organism, but all the DNA in an environment at large. A vexing problem with these surveys is the overwhelming number of DNA sequences detected that are so different from any known microbe that they cannot be classified using traditional approaches. However, some of these “known unknowns” are undoubtedly viral sequences, because only a fraction of the enormous diversity of viruses has been characterized. This “viral dark matter” is a major obstacle for those studying viruses. This led Tisza et al. to attempt to classify some of the unknown viral sequences in their metagenomic surveys. The search, which specifically focused on viruses with circular DNA genomes, detected over 2,500 circular viral genomes. Intensive analysis revealed that many of these genomes had similar makeup to previously discovered viruses, but hundreds of them were totally different from any known virus, based on typical methods of comparison. Computational analysis of genes that were conserved among some of these brand-new circular sequences often revealed virus-like features. Experiments on a few of these genes showed that they encoded proteins capable of forming particles reminiscent of characteristic viral shells, implying that these new sequences are indeed viruses. Tisza et al. have added the 2,500 newly characterized viral sequences to the publicly accessible GenBank database, and the sequences are being considered for the more authoritative RefSeq database, which currently contains around 9,000 complete viral genomes. The expanded databases will hopefully now better equip scientists to explore the enormous diversity of viruses and help medics and veterinarians to detect disease-causing viruses in humans and other animals.
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Affiliation(s)
- Michael J Tisza
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Diana V Pastrana
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Nicole L Welch
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Brittany Stewart
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Alberto Peretti
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Gabriel J Starrett
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Yuk-Ying S Pang
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Siddharth R Krishnamurthy
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - Patricia A Pesavento
- Department of Pathology, Microbiology, and Immunology, University of California, Davis, Davis, United States
| | - David H McDermott
- Molecular Signaling Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - Philip M Murphy
- Molecular Signaling Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - Jessica L Whited
- Department of Orthopedic Surgery, Harvard Medical School, The Harvard Stem Cell Institute, Brigham and Women's Hospital, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, United States
| | - Bess Miller
- Department of Orthopedic Surgery, Harvard Medical School, The Harvard Stem Cell Institute, Brigham and Women's Hospital, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Jason Brenchley
- Barrier Immunity Section, Lab of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Cambridge, United States
| | - Stephan P Rosshart
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Barbara Rehermann
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - John Doorbar
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | | | - Olga Pletnikova
- Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, United States
| | - Juan C Troncoso
- Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, United States
| | - Susan M Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, United States
| | - Ben Bolduc
- Department of Microbiology, Ohio State University, Columbus, United States
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, United States.,Civil Environmental and Geodetic Engineering, Ohio State University, Columbus, United States
| | - Arvind Varsani
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, United States.,Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, South Africa
| | - Anca M Segall
- Viral Information Institute and Department of Biology, San Diego State University, San Diego, United States
| | - Christopher B Buck
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
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10
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de Villiers EM, Gunst K, Chakraborty D, Ernst C, Bund T, Zur Hausen H. A specific class of infectious agents isolated from bovine serum and dairy products and peritumoral colon cancer tissue. Emerg Microbes Infect 2019; 8:1205-1218. [PMID: 31409221 PMCID: PMC6713099 DOI: 10.1080/22221751.2019.1651620] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The in silico analyses of 109 replication-competent genomic DNA sequences isolated from cow milk and its products (97 in the bovine meat and milk factors 2 group – BMMF2, and additional 4 in BMMF1) seems to place these in a specific class of infectious agents spanning between bacterial plasmid and circular ssDNA viruses. Satellite-type small plasmids with partial homology to larger genomes, were also isolated in both groups. A member of the BMMF1 group H1MBS.1 was recovered in a distinctly modified form from colon tissue by laser microdissection. Although the evolutionary origin is unknown, it draws the attention to the existence of a hitherto unrecognized, broad spectrum of potential pathogens. Indirect hints to the origin and structure of our isolates, as well as to their replicative behaviour, result from parallels drawn to the Hepatitis deltavirus genome structure and replication.
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Affiliation(s)
- Ethel-Michele de Villiers
- a Episomal-Persistent DNA in Cancer- and Chronic Diseases, Deutsches Krebsforschungszentrum , Heidelberg , Germany
| | - Karin Gunst
- a Episomal-Persistent DNA in Cancer- and Chronic Diseases, Deutsches Krebsforschungszentrum , Heidelberg , Germany
| | - Deblina Chakraborty
- a Episomal-Persistent DNA in Cancer- and Chronic Diseases, Deutsches Krebsforschungszentrum , Heidelberg , Germany
| | - Claudia Ernst
- a Episomal-Persistent DNA in Cancer- and Chronic Diseases, Deutsches Krebsforschungszentrum , Heidelberg , Germany
| | - Timo Bund
- a Episomal-Persistent DNA in Cancer- and Chronic Diseases, Deutsches Krebsforschungszentrum , Heidelberg , Germany
| | - Harald Zur Hausen
- a Episomal-Persistent DNA in Cancer- and Chronic Diseases, Deutsches Krebsforschungszentrum , Heidelberg , Germany
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11
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Abstract
PURPOSE OF REVIEW Posttransplantation infections are common. It is anticipated that infection will be no less common in xenotransplantation recipients. Prolonged xenograft survivals have resulted from advances in immunosuppressive strategies and development of swine that decrease host immune responses via genetic manipulation, notably CRISPR/cas9 manipulation. As prospects for clinical trials improve, consideration of the unique infectious risks posed by xenotransplantation reemerge. RECENT FINDINGS Organisms likely to cause infection in human recipients of porcine xenografts are unknown in advance of clinical trials. Microbiological screening of swine intended as xenograft donors can be more intensive than is currently feasible for human allograft donors. Monitoring infection in recipients will also be more intensive. Key opportunities in infectious diseases of xenotransplantation include major technological advances in evaluation of the microbiome by unbiased metagenomic sequencing, assessments of some risks posed by porcine endogenous retroviruses (PERVs) including antiretroviral susceptibilities, availability of swine with deletion of genomic PERVs, and recognition of the rapidly changing epidemiology of infection in swine worldwide. SUMMARY Unknown infectious risks in xenotransplantation requires application of advanced microbiological techniques to discern and prevent infection in graft recipients. Clinical trials will provide an opportunity to advance the safety of all of organ transplantation.
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Affiliation(s)
- Jay A Fishman
- Transplantation Infectious Disease and Compromised Host Program, Infectious Disease Division and MGH Transplant Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
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12
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Viral metagenomics reveals significant viruses in the genital tract of apparently healthy dairy cows. Arch Virol 2019; 164:1059-1067. [PMID: 30783771 DOI: 10.1007/s00705-019-04158-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 01/03/2019] [Indexed: 01/03/2023]
Abstract
The virome in genital tract secretion samples collected from 80 dairy cattle in Shanghai, China, was characterized. Viruses detected included members of the families Papillomaviridae, Polyomaviridae, Hepeviridae, Parvoviridae, Astroviridae, Picornaviridae, and Picobirnaviridae. A member of a new species within the genus Dyoxipapillomavirus and six circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) viral genomes were fully sequenced and phylogenetically analyzed. The prevalence of bovine polyomaviruses 1 and 2 was measured by PCR to be 10% (8/80) and 6.25% (5/80), respectively. PCR screening also indicated that the novel papillomavirus ujs-21015 and bovine herpesvirus 6 were present in three and two out of the 80 samples, respectively.
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13
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McDermott DH, Pastrana DV, Calvo KR, Pittaluga S, Velez D, Cho E, Liu Q, Trout HH, Neves JF, Gardner PJ, Bianchi DA, Blair EA, Landon EM, Silva SL, Buck CB, Murphy PM. Plerixafor for the Treatment of WHIM Syndrome. N Engl J Med 2019; 380:163-170. [PMID: 30625055 PMCID: PMC6425947 DOI: 10.1056/nejmoa1808575] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
WHIM syndrome (warts, hypogammaglobulinemia, infections, and myelokathexis), a primary immunodeficiency disorder involving panleukopenia, is caused by autosomal dominant gain-of-function mutations in CXC chemokine receptor 4 (CXCR4). Myelokathexis is neutropenia caused by neutrophil retention in bone marrow. Patients with WHIM syndrome are often treated with granulocyte colony-stimulating factor (G-CSF), which can increase neutrophil counts but does not affect cytopenias other than neutropenia. In this investigator-initiated, open-label study, three severely affected patients with WHIM syndrome who could not receive G-CSF were treated with low-dose plerixafor, a CXCR4 antagonist, for 19 to 52 months. Myelofibrosis, panleukopenia, anemia, and thrombocytopenia were ameliorated, the wart burden and frequency of infection declined, human papillomavirus-associated oropharyngeal squamous-cell carcinoma stabilized, and quality of life improved markedly. Adverse events were mainly infections attributable to the underlying immunodeficiency. One patient died from complications of elective reconstructive surgery. (Funded by the National Institutes of Health.).
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Affiliation(s)
- David H McDermott
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Diana V Pastrana
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Katherine R Calvo
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Stefania Pittaluga
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Daniel Velez
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Elena Cho
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Qian Liu
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Hugh H Trout
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - João F Neves
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Pamela J Gardner
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - David A Bianchi
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Elizabeth A Blair
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Emily M Landon
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Susana L Silva
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Christopher B Buck
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Philip M Murphy
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
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14
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Abstract
Although some members of the viral family Papillomaviridae cause benign skin warts (papillomas), many human papillomavirus (HPV) infections are not associated with visible symptoms. For example, most healthy adults chronically shed Gammapapillomavirus (Gamma) virions from apparently healthy skin surfaces. To further explore the diversity of papillomaviruses, we performed viromic surveys on immunodeficient individuals suffering from florid skin warts. Our results nearly double the number of known Gamma HPV types and suggest that WHIM syndrome patients are uniquely susceptible to Gamma HPV-associated skin warts. Preliminary results suggest that treatment with the drug plerixafor may promote resolution of the unusual Gamma HPV skin warts observed in WHIM patients. Several immunodeficiencies are associated with high susceptibility to persistent and progressive human papillomavirus (HPV) infection leading to a wide range of cutaneous and mucosal lesions. However, the HPV types most commonly associated with such clinical manifestations in these patients have not been systematically defined. Here, we used virion enrichment, rolling circle amplification, and deep sequencing to identify circular DNA viruses present in skin swabs and/or wart biopsy samples from 48 patients with rare genetic immunodeficiencies, including patients with warts, hypogammaglobulinemia, infections, myelokathexis (WHIM) syndrome, or epidermodysplasia verruciformis (EV). Their profiles were compared with the profiles of swabs from 14 healthy adults and warts from 6 immunologically normal children. Individual patients were typically infected with multiple HPV types; up to 26 different types were isolated from a single patient (multiple anatomical sites, one time point). Among these, we identified the complete genomes of 83 previously unknown HPV types and 35 incomplete genomes representing possible additional new types. HPV types in the genus Gammapapillomavirus were common in WHIM patients, whereas EV patients mainly shed HPVs from the genus Betapapillomavirus. Preliminary evidence based on three WHIM patients treated with plerixafor, a leukocyte mobilizing agent, suggest that longer-term therapy may correlate with decreased HPV diversity and increased predominance of HPV types associated with childhood skin warts. IMPORTANCE Although some members of the viral family Papillomaviridae cause benign skin warts (papillomas), many human papillomavirus (HPV) infections are not associated with visible symptoms. For example, most healthy adults chronically shed Gammapapillomavirus (Gamma) virions from apparently healthy skin surfaces. To further explore the diversity of papillomaviruses, we performed viromic surveys on immunodeficient individuals suffering from florid skin warts. Our results nearly double the number of known Gamma HPV types and suggest that WHIM syndrome patients are uniquely susceptible to Gamma HPV-associated skin warts. Preliminary results suggest that treatment with the drug plerixafor may promote resolution of the unusual Gamma HPV skin warts observed in WHIM patients.
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15
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Viral tools for detection of fecal contamination and microbial source tracking in wastewater from food industries and domestic sewage. J Virol Methods 2018; 262:79-88. [PMID: 30336954 DOI: 10.1016/j.jviromet.2018.10.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/28/2018] [Accepted: 10/07/2018] [Indexed: 12/27/2022]
Abstract
Alternative indicators may be more suitable than thermotolerant coliform bacteria to assess enteric virus pollution in environmental waters and their removal from wastewaters. In this study, F-specific RNA bacteriophages (F-RNAPh) showed to be potential viral indicators of fecal contamination when they were quantified from domestic and food-industrial effluents containing human, chicken, swine or bovine wastes. In addition, they showed to be resistant to the primary and secondary treatments of the wastewater treatment plants. The viable F-RNAPh count showed correlation with viable thermotolerant coliforms but also with human polyomaviruses (HPyV) quantified by a new molecular method. In domestic effluents, F-RNAPh and HPyV indicators significantly correlated with a human viral pathogen, norovirus, while the bacterial indicator did not, being then better predictors of the behavior of enteric pathogenic viruses. In addition, we assessed human, bovine and fowl microbial source tracking markers, based on the molecular detections of human polyomavirus, bovine polyomavirus, and fowl adenovirus, respectively. The techniques implemented extend the range of viruses detected, since they target different viral types simultaneously. These markers could be applied when multiple source pollution is suspected, contributing to making decisions on public health interventions.
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16
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Peretti A, Geoghegan EM, Pastrana DV, Smola S, Feld P, Sauter M, Lohse S, Ramesh M, Lim ES, Wang D, Borgogna C, FitzGerald PC, Bliskovsky V, Starrett GJ, Law EK, Harris RS, Killian JK, Zhu J, Pineda M, Meltzer PS, Boldorini R, Gariglio M, Buck CB. Characterization of BK Polyomaviruses from Kidney Transplant Recipients Suggests a Role for APOBEC3 in Driving In-Host Virus Evolution. Cell Host Microbe 2018; 23:628-635.e7. [PMID: 29746834 PMCID: PMC5953553 DOI: 10.1016/j.chom.2018.04.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 12/05/2017] [Accepted: 03/19/2018] [Indexed: 12/31/2022]
Abstract
BK polyomavirus (BKV) frequently causes nephropathy (BKVN) in kidney transplant recipients (KTRs). BKV has also been implicated in the etiology of bladder and kidney cancers. We characterized BKV variants from two KTRs who developed BKVN followed by renal carcinoma. Both patients showed a swarm of BKV sequence variants encoding non-silent mutations in surface loops of the viral major capsid protein. The temporal appearance and disappearance of these mutations highlights the intra-patient evolution of BKV. Some of the observed mutations conferred resistance to antibody-mediated neutralization. The mutations also modified the spectrum of receptor glycans engaged by BKV during host cell entry. Intriguingly, all observed mutations were consistent with DNA damage caused by antiviral APOBEC3 cytosine deaminases. Moreover, APOBEC3 expression was evident upon immunohistochemical analysis of renal biopsies from KTRs. These results provide a snapshot of in-host BKV evolution and suggest that APOBEC3 may drive BKV mutagenesis in vivo.
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Affiliation(s)
- Alberto Peretti
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eileen M Geoghegan
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Diana V Pastrana
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sigrun Smola
- Institute of Virology, Saarland University, Homburg/Saar 66421, Germany
| | - Pascal Feld
- Institute of Virology, Saarland University, Homburg/Saar 66421, Germany
| | - Marlies Sauter
- Institute of Virology, Saarland University, Homburg/Saar 66421, Germany
| | - Stefan Lohse
- Institute of Virology, Saarland University, Homburg/Saar 66421, Germany
| | - Mayur Ramesh
- Division of Infectious Diseases, Henry Ford Hospital, Detroit, MI 48202 USA
| | - Efrem S Lim
- Departments of Molecular Microbiology and Pathology & Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - David Wang
- Departments of Molecular Microbiology and Pathology & Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Cinzia Borgogna
- Virology Unit, Department of Translational Medicine, Novara Medical School, Novara 28100, Italy
| | - Peter C FitzGerald
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Valery Bliskovsky
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gabriel J Starrett
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Emily K Law
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - J Keith Killian
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jack Zhu
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marbin Pineda
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul S Meltzer
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Renzo Boldorini
- Pathology Unit, Department of Health Sciences, Novara Medical School, Novara 28100, Italy
| | - Marisa Gariglio
- Virology Unit, Department of Translational Medicine, Novara Medical School, Novara 28100, Italy
| | - Christopher B Buck
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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17
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Panou MM, Prescott EL, Hurdiss DL, Swinscoe G, Hollinshead M, Caller LG, Morgan EL, Carlisle L, Müller M, Antoni M, Kealy D, Ranson NA, Crump CM, Macdonald A. Agnoprotein Is an Essential Egress Factor during BK Polyomavirus Infection. Int J Mol Sci 2018; 19:ijms19030902. [PMID: 29562663 PMCID: PMC5877763 DOI: 10.3390/ijms19030902] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/13/2018] [Accepted: 03/14/2018] [Indexed: 12/16/2022] Open
Abstract
BK polyomavirus (BKPyV; hereafter referred to as BK) causes a lifelong chronic infection and is associated with debilitating disease in kidney transplant recipients. Despite its importance, aspects of the virus life cycle remain poorly understood. In addition to the structural proteins, the late region of the BK genome encodes for an auxiliary protein called agnoprotein. Studies on other polyomavirus agnoproteins have suggested that the protein may contribute to virion infectivity. Here, we demonstrate an essential role for agnoprotein in BK virus release. Viruses lacking agnoprotein fail to release from host cells and do not propagate to wild-type levels. Despite this, agnoprotein is not essential for virion infectivity or morphogenesis. Instead, agnoprotein expression correlates with nuclear egress of BK virions. We demonstrate that the agnoprotein binding partner α-soluble N-ethylmaleimide sensitive fusion (NSF) attachment protein (α-SNAP) is necessary for BK virion release, and siRNA knockdown of α-SNAP prevents nuclear release of wild-type BK virions. These data highlight a novel role for agnoprotein and begin to reveal the mechanism by which polyomaviruses leave an infected cell.
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Affiliation(s)
- Margarita-Maria Panou
- Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
| | - Emma L Prescott
- Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
| | - Daniel L Hurdiss
- Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
| | - Gemma Swinscoe
- Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
| | - Michael Hollinshead
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK.
| | - Laura G Caller
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK.
| | - Ethan L Morgan
- Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
| | - Louisa Carlisle
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK.
| | - Marietta Müller
- Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
| | - Michelle Antoni
- Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
| | - David Kealy
- Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
| | - Neil A Ranson
- Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
| | - Colin M Crump
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK.
| | - Andrew Macdonald
- Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
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18
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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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19
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Identification of a Second Raccoon-Associated Polyomavirus. GENOME ANNOUNCEMENTS 2017; 5:5/26/e00548-17. [PMID: 28663292 PMCID: PMC5638276 DOI: 10.1128/genomea.00548-17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Raccoon polyomavirus 1 (RacPyV1) is the suspected cause of an outbreak of fatal brain tumors among raccoons (Procyon lotor) in the western United States. Spleen samples from Georgia raccoons were screened for polyomaviruses. Although RacPyV1 was not detected, a previously unknown polyomavirus, which we designate RacPyV2, was identified and sequenced.
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20
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Detection and genome characterization of bovine polyomaviruses in beef muscle and ground beef samples from Germany. Int J Food Microbiol 2017; 241:168-172. [DOI: 10.1016/j.ijfoodmicro.2016.10.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/05/2016] [Accepted: 10/19/2016] [Indexed: 11/17/2022]
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21
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Nguyen KD, Lee EE, Yue Y, Stork J, Pock L, North JP, Vandergriff T, Cockerell C, Hosler GA, Pastrana DV, Buck CB, Wang RC. Human polyomavirus 6 and 7 are associated with pruritic and dyskeratotic dermatoses. J Am Acad Dermatol 2016; 76:932-940.e3. [PMID: 28040372 DOI: 10.1016/j.jaad.2016.11.035] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/08/2016] [Accepted: 11/15/2016] [Indexed: 01/21/2023]
Abstract
BACKGROUND Human polyomavirus (HPyV)6 and HPyV7 are shed chronically from human skin. HPyV7, but not HPyV6, has been linked to a pruritic skin eruption of immunosuppression. OBJECTIVE We determined whether biopsy specimens showing a characteristic pattern of dyskeratosis and parakeratosis might be associated with polyomavirus infection. METHODS We screened biopsy specimens showing "peacock plumage" histology by polymerase chain reaction for HPyVs. Cases positive for HPyV6 or HPyV7 were then analyzed by immunohistochemistry, electron microscopy, immunofluorescence, quantitative polymerase chain reaction, and complete sequencing, including unbiased, next-generation sequencing. RESULTS We identified 3 additional cases of HPyV6 or HPyV7 skin infections. Expression of T antigen and viral capsid was abundant in lesional skin. Dual immunofluorescence staining experiments confirmed that HPyV7 primarily infects keratinocytes. High viral loads in lesional skin compared with normal-appearing skin and the identification of intact virions by both electron microscopy and next-generation sequencing support a role for active viral infections in these skin diseases. LIMITATION This was a small case series of archived materials. CONCLUSION We have found that HPyV6 and HPyV7 are associated with rare, pruritic skin eruptions with a distinctive histologic pattern and describe this entity as "HPyV6- and HPyV7-associated pruritic and dyskeratotic dermatoses."
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Affiliation(s)
- Khang D Nguyen
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Eunice E Lee
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yangbo Yue
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jiri Stork
- Dermatohistopathological Laboratory, Charles University in Prague, Prague, Czech Republic
| | - Lumir Pock
- Bioptical Laboratory, Pilsen, Czech Republic
| | - Jeffrey P North
- Dermatology and Pathology, University of California, San Francisco, California
| | - Travis Vandergriff
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Clay Cockerell
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, Texas; Cockerell Dermatopathology, Dallas, Texas
| | - Gregory A Hosler
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, Texas; ProPath, Dallas, Texas
| | | | | | - Richard C Wang
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, Texas.
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22
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Ronholm J, Nasheri N, Petronella N, Pagotto F. Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing. Clin Microbiol Rev 2016; 29:837-57. [PMID: 27559074 PMCID: PMC5010751 DOI: 10.1128/cmr.00056-16] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The epidemiological investigation of a foodborne outbreak, including identification of related cases, source attribution, and development of intervention strategies, relies heavily on the ability to subtype the etiological agent at a high enough resolution to differentiate related from nonrelated cases. Historically, several different molecular subtyping methods have been used for this purpose; however, emerging techniques, such as single nucleotide polymorphism (SNP)-based techniques, that use whole-genome sequencing (WGS) offer a resolution that was previously not possible. With WGS, unlike traditional subtyping methods that lack complete information, data can be used to elucidate phylogenetic relationships and disease-causing lineages can be tracked and monitored over time. The subtyping resolution and evolutionary context provided by WGS data allow investigators to connect related illnesses that would be missed by traditional techniques. The added advantage of data generated by WGS is that these data can also be used for secondary analyses, such as virulence gene detection, antibiotic resistance gene profiling, synteny comparisons, mobile genetic element identification, and geographic attribution. In addition, several software packages are now available to generate in silico results for traditional molecular subtyping methods from the whole-genome sequence, allowing for efficient comparison with historical databases. Metagenomic approaches using next-generation sequencing have also been successful in the detection of nonculturable foodborne pathogens. This review addresses state-of-the-art techniques in microbial WGS and analysis and then discusses how this technology can be used to help support food safety investigations. Retrospective outbreak investigations using WGS are presented to provide organism-specific examples of the benefits, and challenges, associated with WGS in comparison to traditional molecular subtyping techniques.
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Affiliation(s)
- J Ronholm
- Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, ON, Canada
| | - Neda Nasheri
- Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, ON, Canada
| | - Nicholas Petronella
- Biostatistics and Modelling Division, Bureau of Food Surveillance and Science Integration, Food Directorate, Health Canada, Ottawa, ON, Canada
| | - Franco Pagotto
- Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, ON, Canada Listeriosis Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, ON, Canada
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23
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Uberoi A, Yoshida S, Frazer IH, Pitot HC, Lambert PF. Role of Ultraviolet Radiation in Papillomavirus-Induced Disease. PLoS Pathog 2016; 12:e1005664. [PMID: 27244228 PMCID: PMC4887022 DOI: 10.1371/journal.ppat.1005664] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 05/06/2016] [Indexed: 01/16/2023] Open
Abstract
Human papillomaviruses are causally associated with 5% of human cancers. The recent discovery of a papillomavirus (MmuPV1) that infects laboratory mice provides unique opportunities to study the life cycle and pathogenesis of papillomaviruses in the context of a genetically manipulatable host organism. To date, MmuPV1-induced disease has been found largely to be restricted to severely immunodeficient strains of mice. In this study, we report that ultraviolet radiation (UVR), specifically UVB spectra, causes wild-type strains of mice to become highly susceptible to MmuPV1-induced disease. MmuPV1-infected mice treated with UVB develop warts that progress to squamous cell carcinoma. Our studies further indicate that UVB induces systemic immunosuppression in mice that correlates with susceptibility to MmuPV1-associated disease. These findings provide new insight into how MmuPV1 can be used to study the life cycle of papillomaviruses and their role in carcinogenesis, the role of host immunity in controlling papillomavirus-associated pathogenesis, and a basis for understanding in part the role of UVR in promoting HPV infection in humans.
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Affiliation(s)
- Aayushi Uberoi
- McArdle Laboratory for Cancer Research, Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Satoshi Yoshida
- McArdle Laboratory for Cancer Research, Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ian H. Frazer
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Henry C. Pitot
- McArdle Laboratory for Cancer Research, Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Paul F. Lambert
- McArdle Laboratory for Cancer Research, Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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24
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Buck CB, Van Doorslaer K, Peretti A, Geoghegan EM, Tisza MJ, An P, Katz JP, Pipas JM, McBride AA, Camus AC, McDermott AJ, Dill JA, Delwart E, Ng TFF, Farkas K, Austin C, Kraberger S, Davison W, Pastrana DV, Varsani A. The Ancient Evolutionary History of Polyomaviruses. PLoS Pathog 2016; 12:e1005574. [PMID: 27093155 PMCID: PMC4836724 DOI: 10.1371/journal.ppat.1005574] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/23/2016] [Indexed: 12/21/2022] Open
Abstract
Polyomaviruses are a family of DNA tumor viruses that are known to infect mammals and birds. To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods. Analyses drawing upon the divergent new sequences indicate that polyomaviruses have been gradually co-evolving with their animal hosts for at least half a billion years. Phylogenetic analyses of individual polyomavirus genes suggest that some modern polyomavirus species arose after ancient recombination events involving distantly related polyomavirus lineages. The improved evolutionary model provides a useful platform for developing a more accurate taxonomic classification system for the viral family Polyomaviridae. Polyomaviruses are a family of DNA-based viruses that are known to infect various terrestrial vertebrates, including humans. In this report, we describe our discovery of highly divergent polyomaviruses associated with various marine fish. Searches of public deep sequencing databases unexpectedly revealed the existence of polyomavirus-like sequences in scorpion and spider datasets. Our analysis of these new sequences suggests that polyomaviruses have slowly co-evolved with individual host animal lineages through an established mechanism known as intrahost divergence. The proposed model is similar to the mechanisms through with other DNA viruses, such as papillomaviruses, are thought to have evolved. Our analysis also suggests that distantly related polyomaviruses sometimes recombine to produce new chimeric lineages. We propose a possible taxonomic scheme that can account for these inferred ancient recombination events.
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Affiliation(s)
- Christopher B. Buck
- Lab of Cellular Oncology, NCI, NIH, Bethesda, Maryland, United States of America
- * E-mail:
| | | | - Alberto Peretti
- Lab of Cellular Oncology, NCI, NIH, Bethesda, Maryland, United States of America
| | - Eileen M. Geoghegan
- Lab of Cellular Oncology, NCI, NIH, Bethesda, Maryland, United States of America
| | - Michael J. Tisza
- Lab of Cellular Oncology, NCI, NIH, Bethesda, Maryland, United States of America
| | - Ping An
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Joshua P. Katz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - James M. Pipas
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Alison A. McBride
- Lab of Viral Diseases, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Alvin C. Camus
- Department of Pathology, University of Georgia, Athens, Georgia, United States of America
| | - Alexa J. McDermott
- Animal Health Department, Georgia Aquarium, Inc., Atlanta, Georgia, United States of America
| | - Jennifer A. Dill
- Department of Pathology, University of Georgia, Athens, Georgia, United States of America
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Terry F. F. Ng
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Kata Farkas
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Charlotte Austin
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Simona Kraberger
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - William Davison
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Diana V. Pastrana
- Lab of Cellular Oncology, NCI, NIH, Bethesda, Maryland, United States of America
| | - Arvind Varsani
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
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Exploring the virome of cattle with non-suppurative encephalitis of unknown etiology by metagenomics. Virology 2016; 493:22-30. [PMID: 26994586 DOI: 10.1016/j.virol.2016.03.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 02/17/2016] [Accepted: 03/10/2016] [Indexed: 11/20/2022]
Abstract
Non-suppurative encephalitis is one of the most frequent pathological diagnosis in cattle with neurological disease, but there is a gap in the knowledge on disease-associated pathogens. In order to identify viruses that are associated with non-suppurative encephalitis in cattle, we used a viral metagenomics approach on a sample set of 16 neurologically-diseased cows. We detected six virus candidates: parainfluenza virus 5 (PIV-5), bovine astrovirus CH13/NeuroS1 (BoAstV-CH13/NeuroS1), bovine polyomavirus 2 (BPyV-2 SF), ovine herpesvirus 2 (OvHV-2), bovine herpesvirus 6 (BHV-6) and a novel bovine betaretrovirus termed BoRV-CH15. In a case-control study using PCR, BoAstV-CH13 (p=0.046), BoPV-2 SF (p=0.005) and BoHV-6 (p=4.3E-05) were statistically associated with the disease. These data expand our knowledge on encephalitis-associated pathogens in cattle and point to the value of NGS in resolving complex infection scenarios in a clinical disease setting.
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26
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Complete Genome Sequence of Bovine Polyomavirus Type 1 from Aborted Cattle, Isolated in Belgium in 2014. GENOME ANNOUNCEMENTS 2016; 4:4/2/e01646-15. [PMID: 26941154 PMCID: PMC4777765 DOI: 10.1128/genomea.01646-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The complete and fully annotated genome sequence of a bovine polyomavirus type 1 (BPyV/BEL/1/2014) from aborted cattle was assembled from a metagenomics data set. The 4,697-bp circular dsDNA genome contains 6 protein-coding genes. Bovine polyomavirus is unlikely to be causally related to the abortion cases.
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27
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Genome Sequence of Bovine Polyomavirus 1 Detected in a Salers Cow (Bos taurus) from Catalonia, Spain. GENOME ANNOUNCEMENTS 2016; 4:4/1/e01658-15. [PMID: 26823593 PMCID: PMC4732346 DOI: 10.1128/genomea.01658-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We identified a variant of the first bovine polyomavirus (BPyV1; family Polyomaviridae) in a lymph node of a Salers cow. As the 2 previously published genome sequences of this virus originated from fetal bovine serum and ground beef, respectively, this is the first BPyV1 genome that could be traced back to an individual.
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28
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Li L, Deng X, Da Costa AC, Bruhn R, Deeks SG, Delwart E. Virome analysis of antiretroviral-treated HIV patients shows no correlation between T-cell activation and anelloviruses levels. J Clin Virol 2015; 72:106-13. [PMID: 26479202 DOI: 10.1016/j.jcv.2015.09.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/01/2015] [Accepted: 09/16/2015] [Indexed: 01/29/2023]
Abstract
BACKGROUND Abnormally high levels of T-cell activation can persist in HIV-infected subjects despite effective anti-retroviral therapy (ART) and has been associated with negative health outcomes. The nature of the antigenic drivers or other causes of this residual T-cell activation remain uncertain. Anelloviruses are universally acquired soon after birth, resulting in persistent viremia, and considered part of the commensal human virome. Reduced immunocompetence results in increased anellovirus levels. OBJECTIVES To test whether increased levels of anelloviruses or other viruses in plasma are associated with higher levels of persistent T-cell activation during ART. STUDY DESIGN Two amplification methods combined with next generation sequencing were used to detect all viruses and estimate relative anellovirus levels in plasma from 19 adults on effective ART who exhibited a wide range of T-cell activation levels. RESULTS Nucleic acids from HBV and HCV were detected in one patient each while pegivirus A (GBV-C) was found in three patients. Anellovirus DNA was detected in all patients with some individuals carrying up to eight different genotypes. Specific anellovirus genotypes or higher level of co-infections were not detected in subjects with higher levels of T-cell activation. No association was detected between relative plasma anellovirus DNA levels and the percentage of activated CD4 or CD8 T cells. CONCLUSIONS Human anelloviruses were detected in all HIV suppressed subjects, exhibited a wide range of viremia levels, and were genetically highly diverse. The level of persistent T-cell activation was not correlated with the level of viremia or genotypes present indicating that anellovirus antigens are unlikely to be a dominant source of antigens driving chronic T-cell activation.
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Affiliation(s)
- Linlin Li
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Antonio Charlys Da Costa
- Blood Systems Research Institute, San Francisco, CA, USA; Institute of Tropical Medicine, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Roberta Bruhn
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Steven G Deeks
- Positive Health Program, San Francisco General Hospital, San Francisco, CA, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
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29
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The role of Merkel cell polyomavirus and other human polyomaviruses in emerging hallmarks of cancer. Viruses 2015; 7:1871-901. [PMID: 25866902 PMCID: PMC4411681 DOI: 10.3390/v7041871] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/01/2015] [Accepted: 04/07/2015] [Indexed: 12/24/2022] Open
Abstract
Polyomaviruses are non-enveloped, dsDNA viruses that are common in mammals, including humans. All polyomaviruses encode the large T-antigen and small t-antigen proteins that share conserved functional domains, comprising binding motifs for the tumor suppressors pRb and p53, and for protein phosphatase 2A, respectively. At present, 13 different human polyomaviruses are known, and for some of them their large T-antigen and small t-antigen have been shown to possess oncogenic properties in cell culture and animal models, while similar functions are assumed for the large T- and small t-antigen of other human polyomaviruses. However, so far the Merkel cell polyomavirus seems to be the only human polyomavirus associated with cancer. The large T- and small t-antigen exert their tumorigenic effects through classical hallmarks of cancer: inhibiting tumor suppressors, activating tumor promoters, preventing apoptosis, inducing angiogenesis and stimulating metastasis. This review elaborates on the putative roles of human polyomaviruses in some of the emerging hallmarks of cancer. The reciprocal interactions between human polyomaviruses and the immune system response are discussed, a plausible role of polyomavirus-encoded and polyomavirus-induced microRNA in cancer is described, and the effect of polyomaviruses on energy homeostasis and exosomes is explored. Therapeutic strategies against these emerging hallmarks of cancer are also suggested.
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30
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Hill SC, Murphy AA, Cotten M, Palser AL, Benson P, Lesellier S, Gormley E, Richomme C, Grierson S, Bhuachalla DN, Chambers M, Kellam P, Boschiroli ML, Ehlers B, Jarvis MA, Pybus OG. Discovery of a polyomavirus in European badgers (Meles meles) and the evolution of host range in the family Polyomaviridae. J Gen Virol 2015; 96:1411-1422. [PMID: 25626684 PMCID: PMC4635489 DOI: 10.1099/vir.0.000071] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 01/23/2015] [Indexed: 12/25/2022] Open
Abstract
Polyomaviruses infect a diverse range of mammalian and avian hosts, and are associated with a variety of symptoms. However, it is unknown whether the viruses are found in all mammalian families and the evolutionary history of the polyomaviruses is still unclear. Here, we report the discovery of a novel polyomavirus in the European badger (Meles meles), which to our knowledge represents the first polyomavirus to be characterized in the family Mustelidae, and within a European carnivoran. Although the virus was discovered serendipitously in the supernatant of a cell culture inoculated with badger material, we subsequently confirmed its presence in wild badgers. The European badger polyomavirus was tentatively named Meles meles polyomavirus 1 (MmelPyV1). The genome is 5187 bp long and encodes proteins typical of polyomaviruses. Phylogenetic analyses including all known polyomavirus genomes consistently group MmelPyV1 with California sea lion polyomavirus 1 across all regions of the genome. Further evolutionary analyses revealed phylogenetic discordance amongst polyomavirus genome regions, possibly arising from evolutionary rate heterogeneity, and a complex association between polyomavirus phylogeny and host taxonomic groups.
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Affiliation(s)
| | - Aisling A Murphy
- School of Biomedical and Healthcare Sciences, Plymouth University, UK
| | | | | | - Phillip Benson
- School of Biomedical and Healthcare Sciences, Plymouth University, UK
| | | | - Eamonn Gormley
- School of Veterinary Medicine, University College Dublin (UCD), Ireland
| | | | | | | | - Mark Chambers
- School of Veterinary Medicine, University of Surrey, UK.,Bacteriology Department, Animal and Plant Health Agency, UK
| | - Paul Kellam
- MRC/UCL Centre for Medical Molecular Virology, University College London, UK.,Wellcome Trust Sanger Institute, UK
| | - María-Laura Boschiroli
- University Paris-Est, ANSES, Laboratory for Animal Health, Bovine Tuberculosis National Reference Laboratory, France
| | - Bernhard Ehlers
- Robert Koch Institute, Division 12 'Measles, Mumps, Rubella and Viruses Affecting Immunocompromised Patients', Germany
| | - Michael A Jarvis
- School of Biomedical and Healthcare Sciences, Plymouth University, UK
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