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Laredo-Tiscareño SV, Garza-Hernandez JA, Tangudu CS, Dankaona W, Rodríguez-Alarcón CA, Adame-Gallegos JR, De Luna Santillana EJ, Huerta H, Gonzalez-Peña R, Rivera-Martínez A, Rubio-Tabares E, Beristain-Ruiz DM, Blitvich BJ. Discovery of Novel Viruses in Culicoides Biting Midges in Chihuahua, Mexico. Viruses 2024; 16:1160. [PMID: 39066322 PMCID: PMC11281482 DOI: 10.3390/v16071160] [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: 06/01/2024] [Revised: 06/24/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Biting midges (Culicoides) are vectors of many pathogens of medical and veterinary importance, but their viromes are poorly characterized compared to certain other hematophagous arthropods, e.g., mosquitoes and ticks. The goal of this study was to use metagenomics to identify viruses in Culicoides from Mexico. A total of 457 adult midges were collected in Chihuahua, northern Mexico, in 2020 and 2021, and all were identified as female Culicoides reevesi. The midges were sorted into five pools and homogenized. An aliquot of each homogenate was subjected to polyethylene glycol precipitation to enrich for virions, then total RNA was extracted and analyzed by unbiased high-throughput sequencing. We identified six novel viruses that are characteristic of viruses from five families (Nodaviridae, Partitiviridae, Solemoviridae, Tombusviridae, and Totiviridae) and one novel virus that is too divergent from all classified viruses to be assigned to an established family. The newly discovered viruses are phylogenetically distinct from their closest known relatives, and their minimal infection rates in female C. reevesi range from 0.22 to 1.09. No previously known viruses were detected, presumably because viral metagenomics had never before been used to study Culicoides from the Western Hemisphere. To conclude, we discovered multiple novel viruses in C. reevesi from Mexico, expanding our knowledge of arthropod viral diversity and evolution.
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Affiliation(s)
- S. Viridiana Laredo-Tiscareño
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (S.V.L.-T.); (C.S.T.); (W.D.)
- Laboratorio Entomología Médica, Instituto de Ciencias Biomédicas, Universidad Autónoma de Ciudad Juárez, Ciudad Juárez, Chihuahua 31125, Mexico; (J.A.G.-H.)
| | - Javier A. Garza-Hernandez
- Laboratorio Entomología Médica, Instituto de Ciencias Biomédicas, Universidad Autónoma de Ciudad Juárez, Ciudad Juárez, Chihuahua 31125, Mexico; (J.A.G.-H.)
| | - Chandra S. Tangudu
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (S.V.L.-T.); (C.S.T.); (W.D.)
| | - Wichan Dankaona
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (S.V.L.-T.); (C.S.T.); (W.D.)
- Animal Virome and Diagnostic Development Research Unit, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Carlos A. Rodríguez-Alarcón
- Departamento de Ciencias Veterinarias, Instituto de Ciencias Biomédicas, Universidad Autónoma de Ciudad Juárez, Ciudad Juárez, Chihuahua 32310, Mexico; (C.A.R.-A.); (D.M.B.-R.)
| | | | - Erick J. De Luna Santillana
- Laboratorio Medicina de la Conservación, Centro de Biotecnología Genómica del Instituto Politécnico Nacional, Reynosa, Tamaulipas 88700, México;
| | - Herón Huerta
- Laboratorio de Entomología, Instituto de Diagnóstico y Referencia Epidemiológicos, Ciudad de México 01480, Mexico;
| | - Rodolfo Gonzalez-Peña
- Laboratorio Entomología Médica, Instituto de Ciencias Biomédicas, Universidad Autónoma de Ciudad Juárez, Ciudad Juárez, Chihuahua 31125, Mexico; (J.A.G.-H.)
- Laboratorio de Arbovirología, Centro de Investigaciones Regionales “Dr. Hideyo Noguchi”, Universidad Autónoma de Yucatán, Mérida, Yucatan 97225, Mexico
| | - Alejandra Rivera-Martínez
- Laboratorio Entomología Médica, Instituto de Ciencias Biomédicas, Universidad Autónoma de Ciudad Juárez, Ciudad Juárez, Chihuahua 31125, Mexico; (J.A.G.-H.)
| | - Ezequiel Rubio-Tabares
- Departamento de Ciencias Veterinarias, Instituto de Ciencias Biomédicas, Universidad Autónoma de Ciudad Juárez, Ciudad Juárez, Chihuahua 32310, Mexico; (C.A.R.-A.); (D.M.B.-R.)
| | - Diana M. Beristain-Ruiz
- Departamento de Ciencias Veterinarias, Instituto de Ciencias Biomédicas, Universidad Autónoma de Ciudad Juárez, Ciudad Juárez, Chihuahua 32310, Mexico; (C.A.R.-A.); (D.M.B.-R.)
| | - Bradley J. Blitvich
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (S.V.L.-T.); (C.S.T.); (W.D.)
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Cebriá-Mendoza M, Díaz W, Sanjuán R, Cuevas JM. Optimized Recovery of Viral DNA and RNA from Blood Plasma for Viral Metagenomics. Methods Mol Biol 2024; 2732:155-164. [PMID: 38060124 DOI: 10.1007/978-1-0716-3515-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Metagenomics is vastly improving our ability to discover new viruses, as well as their possible associations with disease. However, metagenomics has also changed our understanding of viruses in general. This is because we can find viruses in healthy hosts in the absence of disease, which changes the perspective of viruses as mere pathogens and offers a new perspective in which viruses function as important components of ecosystems. In concrete, human blood metagenomics has revealed the presence of different types of viruses in apparently healthy subjects. These viruses are human anelloviruses and, to a lower extent, human pegiviruses. Viral metagenomics' major challenge is the correct isolation of the viral nucleic acids from a specific sample. For the protocol to be successful, all steps must be carefully chosen, in particular those that optimize the recovery of viral nucleic acids. Here, we present a procedure that allows the recovery of both DNA and RNA viruses from plasma samples.
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Affiliation(s)
- María Cebriá-Mendoza
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, València, Spain
| | - Wladimiro Díaz
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, València, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, València, Spain
| | - José M Cuevas
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, València, Spain.
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3
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Zuckerman NS, Shulman LM. Next-Generation Sequencing in the Study of Infectious Diseases. Infect Dis (Lond) 2023. [DOI: 10.1007/978-1-0716-2463-0_1090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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Sandybayev N, Beloussov V, Strochkov V, Solomadin M, Granica J, Yegorov S. Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome. Microorganisms 2022; 10:microorganisms10122327. [PMID: 36557580 PMCID: PMC9785614 DOI: 10.3390/microorganisms10122327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
The COVID-19 pandemic and heightened perception of the risk of emerging viral infections have boosted the efforts to better understand the virome or complete repertoire of viruses in health and disease, with a focus on infectious respiratory diseases. Next-generation sequencing (NGS) is widely used to study microorganisms, allowing the elucidation of bacteria and viruses inhabiting different body systems and identifying new pathogens. However, NGS studies suffer from a lack of standardization, in particular, due to various methodological approaches and no single format for processing the results. Here, we review the main methodological approaches and key stages for studies of the human virome, with an emphasis on virome changes during acute respiratory viral infection, with applications for clinical diagnostics and epidemiologic analyses.
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Affiliation(s)
- Nurlan Sandybayev
- Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
- Correspondence: ; Tel.: +7-778312-2058
| | - Vyacheslav Beloussov
- Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
- Molecular Genetics Laboratory TreeGene, Almaty 050009, Kazakhstan
| | - Vitaliy Strochkov
- Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
| | - Maxim Solomadin
- School of Pharmacy, Karaganda Medical University, Karaganda 100000, Kazakhstan
| | - Joanna Granica
- Molecular Genetics Laboratory TreeGene, Almaty 050009, Kazakhstan
| | - Sergey Yegorov
- Michael G. DeGroote Institute for Infectious Disease Research, Faculty of Health Sciences, McMaster University, Hamilton, ON L8S 4LB, Canada
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Lvov DK, Alkhovsky SV, Zhirnov OP. [130th anniversary of virology]. Vopr Virusol 2022; 67:357-384. [PMID: 36515283 DOI: 10.36233/0507-4088-140] [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: 10/02/2022] [Indexed: 06/17/2023]
Abstract
130 years ago, in 1892, our great compatriot Dmitry Iosifovich Ivanovsky (18641920) discovered a new type of pathogen viruses. Viruses have existed since the birth of life on Earth and for more than three billion years, as the biosphere evolved, they are included in interpopulation interactions with representatives of all kingdoms of life: archaea, bacteria, protozoa, algae, fungi, plants, invertebrates, and vertebrates, including the Homo sapiens (Hominidae, Homininae). Discovery of D.I. Ivanovsky laid the foundation for a new science virology. The rapid development of virology in the 20th century was associated with the fight against emerging and reemerging infections, epidemics (epizootics) and pandemics (panzootics) of which posed a threat to national and global biosecurity (tick-borne and other encephalitis, hemorrhagic fevers, influenza, smallpox, poliomyelitis, HIV, parenteral hepatitis, coronaviral and other infections). Fundamental research on viruses created the basis for the development of effective methods of diagnostics, vaccine prophylaxis, and antiviral drugs. Russian virologists continue to occupy leading positions in some priority areas of modern virology in vaccinology, environmental studies oz zoonotic viruses, studies of viral evolution in various ecosystems, and several other areas. A meaningful combination of theoretical approaches to studying the evolution of viruses with innovative methods for studying their molecular genetic properties and the creation of new generations of vaccines and antiviral drugs on this basis will significantly reduce the consequences of future pandemics or panzootics. The review presents the main stages in the formation and development of virology as a science in Russia with an emphasis on the most significant achievements of soviet and Russian virologists in the fight against viral infectious diseases.
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Affiliation(s)
- D K Lvov
- D.I. Ivanovsky Institute of Virology of N.F Gamaleya National Research Center of Epidemiology and Microbiology of Ministry of Health of the Russian Federation
| | - S V Alkhovsky
- D.I. Ivanovsky Institute of Virology of N.F Gamaleya National Research Center of Epidemiology and Microbiology of Ministry of Health of the Russian Federation
| | - O P Zhirnov
- D.I. Ivanovsky Institute of Virology of N.F Gamaleya National Research Center of Epidemiology and Microbiology of Ministry of Health of the Russian Federation
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Kuchinski KS, Duan J, Himsworth C, Hsiao W, Prystajecky NA. ProbeTools: designing hybridization probes for targeted genomic sequencing of diverse and hypervariable viral taxa. BMC Genomics 2022; 23:579. [PMID: 35953803 PMCID: PMC9371634 DOI: 10.1186/s12864-022-08790-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Sequencing viruses in many specimens is hindered by excessive background material from hosts, microbiota, and environmental organisms. Consequently, enrichment of target genomic material is necessary for practical high-throughput viral genome sequencing. Hybridization probes are widely used for enrichment in many fields, but their application to viral sequencing faces a major obstacle: it is difficult to design panels of probe oligo sequences that broadly target many viral taxa due to their rapid evolution, extensive diversity, and genetic hypervariability. To address this challenge, we created ProbeTools, a package of bioinformatic tools for generating effective viral capture panels, and for assessing coverage of target sequences by probe panel designs in silico. In this study, we validated ProbeTools by designing a panel of 3600 probes for subtyping the hypervariable haemagglutinin (HA) and neuraminidase (NA) genome segments of avian-origin influenza A viruses (AIVs). Using in silico assessment of AIV reference sequences and in vitro capture on egg-cultured viral isolates, we demonstrated effective performance by our custom AIV panel and ProbeTools' suitability for challenging viral probe design applications. RESULTS Based on ProbeTool's in silico analysis, our panel provided broadly inclusive coverage of 14,772 HA and 11,967 NA reference sequences. For each reference sequence, we calculated the percentage of nucleotide positions covered by our panel in silico; 90% of HA and NA references sequences had at least 90.8 and 95.1% of their nucleotide positions covered respectively. We also observed effective in vitro capture on a representative collection of 23 egg-cultured AIVs that included isolates from wild birds, poultry, and humans and representatives from all HA and NA subtypes. Forty-two of forty-six HA and NA segments had over 98.3% of their nucleotide positions significantly enriched by our custom panel. These in vitro results were further used to validate ProbeTools' in silico coverage assessment algorithm; 89.2% of in silico predictions were concordant with in vitro results. CONCLUSIONS ProbeTools generated an effective panel for subtyping AIVs that can be deployed for genomic surveillance, outbreak prevention, and pandemic preparedness. Effective probe design against hypervariable AIV targets also validated ProbeTools' design and coverage assessment algorithms, demonstrating their suitability for other challenging viral capture applications.
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Affiliation(s)
- Kevin S Kuchinski
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
- , Vancouver, Canada.
| | - Jun Duan
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chelsea Himsworth
- Animal Health Centre, British Columbia Ministry of Agriculture, Food, and Fisheries, Abbotsford, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - William Hsiao
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Natalie A Prystajecky
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
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7
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Zhang F, Chase-Topping M, Guo CG, Woolhouse MEJ. Predictors of human-infective RNA virus discovery in the United States, China, and Africa, an ecological study. eLife 2022; 11:e72123. [PMID: 35666108 PMCID: PMC9278958 DOI: 10.7554/elife.72123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Background The variation in the pathogen type as well as the spatial heterogeneity of predictors make the generality of any associations with pathogen discovery debatable. Our previous work confirmed that the association of a group of predictors differed across different types of RNA viruses, yet there have been no previous comparisons of the specific predictors for RNA virus discovery in different regions. The aim of the current study was to close the gap by investigating whether predictors of discovery rates within three regions-the United States, China, and Africa-differ from one another and from those at the global level. Methods Based on a comprehensive list of human-infective RNA viruses, we collated published data on first discovery of each species in each region. We used a Poisson boosted regression tree (BRT) model to examine the relationship between virus discovery and 33 predictors representing climate, socio-economics, land use, and biodiversity across each region separately. The discovery probability in three regions in 2010-2019 was mapped using the fitted models and historical predictors. Results The numbers of human-infective virus species discovered in the United States, China, and Africa up to 2019 were 95, 80, and 107 respectively, with China lagging behind the other two regions. In each region, discoveries were clustered in hotspots. BRT modelling suggested that in all three regions RNA virus discovery was better predicted by land use and socio-economic variables than climatic variables and biodiversity, although the relative importance of these predictors varied by region. Map of virus discovery probability in 2010-2019 indicated several new hotspots outside historical high-risk areas. Most new virus species since 2010 in each region (6/6 in the United States, 19/19 in China, 12/19 in Africa) were discovered in high-risk areas as predicted by our model. Conclusions The drivers of spatiotemporal variation in virus discovery rates vary in different regions of the world. Within regions virus discovery is driven mainly by land-use and socio-economic variables; climate and biodiversity variables are consistently less important predictors than at a global scale. Potential new discovery hotspots in 2010-2019 are identified. Results from the study could guide active surveillance for new human-infective viruses in local high-risk areas. Funding FFZ is funded by the Darwin Trust of Edinburgh (https://darwintrust.bio.ed.ac.uk/). MEJW has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 874735 (VEO) (https://www.veo-europe.eu/).
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Affiliation(s)
- Feifei Zhang
- Usher Institute, University of EdinburghEdinburghUnited Kingdom
| | - Margo Chase-Topping
- Usher Institute, University of EdinburghEdinburghUnited Kingdom
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of EdinburghEdinburghUnited Kingdom
| | - Chuan-Guo Guo
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong KongHong KongChina
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Development of a Multiplex RT-PCR Assay for Simultaneous Detection of Four Potential Zoonotic Swine RNA Viruses. Vet Sci 2022; 9:vetsci9040176. [PMID: 35448674 PMCID: PMC9029180 DOI: 10.3390/vetsci9040176] [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: 03/03/2022] [Revised: 03/26/2022] [Accepted: 04/04/2022] [Indexed: 11/24/2022] Open
Abstract
Swine viruses like porcine sapovirus (SaV), porcine encephalomyocarditis virus (EMCV), porcine rotavirus A (RVA) and porcine astroviruses (AstV) are potentially zoonotic viruses or suspected of potential zoonosis. These viruses have been detected in pigs with or without clinical signs and often occur as coinfections. Despite the potential public health risks, no assay for detecting them all at once has been developed. Hence, in this study, a multiplex RT-PCR (mRT-PCR) assay was developed for the simultaneous detection of SaV, EMCV, RVA and AstV from swine fecal samples. The PCR parameters were optimized using specific primers for each target virus. The assay’s sensitivity, specificity, reproducibility, and application to field samples have been evaluated. Using a pool of plasmids containing the respective viral target fragments as a template, the developed mRT-PCR successfully detected 2.5 × 103 copies of each target virus. The assay’s specificity was tested using six other swine viruses as a template and did not show any cross-reactivity. A total of 280 field samples were tested with the developed mRT-PCR assay. Positive rates for SaV, EMCV, RVA, and AstV were found to be 24.6% (69/280), 5% (14/280), 4.3% (12/280), and 17.5% (49/280), respectively. Compared to performing separate assays for each virus, this mRT-PCR assay is a simple, rapid, and cost-effective method for detecting mixed or single infections of SaV, EMCV, RVA, and AstV.
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Fay EJ, Balla KM, Roach SN, Shepherd FK, Putri DS, Wiggen TD, Goldstein SA, Pierson MJ, Ferris MT, Thefaine CE, Tucker A, Salnikov M, Cortez V, Compton SR, Kotenko SV, Hunter RC, Masopust D, Elde NC, Langlois RA. Natural rodent model of viral transmission reveals biological features of virus population dynamics. J Exp Med 2022; 219:e20211220. [PMID: 34958350 PMCID: PMC8713297 DOI: 10.1084/jem.20211220] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/05/2021] [Accepted: 12/08/2021] [Indexed: 12/21/2022] Open
Abstract
Emerging viruses threaten global health, but few experimental models can characterize the virus and host factors necessary for within- and cross-species transmission. Here, we leverage a model whereby pet store mice or rats-which harbor natural rodent pathogens-are cohoused with laboratory mice. This "dirty" mouse model offers a platform for studying acute transmission of viruses between and within hosts via natural mechanisms. We identified numerous viruses and other microbial species that transmit to cohoused mice, including prospective new members of the Coronaviridae, Astroviridae, Picornaviridae, and Narnaviridae families, and uncovered pathogen interactions that promote or prevent virus transmission. We also evaluated transmission dynamics of murine astroviruses during transmission and spread within a new host. Finally, by cohousing our laboratory mice with the bedding of pet store rats, we identified cross-species transmission of a rat astrovirus. Overall, this model system allows for the analysis of transmission of natural rodent viruses and is a platform to further characterize barriers to zoonosis.
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Affiliation(s)
- Elizabeth J. Fay
- Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
- Center for Immunology, University of Minnesota, Minneapolis, MN
| | - Keir M. Balla
- Department of Human Genetics, University of Utah, Salt Lake City, UT
| | - Shanley N. Roach
- Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
| | - Frances K. Shepherd
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
| | - Dira S. Putri
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
- Microbiology, Immunology and Cancer Biology Graduate Program, University of Minnesota, Minneapolis, MN
| | - Talia D. Wiggen
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
| | | | - Mark J. Pierson
- Center for Immunology, University of Minnesota, Minneapolis, MN
| | - Martin T. Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Claire E. Thefaine
- Microbiology, Immunology and Cancer Biology Graduate Program, University of Minnesota, Minneapolis, MN
| | - Andrew Tucker
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
| | - Mark Salnikov
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
| | - Valerie Cortez
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA
| | - Susan R. Compton
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT
| | - Sergei V. Kotenko
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ
| | - Ryan C. Hunter
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
| | - David Masopust
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
- Center for Immunology, University of Minnesota, Minneapolis, MN
| | - Nels C. Elde
- Department of Human Genetics, University of Utah, Salt Lake City, UT
| | - Ryan A. Langlois
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
- Center for Immunology, University of Minnesota, Minneapolis, MN
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van Zyl GU. New Technological Developments in Identification and Monitoring of New and Emerging Infections. ENCYCLOPEDIA OF INFECTION AND IMMUNITY 2022. [PMCID: PMC8291697 DOI: 10.1016/b978-0-12-818731-9.00094-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Novel RNA Viruses from the Transcriptome of Pheromone Glands in the Pink Bollworm Moth, Pectinophora gossypiella. INSECTS 2021; 12:insects12060556. [PMID: 34203764 PMCID: PMC8232680 DOI: 10.3390/insects12060556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 12/29/2022]
Abstract
Simple Summary The pink bollworm, Pectinophora gossypiella (Lepidoptera: Gelechiidae), is a major pest of cotton. In this study, we analyzed the mRNA from pheromone glands of two populations in Israel. We found several virus sequences that were the same in these populations. We identified these viruses based on high-throughput sequencing data and analysis of the assembled transcripts. Through analysis of the sequences, we identified several unique viral sequences representing possible novel viral species. Two of the viral sequences were found in relatively high abundance in pheromone glands. One of the virus sequences was also found through analysis of previous transcriptome sequencing data from the midgut of pink bollworm larvae. This is the first report of these unique viral sequences found in the pink bollworm, and these viruses could be developed to help control this pest around the world, but more research is needed to determine their utility as biological control agents. Abstract In this study, we analyzed the transcriptome obtained from the pheromone gland isolated from two Israeli populations of the pink bollworm Pectinophora gossypiella to identify viral sequences. The lab population and the field samples carried the same viral sequences. We discovered four novel viruses: two positive-sense single-stranded RNA viruses, Pectinophora gossypiella virus 1 (PecgV1, a virus of Iflaviridae) and Pectinophora gossypiella virus 4 (PecgV4, unclassified), and two negative-sense single-stranded RNA viruses, Pectinophora gossypiella virus 2 (PecgV2, a virus of Phasmaviridae) and Pectinophora gossypiella virus 3 (PecgV3, a virus of Phenuiviridae). In addition, sequences derived from two negative-sense single-stranded RNA viruses that belong to Mononegavirales were found in the data. Analysis of previous transcriptome sequencing data derived from the midgut of pink bollworm larvae of a USA population only identified PecgV1, but no other viruses. High viral sequence coverages of PecgV1 and PecgV4 were observed in both field and lab populations. This is the first report of viral sequences discovered from the pink bollworm. Results from this investigation suggest that the pink bollworm harbors multiple viruses. Further investigation of the viral pathogens may help to develop novel pest management strategies for control of the pink bollworm.
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Current Developments and Challenges in Plant Viral Diagnostics: A Systematic Review. Viruses 2021; 13:v13030412. [PMID: 33807625 PMCID: PMC7999175 DOI: 10.3390/v13030412] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/10/2021] [Accepted: 02/18/2021] [Indexed: 12/24/2022] Open
Abstract
Plant viral diseases are the foremost threat to sustainable agriculture, leading to several billion dollars in losses every year. Many viruses infecting several crops have been described in the literature; however, new infectious viruses are emerging frequently through outbreaks. For the effective treatment and prevention of viral diseases, there is great demand for new techniques that can provide accurate identification on the causative agents. With the advancements in biochemical and molecular biology techniques, several diagnostic methods with improved sensitivity and specificity for the detection of prevalent and/or unknown plant viruses are being continuously developed. Currently, serological and nucleic acid methods are the most widely used for plant viral diagnosis. Nucleic acid-based techniques that amplify target DNA/RNA have been evolved with many variants. However, there is growing interest in developing techniques that can be based in real-time and thus facilitate in-field diagnosis. Next-generation sequencing (NGS)-based innovative methods have shown great potential to detect multiple viruses simultaneously; however, such techniques are in the preliminary stages in plant viral disease diagnostics. This review discusses the recent progress in the use of NGS-based techniques for the detection, diagnosis, and identification of plant viral diseases. New portable devices and technologies that could provide real-time analyses in a relatively short period of time are prime important for in-field diagnostics. Current development and application of such tools and techniques along with their potential limitations in plant virology are likewise discussed in detail.
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Zhu X, Yan S, Yuan F, Wan S. The Applications of Nanopore Sequencing Technology in Pathogenic Microorganism Detection. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2020; 2020:6675206. [PMID: 33488885 PMCID: PMC7790562 DOI: 10.1155/2020/6675206] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/04/2020] [Accepted: 12/18/2020] [Indexed: 12/23/2022]
Abstract
Infectious diseases are major threats to human health and lead to a serious public health burden. The emergence of new pathogens and the mutation of known pathogens challenge our ability to diagnose and control infectious diseases. Nanopore sequencing technology exhibited versatile applications in pathogenic microorganism detection due to its flexible data throughput. This review article introduced the applications of nanopore sequencing in clinical microbiology and infectious diseases management, including the monitoring of emerging infectious diseases outbreak, identification of pathogen drug resistance, and disease-related microbial communities characterization.
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Affiliation(s)
- Xiaojian Zhu
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou 341000, China
| | - Shanshan Yan
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, China
- Department of Publication Health and Health Management, Gannan Medical University, Ganzhou 341000, China
| | - Fenghua Yuan
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou 341000, China
| | - Shaogui Wan
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou 341000, China
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Gleizes A, Laubscher F, Guex N, Iseli C, Junier T, Cordey S, Fellay J, Xenarios I, Kaiser L, Mercier PL. Virosaurus A Reference to Explore and Capture Virus Genetic Diversity. Viruses 2020; 12:v12111248. [PMID: 33139591 PMCID: PMC7693494 DOI: 10.3390/v12111248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 10/29/2020] [Accepted: 10/29/2020] [Indexed: 12/24/2022] Open
Abstract
The huge genetic diversity of circulating viruses is a challenge for diagnostic assays for emerging or rare viral diseases. High-throughput technology offers a new opportunity to explore the global virome of patients without preconception about the culpable pathogens. It requires a solid reference dataset to be accurate. Virosaurus has been designed to offer a non-biased, automatized and annotated database for clinical metagenomics studies and diagnosis. Raw viral sequences have been extracted from GenBank, and cleaned up to remove potentially erroneous sequences. Complete sequences have been identified for all genera infecting vertebrates, plants and other eukaryotes (insect, fungus, etc.). To facilitate the analysis of clinically relevant viruses, we have annotated all sequences with official and common virus names, acronym, genotypes, and genomic features (linear, circular, DNA, RNA, etc.). Sequences have been clustered to remove redundancy at 90% or 98% identity. The analysis of clustering results reveals the state of the virus genetic landscape knowledge. Because herpes and poxviruses were under-represented in complete genomes considering their potential diversity in nature, we used genes instead of complete genomes for those in Virosaurus.
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Affiliation(s)
- Anne Gleizes
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; (A.G.); (T.J.)
| | - Florian Laubscher
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland; (F.L.); (S.C.); (L.K.)
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, 1015 Lausanne, Switzerland; (N.G.); (C.I.)
| | - Christian Iseli
- Bioinformatics Competence Center, University of Lausanne, 1015 Lausanne, Switzerland; (N.G.); (C.I.)
| | - Thomas Junier
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; (A.G.); (T.J.)
- Laboratory of Microbiology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Samuel Cordey
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland; (F.L.); (S.C.); (L.K.)
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
| | - Jacques Fellay
- Unité de Médecine de Précision, CHUV, 1015 Lausanne, Switzerland;
- School of Life Sciences, EPFL, 1015 Lausanne, Switzerland
- Host-Pathogen Genomics Laboratory, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Ioannis Xenarios
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland;
| | - Laurent Kaiser
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland; (F.L.); (S.C.); (L.K.)
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Philippe Le Mercier
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, 1011 Geneva, Switzerland
- Correspondence:
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Genome reconstruction of white spot syndrome virus (WSSV) from archival Davidson's-fixed paraffin embedded shrimp (Penaeus vannamei) tissue. Sci Rep 2020; 10:13425. [PMID: 32778727 PMCID: PMC7417530 DOI: 10.1038/s41598-020-70435-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 07/27/2020] [Indexed: 12/18/2022] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are a priceless resource for diagnostic laboratories worldwide. However, DNA extracted from these tissues is often not optimal for most downstream molecular analysis due to fragmentation and chemical modification. In this study, the complete genome of white spot syndrome virus (WSSV) was reconstructed from ~ 2-year-old archived Davidson’s-fixed paraffin-embedded (DFPE) shrimp tissue using Next Generation Sequencing (NGS). A histological analysis was performed on archived DFPE shrimp tissue and a sample showing a high level of WSSV infection was selected for molecular analysis. The viral infection was further confirmed by molecular methods. DNA isolated from DFPE and fresh frozen (FF) tissues were sequenced by NGS. The complete genome reconstruction of WSSV (~ 305 kbp) was achieved from both DFPE and FF tissue. Single nucleotide polymorphisms, insertion and deletions were compared between the genomes. Thirty-eight mutations were identified in the WSSV genomes from the DFPE and FF that differed from the reference genome. This is the first study that has successfully sequenced the complete genome of a virus of over 300 kbp from archival DFPE tissue. These findings demonstrate that DFPE shrimp tissue represents an invaluable resource for prospective and retrospective studies, evolutionary studies and opens avenues for pathogen discovery.
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Tse LV, Meganck RM, Graham RL, Baric RS. The Current and Future State of Vaccines, Antivirals and Gene Therapies Against Emerging Coronaviruses. Front Microbiol 2020; 11:658. [PMID: 32390971 PMCID: PMC7193113 DOI: 10.3389/fmicb.2020.00658] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/23/2020] [Indexed: 12/31/2022] Open
Abstract
Emerging coronaviruses (CoV) are constant global public health threats to society. Multiple ongoing clinical trials for vaccines and antivirals against CoVs showcase the availability of medical interventions to both prevent and treat the future emergence of highly pathogenic CoVs in human. However, given the diverse nature of CoVs and our close interactions with wild, domestic and companion animals, the next epidemic zoonotic CoV could resist the existing vaccines and antivirals developed, which are primarily focused on Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle East Respiratory Syndrome Coronavirus (MERS CoV). In late 2019, the novel CoV (SARS-CoV-2) emerged in Wuhan, China, causing global public health concern. In this review, we will summarize the key advancements of current vaccines and antivirals against SARS-CoV and MERS-CoV as well as discuss the challenge and opportunity in the current SARS-CoV-2 crisis. At the end, we advocate the development of a "plug-and-play" platform technologies that could allow quick manufacturing and administration of broad-spectrum countermeasures in an outbreak setting. We will discuss the potential of AAV-based gene therapy technology for in vivo therapeutic antibody delivery to combat SARS-CoV-2 outbreak and the future emergence of severe CoVs.
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Affiliation(s)
- Longping V. Tse
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Rita M. Meganck
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Rachel L. Graham
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ralph S. Baric
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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17
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Tangudu CS, Charles J, Hurt SL, Dunphy BM, Smith RC, Bartholomay LC, Blitvich BJ. Skunk River virus, a novel orbivirus isolated from Aedes trivittatus in the United States. J Gen Virol 2019; 100:295-300. [DOI: 10.1099/jgv.0.001219] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Chandra S. Tangudu
- 1Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Jermilia Charles
- 1Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Stefanie L. Hurt
- 1Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Brendan M. Dunphy
- 2Department of Entomology, College of Agriculture and Life Sciences, Iowa State University, Ames, Iowa, USA
| | - Ryan C. Smith
- 2Department of Entomology, College of Agriculture and Life Sciences, Iowa State University, Ames, Iowa, USA
| | - Lyric C. Bartholomay
- 2Department of Entomology, College of Agriculture and Life Sciences, Iowa State University, Ames, Iowa, USA
- 3Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Bradley J. Blitvich
- 1Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
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18
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Charles J, Tangudu CS, Hurt SL, Tumescheit C, Firth AE, Garcia-Rejon JE, Machain-Williams C, Blitvich BJ. Detection of novel and recognized RNA viruses in mosquitoes from the Yucatan Peninsula of Mexico using metagenomics and characterization of their in vitro host ranges. J Gen Virol 2018; 99:1729-1738. [PMID: 30412047 DOI: 10.1099/jgv.0.001165] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
A metagenomics approach was used to detect novel and recognized RNA viruses in mosquitoes from the Yucatan Peninsula of Mexico. A total of 1359 mosquitoes of 7 species and 5 genera (Aedes, Anopheles, Culex, Mansonia and Psorophora) were sorted into 37 pools, homogenized and inoculated onto monolayers of Aedes albopictus (C6/36) cells. A second blind passage was performed and then total RNA was extracted and analysed by RNA-seq. Two novel viruses, designated Uxmal virus and Mayapan virus, were identified. Uxmal virus was isolated from three pools of Aedes (Ochlerotatus) taeniorhynchus and phylogenetic data indicate that it should be classified within the recently proposed taxon Negevirus. Mayapan virus was recovered from two pools of Psorophora ferox and is most closely related to unclassified Nodaviridae-like viruses. Two recognized viruses were also detected: Culex flavivirus (family Flaviviridae) and Houston virus (family Mesoniviridae), with one and two isolates being recovered, respectively. The in vitro host ranges of all four viruses were determined by assessing their replicative abilities in cell lines of avian, human, monkey, hamster, murine, lepidopteran and mosquito (Aedes, Anopheles and Culex) origin, revealing that all viruses possess vertebrate replication-incompetent phenotypes. In conclusion, we report the isolation of both novel and recognized RNA viruses from mosquitoes collected in Mexico, and add to the growing plethora of viruses discovered recently through the use of metagenomics.
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Affiliation(s)
- Jermilia Charles
- 1Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Chandra S Tangudu
- 1Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Stefanie L Hurt
- 1Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | | | - Andrew E Firth
- 2Department of Pathology, University of Cambridge, Cambridge, UK
| | - Julian E Garcia-Rejon
- 3Laboratorio de Arbovirologia, Centro de Investigaciones Regionales 'Dr Hideyo Noguchi', Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Carlos Machain-Williams
- 3Laboratorio de Arbovirologia, Centro de Investigaciones Regionales 'Dr Hideyo Noguchi', Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Bradley J Blitvich
- 1Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
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19
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Singh S. Alignment-Free Analyses of Nucleic Acid Sequences Using Graphical Representation (with Special Reference to Pandemic Bird Flu and Swine Flu). Synth Biol (Oxf) 2018. [PMCID: PMC7121243 DOI: 10.1007/978-981-10-8693-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The exponential growth in database of bio-molecular sequences have spawned many approaches towards storage, retrieval, classification and analyses requirements. Alignment-free techniques such as graphical representations and numerical characterisation (GRANCH) methods have enabled some detailed analyses of large sequences and found a number of different applications in the eukaryotic and prokaryotic domain. In particular, recalling the history of pandemic influenza in brief, we have followed the progress of viral infections such as bird flu of 1997 onwards and determined that the virus can spread conserved over space and time, that influenza virus can undergo fairly conspicuous recombination-like events in segmented genes, that certain segments of the neuraminidase and hemagglutinin surface proteins remain conserved and can be targeted for peptide vaccines. We recount in some detail a few of the representative GRANCH techniques to provide a glimpse of how these methods are used in formulating quantitative sequence descriptors to analyse DNA, RNA and protein sequences to derive meaningful results. Finally, we survey the surveillance techniques with a special reference to how the GRANCH techniques can be used for the purpose and recount the forecasts made of possible metamorphosis of pandemic bird flu to pandemic human infecting agents.
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Affiliation(s)
- Shailza Singh
- Department of Pathogenesis and Cellular Response, National Centre for Cell Science, Computational and Systems Biology Lab, Pune, Maharashtra India
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20
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Insect-specific viruses: from discovery to potential translational applications. Curr Opin Virol 2018; 33:33-41. [PMID: 30048906 DOI: 10.1016/j.coviro.2018.07.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 06/29/2018] [Accepted: 07/04/2018] [Indexed: 12/17/2022]
Abstract
Over the past decade the scientific community has experienced a new age of virus discovery in arthropods in general, and in insects in particular. Next generation sequencing and advanced bioinformatics tools have provided new insights about insect viromes and viral evolution. In this review, we discuss some high-throughput sequencing technologies used to discover viruses in insects and the challenges raised in data interpretations. Additionally, the discovery of these novel viruses that are considered as insect-specific viruses (ISVs) has gained increasing attention in their potential use as biological agents. As example, we show how the ISV Nhumirim virus was used to reduce West Nile virus transmission when co-infecting the mosquito vector. We also discuss new translational opportunities of using ISVs to limit insect vector competence by using them to interfere with pathogen acquisition, to directly target the insect vector or to confer pathogen resistance by the insect vector.
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21
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Varghese FS, van Rij RP. Insect Virus Discovery by Metagenomic and Cell Culture-Based Approaches. Methods Mol Biol 2018; 1746:197-213. [PMID: 29492897 DOI: 10.1007/978-1-4939-7683-6_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Insects are the most abundant and diverse group of animals on earth, but our knowledge of their viruses is biased toward insect-borne viruses that cause disease in plants, animals, or humans. Recent metagenomic studies and systematic surveys of viruses in wild-caught insects have identified an unanticipated large repertoire of novel viruses and viral sequences. These include new members of existing clades, new clades, and even entirely new virus families. These studies greatly expand the known virosphere in insects, provide opportunities to study virus-host interactions, and generate new insights into virus evolution. In this chapter, we discuss the methods used to identify novel viruses in insects and highlight some notable surprises arising from these studies.
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Affiliation(s)
- Finny S Varghese
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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22
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The Human Virome: Implications for Clinical Practice in Transplantation Medicine. J Clin Microbiol 2017; 55:2884-2893. [PMID: 28724557 DOI: 10.1128/jcm.00489-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Advances in DNA sequencing technology have provided an unprecedented opportunity to study the human virome. Transplant recipients and other immunocompromised hosts are at particular risk for developing virus-related pathology; thus, the impact of the virome on health and disease may be even more relevant in this population. Here, we discuss technical considerations in studying the human virome, the current literature on the virome in transplant recipients, and near-future applications of sequence-based findings that can further our understanding of viruses in transplantation medicine.
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Kandathil AJ, Breitwieser FP, Sachithanandham J, Robinson M, Mehta SH, Timp W, Salzberg SL, Thomas DL, Balagopal A. Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs. Ann Intern Med 2017; 167:1-7. [PMID: 28586923 PMCID: PMC5721525 DOI: 10.7326/m17-0085] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Next-generation metagenomic sequencing (NGMS) has opened new frontiers in microbial discovery but has been clinically characterized in only a few settings. OBJECTIVE To explore the plasma virome of persons who inject drugs and to characterize the sensitivity and accuracy of NGMS compared with quantitative clinical standards. DESIGN Longitudinal and cross-sectional studies. SETTING A clinical trial (ClinicalTrials.gov: NCT01285050) and a well-characterized cohort study of persons who have injected drugs. PARTICIPANTS Persons co-infected with hepatitis C virus (HCV) and HIV. MEASUREMENTS Viral nucleic acid in plasma by NGMS and quantitative polymerase chain reaction (PCR). RESULTS Next-generation metagenomic sequencing generated a total of 600 million reads, which included the expected HIV and HCV RNA sequences. HIV and HCV reads were consistently identified only when samples contained more than 10 000 copies/mL or IU/mL, respectively, as determined by quantitative PCR. A novel RNA virus, human hepegivirus-1 (HHpgV-1), was also detected by NGMS in 4 samples from 2 persons in the clinical trial. Through use of a quantitative PCR assay for HHpgV-1, infection was also detected in 17 (10.9%) of 156 members of a cohort of persons who injected drugs. In these persons, HHpgV-1 viremia persisted for a median of at least 4538 days and was associated with detection of other bloodborne viruses, such as HCV RNA and SEN virus D. LIMITATION The medical importance of HHpgV-1 infection is unknown. CONCLUSION Although NGMS is insensitive for detection of viruses with relatively low plasma nucleic acid concentrations, it may have broad potential for discovery of new viral infections of possible medical importance, such as HHpgV-1. PRIMARY FUNDING SOURCE National Institutes of Health.
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Affiliation(s)
- Abraham J Kandathil
- From Johns Hopkins University and Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Florian P Breitwieser
- From Johns Hopkins University and Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Matthew Robinson
- From Johns Hopkins University and Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Shruti H Mehta
- From Johns Hopkins University and Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Winston Timp
- From Johns Hopkins University and Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Steven L Salzberg
- From Johns Hopkins University and Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - David L Thomas
- From Johns Hopkins University and Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Ashwin Balagopal
- From Johns Hopkins University and Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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24
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Bonsall D, Gregory WF, Ip CLC, Donfield S, Iles J, Ansari MA, Piazza P, Trebes A, Brown A, Frater J, Pybus OG, Goulder P, Klenerman P, Bowden R, Gomperts ED, Barnes E, Kapoor A, Sharp CP, Simmonds P. Evaluation of Viremia Frequencies of a Novel Human Pegivirus by Using Bioinformatic Screening and PCR. Emerg Infect Dis 2016; 22:671-8. [PMID: 26982117 PMCID: PMC4806942 DOI: 10.3201/eid2204.151812] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Bioinformatic screening and PCR-based approaches detected active infection with human hepegivirus-1 in exposed populations. Next-generation sequencing has critical applications in virus discovery, diagnostics, and environmental surveillance. We used metagenomic sequence libraries for retrospective screening of plasma samples for the recently discovered human hepegivirus 1 (HHpgV-1). From a cohort of 150 hepatitis C virus (HCV)–positive case-patients, we identified 2 persons with HHpgV-1 viremia and a high frequency of human pegivirus (HPgV) viremia (14%). Detection of HHpgV-1 and HPgV was concordant with parallel PCR-based screening using conserved primers matching groups 1 (HPgV) and 2 (HHPgV-1) nonstructural 3 region sequences. PCR identified 1 HHPgV-1–positive person with viremia from a group of 195 persons with hemophilia who had been exposed to nonvirally inactivated factor VII/IX; 18 (9%) were HPgV-positive. Relative to HCV and HPgV, active infections with HHpgV-1 were infrequently detected in blood, even in groups that had substantial parenteral exposure. Our findings are consistent with lower transmissibility or higher rates of virus clearance for HHpgV-1 than for other bloodborne human flaviviruses.
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Viral metagenomics applied to blood donors and recipients at high risk for blood-borne infections. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2016; 14:400-7. [PMID: 27136432 DOI: 10.2450/2016.0160-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 01/18/2016] [Indexed: 02/08/2023]
Abstract
BACKGROUND Characterisation of human-associated viral communities is essential for epidemiological surveillance and to be able to anticipate new potential threats for blood transfusion safety. In high-resource countries, the risk of blood-borne agent transmission of well-known viruses (HBV, HCV, HIV and HTLV) is currently considered to be under control. However, other unknown or unsuspected viruses may be transmitted to recipients by blood-derived products. To investigate this, the virome of plasma from individuals at high risk for parenterally and sexually transmitted infections was analysed by high throughput sequencing (HTS). MATERIALS AND METHODS Purified nucleic acids from two pools of 50 samples from recipients of multiple transfusions, and three pools containing seven plasma samples from either HBV-, HCV- or HIV-infected blood donors, were submitted to HTS. RESULTS Sequences from resident anelloviruses and HPgV were evidenced in all pools. HBV and HCV sequences were detected in pools containing 3.8×10(3) IU/mL of HBV-DNA and 1.7×10(5) IU/mL of HCV-RNA, respectively, whereas no HIV sequence was found in a pool of 150 copies/mL of HIV-RNA. This suggests a lack of sensitivity in HTS performance in detecting low levels of virus. In addition, this study identified other issues, including laboratory contaminants and the uncertainty of taxonomic assignment of short sequence. No sequence suggestive of a new viral species was identified. DISCUSSION This study did not identify any new blood-borne virus in high-risk individuals. However, rare and/or viruses present at very low titre could have escaped our protocol. Our results demonstrate the positive contribution of HTS in the detection of viral sequences in blood donations.
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Alves JMP, de Oliveira AL, Sandberg TOM, Moreno-Gallego JL, de Toledo MAF, de Moura EMM, Oliveira LS, Durham AM, Mehnert DU, Zanotto PMDA, Reyes A, Gruber A. GenSeed-HMM: A Tool for Progressive Assembly Using Profile HMMs as Seeds and its Application in Alpavirinae Viral Discovery from Metagenomic Data. Front Microbiol 2016; 7:269. [PMID: 26973638 PMCID: PMC4777721 DOI: 10.3389/fmicb.2016.00269] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/19/2016] [Indexed: 01/01/2023] Open
Abstract
This work reports the development of GenSeed-HMM, a program that implements seed-driven progressive assembly, an approach to reconstruct specific sequences from unassembled data, starting from short nucleotide or protein seed sequences or profile Hidden Markov Models (HMM). The program can use any one of a number of sequence assemblers. Assembly is performed in multiple steps and relatively few reads are used in each cycle, consequently the program demands low computational resources. As a proof-of-concept and to demonstrate the power of HMM-driven progressive assemblies, GenSeed-HMM was applied to metagenomic datasets in the search for diverse ssDNA bacteriophages from the recently described Alpavirinae subfamily. Profile HMMs were built using Alpavirinae-specific regions from multiple sequence alignments (MSA) using either the viral protein 1 (VP1; major capsid protein) or VP4 (genome replication initiation protein). These profile HMMs were used by GenSeed-HMM (running Newbler assembler) as seeds to reconstruct viral genomes from sequencing datasets of human fecal samples. All contigs obtained were annotated and taxonomically classified using similarity searches and phylogenetic analyses. The most specific profile HMM seed enabled the reconstruction of 45 partial or complete Alpavirinae genomic sequences. A comparison with conventional (global) assembly of the same original dataset, using Newbler in a standalone execution, revealed that GenSeed-HMM outperformed global genomic assembly in several metrics employed. This approach is capable of detecting organisms that have not been used in the construction of the profile HMM, which opens up the possibility of diagnosing novel viruses, without previous specific information, constituting a de novo diagnosis. Additional applications include, but are not limited to, the specific assembly of extrachromosomal elements such as plastid and mitochondrial genomes from metagenomic data. Profile HMM seeds can also be used to reconstruct specific protein coding genes for gene diversity studies, and to determine all possible gene variants present in a metagenomic sample. Such surveys could be useful to detect the emergence of drug-resistance variants in sensitive environments such as hospitals and animal production facilities, where antibiotics are regularly used. Finally, GenSeed-HMM can be used as an adjunct for gap closure on assembly finishing projects, by using multiple contig ends as anchored seeds.
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Affiliation(s)
- João M P Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - André L de Oliveira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Tatiana O M Sandberg
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | | | - Marcelo A F de Toledo
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Elisabeth M M de Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Liliane S Oliveira
- Department of Parasitology, Institute of Biomedical Sciences, University of São PauloSão Paulo, Brazil; Department of Computer Science, Institute of Mathematics and Statistics, University of São PauloSão Paulo, Brazil
| | - Alan M Durham
- Department of Computer Science, Institute of Mathematics and Statistics, University of São Paulo São Paulo, Brazil
| | - Dolores U Mehnert
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Paolo M de A Zanotto
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Alejandro Reyes
- Department of Biological Sciences, Universidad de los AndesBogotá, Colombia; Center for Genome Sciences and Systems Biology, Department of Pathology and Immunology, Washington University in Saint LouisMO, USA
| | - Arthur Gruber
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
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Teixeira M, Sela N, Ng J, Casteel CL, Peng HC, Bekal S, Girke T, Ghanim M, Kaloshian I. A novel virus from Macrosiphum euphorbiae with similarities to members of the family Flaviviridae. J Gen Virol 2016; 97:1261-1271. [PMID: 26822322 DOI: 10.1099/jgv.0.000414] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A virus with a large genome was identified in the transcriptome of the potato aphid (Macrosiphum euphorbiae) and was named Macrosiphum euphorbiae virus 1 (MeV-1). The MeV-1 genome is 22 780 nt in size, including 3' and 5' non-coding regions, with a single large ORF encoding a putative polyprotein of 7333 aa. The C-terminal region of the predicted MeV-1 polyprotein contained sequences with similarities to helicase, methyltransferase and RNA-dependent RNA polymerase (RdRp) motifs, while the N-terminal region lacked any motifs including structural proteins. Phylogenetic analysis of the helicase placed MeV-1 close to pestiviruses, while the RdRp region placed it close to pestiviruses and flaviviruses, suggesting MeV-1 has a positive-polarity ssRNA genome and is a member of the family Flaviviridae. Since the MeV-1 genome is predicted to contain a methyltransferase, a gene present typically in flaviviruses but not pestiviruses, MeV-1 is likely a member of the genus Flavivirus. MeV-1 was present in nymphal and adult stages of the aphid, aphid saliva and plant tissues fed upon by aphids. However, the virus was unable to multiply and spread in tomato plants. In addition, dsRNA, the replication intermediate of RNA viruses, was isolated from virus-infected M. euphorbiae and not from tomato plants infested with the aphid. Furthermore, nymphs laid without exposure to infected plants harboured the virus, indicating that MeV-1 is an aphid-infecting virus likely transmitted transovarially. The virus was present in M. euphorbiae populations from Europe but not from North America and was absent in all other aphid species tested.
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Affiliation(s)
- Marcella Teixeira
- Department of Nematology,University of California, Riverside, California,USA
| | - Noa Sela
- Department of Plant Pathology and Weed Research,Volcani Center, Bet Dagan,Israel
| | - James Ng
- Plant Pathology and Microbiology,University of California, Riverside, California,USA.,Institute of Integrative Genome Biology,University of California, Riverside, California,USA
| | - Clare L Casteel
- Department of Plant Pathology,University of California, Davis, California,USA
| | - Hsuan-Chieh Peng
- Plant Pathology and Microbiology,University of California, Riverside, California,USA
| | - Sadia Bekal
- Department of Agricultural and Biological Engineering,University of Illinois, Urbana, IL,USA
| | - Thomas Girke
- Institute of Integrative Genome Biology,University of California, Riverside, California,USA.,Department of Botany and Plant Sciences,University of California, Riverside, California,USA
| | - Murad Ghanim
- Department of Entomology,Volcani Center, Bet Dagan,Israel
| | - Isgouhi Kaloshian
- Institute of Integrative Genome Biology,University of California, Riverside, California,USA.,Department of Nematology,University of California, Riverside, California,USA
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Abstract
This chapter profiles some examples of past and current viral infections that have levied a high toll in human misery and mortality, and derives a number of lessons about the dynamics of viral pandemics. Viral epidemics can be very disruptive to civil society, and—conversely—civil disasters can trigger viral epidemics. Furthermore, viruses likely play an insidious role in initiating a number of chronic diseases whose burden is ever increasing. Evolving technologies have led to much more rapid detection of emerging viral diseases anywhere in the world. However, current efforts to mitigate the toll of viral diseases are less than satisfactory, and futurists predict the emergence of new pandemics particularly of zoonotic origin. Pathogenesis—the subject of this book—informs ongoing efforts to mitigate the toll of viral disease.
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Kilianski A, Carcel P, Yao S, Roth P, Schulte J, Donarum GB, Fochler ET, Hill JM, Liem AT, Wiley MR, Ladner JT, Pfeffer BP, Elliot O, Petrosov A, Jima DD, Vallard TG, Melendrez MC, Skowronski E, Quan PL, Lipkin WI, Gibbons HS, Hirschberg DL, Palacios GF, Rosenzweig CN. Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform. BMC Bioinformatics 2015; 16:416. [PMID: 26714571 PMCID: PMC4696252 DOI: 10.1186/s12859-015-0840-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 12/08/2015] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The detection of pathogens in complex sample backgrounds has been revolutionized by wide access to next-generation sequencing (NGS) platforms. However, analytical methods to support NGS platforms are not as uniformly available. Pathosphere (found at Pathosphere.org) is a cloud - based open - sourced community tool that allows for communication, collaboration and sharing of NGS analytical tools and data amongst scientists working in academia, industry and government. The architecture allows for users to upload data and run available bioinformatics pipelines without the need for onsite processing hardware or technical support. RESULTS The pathogen detection capabilities hosted on Pathosphere were tested by analyzing pathogen-containing samples sequenced by NGS with both spiked human samples as well as human and zoonotic host backgrounds. Pathosphere analytical pipelines developed by Edgewood Chemical Biological Center (ECBC) identified spiked pathogens within a common sample analyzed by 454, Ion Torrent, and Illumina sequencing platforms. ECBC pipelines also correctly identified pathogens in human samples containing arenavirus in addition to animal samples containing flavivirus and coronavirus. These analytical methods were limited in the detection of sequences with limited homology to previous annotations within NCBI databases, such as parvovirus. Utilizing the pipeline-hosting adaptability of Pathosphere, the analytical suite was supplemented by analytical pipelines designed by the United States Army Medical Research Insititute of Infectious Diseases and Walter Reed Army Institute of Research (USAMRIID-WRAIR). These pipelines were implemented and detected parvovirus sequence in the sample that the ECBC iterative analysis previously failed to identify. CONCLUSIONS By accurately detecting pathogens in a variety of samples, this work demonstrates the utility of Pathosphere and provides a platform for utilizing, modifying and creating pipelines for a variety of NGS technologies developed to detect pathogens in complex sample backgrounds. These results serve as an exhibition for the existing pipelines and web-based interface of Pathosphere as well as the plug-in adaptability that allows for integration of newer NGS analytical software as it becomes available.
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Affiliation(s)
- Andy Kilianski
- Biosciences Division, Edgewood Chemical and Biological Center, 5183 Blackhawk Rd, Aberdeen Proving Ground, Edgewood, MD, 21010, USA.
| | | | - Shijie Yao
- OptiMetrics, Inc, Abingdon, MD, USA. .,Joint Genome Institute, Department of Energy, LBNL, Berkley, CA, USA.
| | - Pierce Roth
- Biosciences Division, Edgewood Chemical and Biological Center, 5183 Blackhawk Rd, Aberdeen Proving Ground, Edgewood, MD, 21010, USA. .,OptiMetrics, Inc, Abingdon, MD, USA.
| | | | | | | | - Jessica M Hill
- Biosciences Division, Edgewood Chemical and Biological Center, 5183 Blackhawk Rd, Aberdeen Proving Ground, Edgewood, MD, 21010, USA. .,OptiMetrics, Inc, Abingdon, MD, USA.
| | - Alvin T Liem
- Biosciences Division, Edgewood Chemical and Biological Center, 5183 Blackhawk Rd, Aberdeen Proving Ground, Edgewood, MD, 21010, USA. .,OptiMetrics, Inc, Abingdon, MD, USA.
| | - Michael R Wiley
- Center for Genome Sciences, United States Medical Research Institute of Infectious Diseases, Ft. Detrick, Frederick, MD, USA.
| | - Jason T Ladner
- Center for Genome Sciences, United States Medical Research Institute of Infectious Diseases, Ft. Detrick, Frederick, MD, USA.
| | - Bradley P Pfeffer
- Center for Genome Sciences, United States Medical Research Institute of Infectious Diseases, Ft. Detrick, Frederick, MD, USA.
| | - Oliver Elliot
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.
| | - Alexandra Petrosov
- The Center for Infection and Immunity, Columbia University, New York, NY, USA.
| | - Dereje D Jima
- Walter Reed Army Institute of Research, Viral Diseases Branch, Silver Spring, MD, USA.
| | - Tyghe G Vallard
- Walter Reed Army Institute of Research, Viral Diseases Branch, Silver Spring, MD, USA.
| | - Melanie C Melendrez
- Walter Reed Army Institute of Research, Viral Diseases Branch, Silver Spring, MD, USA.
| | | | - Phenix-Lan Quan
- The Center for Infection and Immunity, Columbia University, New York, NY, USA.
| | - W Ian Lipkin
- The Center for Infection and Immunity, Columbia University, New York, NY, USA.
| | - Henry S Gibbons
- Biosciences Division, Edgewood Chemical and Biological Center, 5183 Blackhawk Rd, Aberdeen Proving Ground, Edgewood, MD, 21010, USA.
| | - David L Hirschberg
- The Center for Infection and Immunity, Columbia University, New York, NY, USA. .,Department of Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, WA, USA.
| | - Gustavo F Palacios
- Center for Genome Sciences, United States Medical Research Institute of Infectious Diseases, Ft. Detrick, Frederick, MD, USA.
| | - C Nicole Rosenzweig
- Biosciences Division, Edgewood Chemical and Biological Center, 5183 Blackhawk Rd, Aberdeen Proving Ground, Edgewood, MD, 21010, USA.
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30
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Nouri S, Salem N, Nigg JC, Falk BW. Diverse Array of New Viral Sequences Identified in Worldwide Populations of the Asian Citrus Psyllid (Diaphorina citri) Using Viral Metagenomics. J Virol 2015; 90:2434-45. [PMID: 26676774 PMCID: PMC4810699 DOI: 10.1128/jvi.02793-15] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 12/08/2015] [Indexed: 12/26/2022] Open
Abstract
UNLABELLED The Asian citrus psyllid, Diaphorina citri, is the natural vector of the causal agent of Huanglongbing (HLB), or citrus greening disease. Together; HLB and D. citri represent a major threat to world citrus production. As there is no cure for HLB, insect vector management is considered one strategy to help control the disease, and D. citri viruses might be useful. In this study, we used a metagenomic approach to analyze viral sequences associated with the global population of D. citri. By sequencing small RNAs and the transcriptome coupled with bioinformatics analysis, we showed that the virus-like sequences of D. citri are diverse. We identified novel viral sequences belonging to the picornavirus superfamily, the Reoviridae, Parvoviridae, and Bunyaviridae families, and an unclassified positive-sense single-stranded RNA virus. Moreover, a Wolbachia prophage-related sequence was identified. This is the first comprehensive survey to assess the viral community from worldwide populations of an agricultural insect pest. Our results provide valuable information on new putative viruses, some of which may have the potential to be used as biocontrol agents. IMPORTANCE Insects have the most species of all animals, and are hosts to, and vectors of, a great variety of known and unknown viruses. Some of these most likely have the potential to be important fundamental and/or practical resources. In this study, we used high-throughput next-generation sequencing (NGS) technology and bioinformatics analysis to identify putative viruses associated with Diaphorina citri, the Asian citrus psyllid. D. citri is the vector of the bacterium causing Huanglongbing (HLB), currently the most serious threat to citrus worldwide. Here, we report several novel viral sequences associated with D. citri.
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Affiliation(s)
- Shahideh Nouri
- Department of Plant Pathology, University of California, Davis, California, USA
| | - Nidá Salem
- Department of Plant Protection, The University of Jordan, Amman, Jordan
| | - Jared C Nigg
- Department of Plant Pathology, University of California, Davis, California, USA
| | - Bryce W Falk
- Department of Plant Pathology, University of California, Davis, California, USA
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31
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Datta S, Budhauliya R, Das B, Chatterjee S, Vanlalhmuaka, Veer V. Next-generation sequencing in clinical virology: Discovery of new viruses. World J Virol 2015; 4:265-276. [PMID: 26279987 PMCID: PMC4534817 DOI: 10.5501/wjv.v4.i3.265] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Revised: 03/23/2015] [Accepted: 05/08/2015] [Indexed: 02/05/2023] Open
Abstract
Viruses are a cause of significant health problem worldwide, especially in the developing nations. Due to different anthropological activities, human populations are exposed to different viral pathogens, many of which emerge as outbreaks. In such situations, discovery of novel viruses is utmost important for deciding prevention and treatment strategies. Since last century, a number of different virus discovery methods, based on cell culture inoculation, sequence-independent PCR have been used for identification of a variety of viruses. However, the recent emergence and commercial availability of next-generation sequencers (NGS) has entirely changed the field of virus discovery. These massively parallel sequencing platforms can sequence a mixture of genetic materials from a very heterogeneous mix, with high sensitivity. Moreover, these platforms work in a sequence-independent manner, making them ideal tools for virus discovery. However, for their application in clinics, sample preparation or enrichment is necessary to detect low abundance virus populations. A number of techniques have also been developed for enrichment or viral nucleic acids. In this manuscript, we review the evolution of sequencing; NGS technologies available today as well as widely used virus enrichment technologies. We also discuss the challenges associated with their applications in the clinical virus discovery.
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32
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Punina NV, Makridakis NM, Remnev MA, Topunov AF. Whole-genome sequencing targets drug-resistant bacterial infections. Hum Genomics 2015; 9:19. [PMID: 26243131 PMCID: PMC4525730 DOI: 10.1186/s40246-015-0037-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/03/2015] [Indexed: 01/07/2023] Open
Abstract
During the past two decades, the technological progress of whole-genome sequencing (WGS) had changed the fields of Environmental Microbiology and Biotechnology, and, currently, is changing the underlying principles, approaches, and fundamentals of Public Health, Epidemiology, Health Economics, and national productivity. Today’s WGS technologies are able to compete with conventional techniques in cost, speed, accuracy, and resolution for day-to-day control of infectious diseases and outbreaks in clinical laboratories and in long-term epidemiological investigations. WGS gives rise to an exciting future direction for personalized Genomic Epidemiology. One of the most vital and growing public health problems is the emerging and re-emerging of multidrug-resistant (MDR) bacterial infections in the communities and healthcare settings, reinforced by a decline in antimicrobial drug discovery. In recent years, retrospective analysis provided by WGS has had a great impact on the identification and tracking of MDR microorganisms in hospitals and communities. The obtained genomic data are also important for developing novel easy-to-use diagnostic assays for clinics, as well as for antibiotic and therapeutic development at both the personal and population levels. At present, this technology has been successfully applied as an addendum to the real-time diagnostic methods currently used in clinical laboratories. However, the significance of WGS for public health may increase if: (a) unified and user-friendly bioinformatics toolsets for easy data interpretation and management are established, and (b) standards for data validation and verification are developed. Herein, we review the current and future impact of this technology on diagnosis, prevention, treatment, and control of MDR infectious bacteria in clinics and on the global scale.
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Affiliation(s)
- N V Punina
- Bach Institute of Biochemistry, Russian Academy of Science, Moscow, 119071, Russia.
| | - N M Makridakis
- Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - M A Remnev
- The Federal State Unitary Enterprise All-Russia Research Institute of Automatics, Moscow, 127055, Russia
| | - A F Topunov
- Bach Institute of Biochemistry, Russian Academy of Science, Moscow, 119071, Russia
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33
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Bellehumeur C, Boyle B, Charette SJ, Harel J, L'Homme Y, Masson L, Gagnon CA. Propidium monoazide (PMA) and ethidium bromide monoazide (EMA) improve DNA array and high-throughput sequencing of porcine reproductive and respiratory syndrome virus identification. J Virol Methods 2015; 222:182-91. [PMID: 26129867 PMCID: PMC7119533 DOI: 10.1016/j.jviromet.2015.06.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 06/11/2015] [Accepted: 06/25/2015] [Indexed: 11/29/2022]
Abstract
Pan-viral DNA array (PVDA) and high-throughput sequencing (HTS) are useful tools to identify novel viruses of emerging diseases. However, both techniques have difficulties to identify viruses in clinical samples because of the host genomic nucleic acid content (hg/cont). Both propidium monoazide (PMA) and ethidium bromide monoazide (EMA) have the capacity to bind free DNA/RNA, but are cell membrane-impermeable. Thus, both are unable to bind protected nucleic acid such as viral genomes within intact virions. However, EMA/PMA modified genetic material cannot be amplified by enzymes. In order to assess the potential of EMA/PMA to lower the presence of amplifiable hg/cont in samples and improve virus detection, serum and lung tissue homogenates were spiked with porcine reproductive and respiratory virus (PRRSV) and were processed with EMA/PMA. In addition, PRRSV RT-qPCR positive clinical samples were also tested. EMA/PMA treatments significantly decreased amplifiable hg/cont and significantly increased the number of PVDA positive probes and their signal intensity compared to untreated spiked lung samples. EMA/PMA treatments also increased the sensitivity of HTS by increasing the number of specific PRRSV reads and the PRRSV percentage of coverage. Interestingly, EMA/PMA treatments significantly increased the sensitivity of PVDA and HTS in two out of three clinical tissue samples. Thus, EMA/PMA treatments offer a new approach to lower the amplifiable hg/cont in clinical samples and increase the success of PVDA and HTS to identify viruses.
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Affiliation(s)
- Christian Bellehumeur
- Groupe de recherche sur les maladies infectieuses du porc (GREMIP), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada; Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Brian Boyle
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Steve J Charette
- Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada; Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
| | - Josée Harel
- Groupe de recherche sur les maladies infectieuses du porc (GREMIP), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada; Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Yvan L'Homme
- Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada; Canadian Food Inspection Agency, Saint-Hyacinthe, QC, Canada
| | - Luke Masson
- Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada; National Research Council Canada, Montréal, QC, Canada
| | - Carl A Gagnon
- Groupe de recherche sur les maladies infectieuses du porc (GREMIP), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada; Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada.
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34
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Liu S, Chen Y, Bonning BC. RNA virus discovery in insects. CURRENT OPINION IN INSECT SCIENCE 2015; 8:54-61. [PMID: 32846679 DOI: 10.1016/j.cois.2014.12.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 12/05/2014] [Indexed: 06/11/2023]
Abstract
The advent of next generation sequencing (NGS) technology has allowed for significant advances in insect RNA virus discovery, particularly for identification of covert viruses and for identification of previously undescribed virus groups. Recent research has revealed the complexity and diversity both of viral populations within an insect, and of different virus groups infecting insects. While appropriate verification of the ability of a given virus to infect a putative host is essential, this is frequently challenging for newly discovered viruses. In this chapter, we describe recently discovered RNA viruses of insects, optimization of NGS data analysis for virus discovery, and challenges associated with virus nomenclature.
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Affiliation(s)
- Sijun Liu
- Department of Entomology, Iowa State University, Ames, IA 50011, USA.
| | - Yuting Chen
- Department of Entomology, Iowa State University, Ames, IA 50011, USA
| | - Bryony C Bonning
- Department of Entomology, Iowa State University, Ames, IA 50011, USA
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35
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Virus characterization and discovery in formalin-fixed paraffin-embedded tissues. J Virol Methods 2015; 214:54-9. [PMID: 25681526 PMCID: PMC7119673 DOI: 10.1016/j.jviromet.2015.02.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/04/2014] [Accepted: 02/05/2015] [Indexed: 01/09/2023]
Abstract
Detection and characterization of novel viruses is often hampered by the lack of adequately stored materials. Formalin-fixed paraffin embedded (FFPE) tissues can be used to detect known viral sequences. The application of FFPE tissues for detection of novel viral sequences is currently unclear. Sequence-independent amplification and next-generation was performed on FFPE tissues. Sequences of known viruses and a novel rotavirus were detected, with relatively low sensitivity but standard accuracy.
Detection and characterization of novel viruses is hampered frequently by the lack of properly stored materials. Especially for the retrospective identification of viruses responsible for past disease outbreaks, often only formalin-fixed paraffin-embedded (FFPE) tissue samples are available. Although FFPE tissues can be used to detect known viral sequences, the application of FFPE tissues for detection of novel viruses is currently unclear. In the present study it was shown that sequence-independent amplification in combination with next-generation sequencing can be used to detect sequences of known and unknown viruses, although with relatively low sensitivity. These findings indicate that this technique could be useful for detecting novel viral sequences in FFPE tissues collected from humans and animals with disease of unknown origin, when other samples are not available. In addition, application of this method to FFPE tissues allows to correlate with the presence of histopathological changes in the corresponding tissue sections.
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36
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Aranaz A. Significance and integration of molecular diagnostics in the framework of veterinary practice. Methods Mol Biol 2015; 1247:19-30. [PMID: 25399085 DOI: 10.1007/978-1-4939-2004-4_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The field of molecular diagnostics in veterinary practice is rapidly evolving. An array of molecular techniques of different complexity is available to facilitate the fast and specific diagnosis of animal diseases. The choice for the adequate technique is dependent on the mission and attributions of the laboratory and requires both a knowledge of the molecular biology basis and of its limitations. The ability to quickly detect pathogens and their characteristics would allow for precise decision-making and target measures such as prophylaxis, appropriate therapy, and biosafety plans to control disease outbreaks. In practice, taking benefit of the huge amount of data that can be obtained using molecular techniques highlights the need of collaboration between veterinarians in the laboratory and practitioners.
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Affiliation(s)
- Alicia Aranaz
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040, Madrid, Spain,
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37
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Li L, Deng X, Mee ET, Collot-Teixeira S, Anderson R, Schepelmann S, Minor PD, Delwart E. Comparing viral metagenomics methods using a highly multiplexed human viral pathogens reagent. J Virol Methods 2014; 213:139-46. [PMID: 25497414 PMCID: PMC4344864 DOI: 10.1016/j.jviromet.2014.12.002] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/26/2014] [Accepted: 12/03/2014] [Indexed: 10/29/2022]
Abstract
Unbiased metagenomic sequencing holds significant potential as a diagnostic tool for the simultaneous detection of any previously genetically described viral nucleic acids in clinical samples. Viral genome sequences can also inform on likely phenotypes including drug susceptibility or neutralization serotypes. In this study, different variables of the laboratory methods often used to generate viral metagenomics libraries were compared for their abilities to detect multiple viruses and generate full genome coverage. A biological reagent consisting of 25 different human RNA and DNA viral pathogens was used to estimate the effect of filtration and nuclease digestion, DNA/RNA extraction methods, pre-amplification and the use of different library preparation kits on the detection of viral nucleic acids. Filtration and nuclease treatment led to slight decreases in the percentage of viral sequence reads and number of viruses detected. For nucleic acid extractions silica spin columns improved viral sequence recovery relative to magnetic beads and Trizol extraction. Pre-amplification using random RT-PCR while generating more viral sequence reads resulted in detection of fewer viruses, more overlapping sequences, and lower genome coverage. The ScriptSeq library preparation method retrieved more viruses and a greater fraction of their genomes than the TruSeq and Nextera methods. Viral metagenomics sequencing was able to simultaneously detect up to 22 different viruses in the biological reagent analyzed including all those detected by qPCR. Further optimization will be required for the detection of viruses in biologically more complex samples such as tissues, blood, or feces.
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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
| | - Edward T Mee
- Division of Virology, National Institute for Biological Reagents and Control, Medicines and Healthcare Products Regulatory Agency, Hertfordshire, UK
| | - Sophie Collot-Teixeira
- Division of Virology, National Institute for Biological Reagents and Control, Medicines and Healthcare Products Regulatory Agency, Hertfordshire, UK
| | - Rob Anderson
- Division of Virology, National Institute for Biological Reagents and Control, Medicines and Healthcare Products Regulatory Agency, Hertfordshire, UK
| | - Silke Schepelmann
- Division of Virology, National Institute for Biological Reagents and Control, Medicines and Healthcare Products Regulatory Agency, Hertfordshire, UK
| | - Philip D Minor
- Division of Virology, National Institute for Biological Reagents and Control, Medicines and Healthcare Products Regulatory Agency, Hertfordshire, UK
| | - 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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Kernbauer E, Ding Y, Cadwell K. An enteric virus can replace the beneficial function of commensal bacteria. Nature 2014; 516:94-8. [PMID: 25409145 PMCID: PMC4257755 DOI: 10.1038/nature13960] [Citation(s) in RCA: 363] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 10/13/2014] [Indexed: 12/18/2022]
Abstract
Intestinal microbial communities have profound effects on host physiology1. Whereas the symbiotic contribution of commensal bacteria is well established, the role of eukaryotic viruses that are present in the gastrointestinal tract under homeostatic conditions is undefined2,3. Here, we demonstrate that a common enteric RNA virus can replace the beneficial function of commensal bacteria in the intestine. Murine norovirus (MNV) infection of germfree or antibiotics-treated mice restored intestinal morphology and lymphocyte function without inducing overt inflammation and disease. The presence of MNV also suppressed an expansion of group 2 innate lymphoid cells (ILCs) observed in the absence of bacteria, and induced transcriptional changes in the intestine associated with immune development and type I interferon (IFN) signaling. Consistent with this observation, the IFNα receptor was essential for the ability of MNV to compensate for bacterial depletion. Importantly, MNV infection offset the deleterious effect of antibiotics-treatment in models of intestinal injury and pathogenic bacterial infection. These data indicate that eukaryotic viruses have the capacity to support intestinal homeostasis and shape mucosal immunity akin to commensal bacteria.
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Affiliation(s)
- Elisabeth Kernbauer
- 1] Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA [2] Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Yi Ding
- 1] New York Presbyterian Hospital, New York, New York 10065, USA [2] Department of Pathology, New York University School of Medicine, New York, New York 10016, USA
| | - Ken Cadwell
- 1] Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA [2] Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
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Lloyd-Smith JO, Funk S, McLean AR, Riley S, Wood JLN. Nine challenges in modelling the emergence of novel pathogens. Epidemics 2014; 10:35-9. [PMID: 25843380 PMCID: PMC4715032 DOI: 10.1016/j.epidem.2014.09.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 08/19/2014] [Accepted: 09/08/2014] [Indexed: 12/28/2022] Open
Abstract
We summarize key challenges in modeling the emergence of novel infectious agents. We focus on connections to data, including epidemiologic and genetic data. Zoonoses are emphasized, because they are the source of most new human pathogens. Challenges span reservoir dynamics, cross-species spillover, and outbreak dynamics. Estimation of fatality rates and overall risk assessment are also addressed.
Studying the emergence of novel infectious agents involves many processes spanning host species, spatial scales, and scientific disciplines. Mathematical models play an essential role in combining insights from these investigations and drawing robust inferences from field and experimental data. We describe nine challenges in modelling the emergence of novel pathogens, emphasizing the interface between models and data.
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Affiliation(s)
- James O Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA; Fogarty International Center, National Institutes of Health, Bethesda, MD, USA.
| | - Sebastian Funk
- Center for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Angela R McLean
- Department of Zoology, Oxford Martin School, University of Oxford, Oxford, United Kingdom
| | - Steven Riley
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA; MRC Centre for Outbreak Analysis and Disease Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, United Kingdom
| | - James L N Wood
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA; Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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Goldberg TL, Gendron-Fitzpatrick A, Deering KM, Wallace RS, Clyde VL, Lauck M, Rosen GE, Bennett AJ, Greiner EC, O'Connor DH. Fatal metacestode infection in Bornean orangutan caused by unknown Versteria species. Emerg Infect Dis 2014; 20:109-13. [PMID: 24377497 PMCID: PMC3884733 DOI: 10.3201/eid2001.131191] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
A captive juvenile Bornean orangutan (Pongo pygmaeus) died from an unknown disseminated parasitic infection. Deep sequencing of DNA from infected tissues, followed by gene-specific PCR and sequencing, revealed a divergent species within the newly proposed genus Versteria (Cestoda: Taeniidae). Versteria may represent a previously unrecognized risk to primate health.
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Quiñones-Mateu ME, Avila S, Reyes-Teran G, Martinez MA. Deep sequencing: becoming a critical tool in clinical virology. J Clin Virol 2014; 61:9-19. [PMID: 24998424 DOI: 10.1016/j.jcv.2014.06.013] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/12/2014] [Accepted: 06/14/2014] [Indexed: 02/07/2023]
Abstract
Population (Sanger) sequencing has been the standard method in basic and clinical DNA sequencing for almost 40 years; however, next-generation (deep) sequencing methodologies are now revolutionizing the field of genomics, and clinical virology is no exception. Deep sequencing is highly efficient, producing an enormous amount of information at low cost in a relatively short period of time. High-throughput sequencing techniques have enabled significant contributions to multiples areas in virology, including virus discovery and metagenomics (viromes), molecular epidemiology, pathogenesis, and studies of how viruses to escape the host immune system and antiviral pressures. In addition, new and more affordable deep sequencing-based assays are now being implemented in clinical laboratories. Here, we review the use of the current deep sequencing platforms in virology, focusing on three of the most studied viruses: human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus.
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Affiliation(s)
- Miguel E Quiñones-Mateu
- University Hospital Translational Laboratory, University Hospitals Case Medical Center, Cleveland, OH, USA; Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Santiago Avila
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Gustavo Reyes-Teran
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Miguel A Martinez
- Fundació irsicaixa, Universitat Autònoma de Barcelona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
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Horton DL, Banyard AC, Marston DA, Wise E, Selden D, Nunez A, Hicks D, Lembo T, Cleaveland S, Peel AJ, Kuzmin IV, Rupprecht CE, Fooks AR. Antigenic and genetic characterization of a divergent African virus, Ikoma lyssavirus. J Gen Virol 2014; 95:1025-1032. [PMID: 24496827 PMCID: PMC3983756 DOI: 10.1099/vir.0.061952-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In 2009, a novel lyssavirus (subsequently named Ikoma lyssavirus, IKOV) was detected in the brain of an African civet (Civettictis civetta) with clinical rabies in the Serengeti National Park of Tanzania. The degree of nucleotide divergence between the genome of IKOV and those of other lyssaviruses predicted antigenic distinction from, and lack of protection provided by, available rabies vaccines. In addition, the index case was considered likely to be an incidental spillover event, and therefore the true reservoir of IKOV remained to be identified. The advent of sensitive molecular techniques has led to a rapid increase in the discovery of novel viruses. Detecting viral sequence alone, however, only allows for prediction of phenotypic characteristics and not their measurement. In the present study we describe the in vitro and in vivo characterization of IKOV, demonstrating that it is (1) pathogenic by peripheral inoculation in an animal model, (2) antigenically distinct from current rabies vaccine strains and (3) poorly neutralized by sera from humans and animals immunized against rabies. In a laboratory mouse model, no protection was elicited by a licensed rabies vaccine. We also investigated the role of bats as reservoirs of IKOV. We found no evidence for infection among 483 individuals of at least 13 bat species sampled across sites in the Serengeti and Southern Kenya.
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Affiliation(s)
- Daniel L Horton
- Animal Health and Veterinary Laboratories Agency (AHVLA), Weybridge, UK
| | - Ashley C Banyard
- Animal Health and Veterinary Laboratories Agency (AHVLA), Weybridge, UK
| | - Denise A Marston
- Animal Health and Veterinary Laboratories Agency (AHVLA), Weybridge, UK
| | - Emma Wise
- Animal Health and Veterinary Laboratories Agency (AHVLA), Weybridge, UK
| | - David Selden
- Animal Health and Veterinary Laboratories Agency (AHVLA), Weybridge, UK
| | - Alejandro Nunez
- Animal Health and Veterinary Laboratories Agency (AHVLA), Weybridge, UK
| | - Daniel Hicks
- Animal Health and Veterinary Laboratories Agency (AHVLA), Weybridge, UK
| | - Tiziana Lembo
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Sarah Cleaveland
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Alison J Peel
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, UK
| | - Ivan V Kuzmin
- Global Alliance for Rabies Control, Manhattan, KS, USA
| | - Charles E Rupprecht
- Ross University School of Veterinary Medicine, St Kitts.,Global Alliance for Rabies Control, Manhattan, KS, USA
| | - Anthony R Fooks
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK.,Animal Health and Veterinary Laboratories Agency (AHVLA), Weybridge, UK
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