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Murphy HL, Ly H. Pathogenicity and virulence mechanisms of Lassa virus and its animal modeling, diagnostic, prophylactic, and therapeutic developments. Virulence 2021; 12:2989-3014. [PMID: 34747339 PMCID: PMC8923068 DOI: 10.1080/21505594.2021.2000290] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Lassa fever (LF) is a deadly viral hemorrhagic disease that is endemic to West Africa. The causative agent of LF is Lassa virus (LASV), which causes approximately 300,000 infections and 5,000 deaths annually. There are currently no approved therapeutics or FDA-approved vaccines against LASV. The high genetic variability between LASV strains and immune evasion mediated by the virus complicate the development of effective therapeutics and vaccines. Here, we aim to provide a comprehensive review of the basic biology of LASV and its mechanisms of disease pathogenesis and virulence in various animal models, as well as an update on prospective vaccines, therapeutics, and diagnostics for LF. Until effective vaccines and/or therapeutics are available for use to prevent or treat LF, a better level of understanding of the basic biology of LASV, its natural genetic variations and immune evasion mechanisms as potential pathogenicity factors, and of the rodent reservoir-vector populations and their geographical distributions, is necessary for the development of accurate diagnostics and effective therapeutics and vaccines against this deadly human viral pathogen.
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Affiliation(s)
- Hannah L Murphy
- Department of Veterinary & Biomedical Sciences, Comparative & Molecular Biosciences Graduate Program, College of Veterinary Medicine, University of Minnesota, Twin Cities
| | - Hinh Ly
- Department of Veterinary & Biomedical Sciences, Comparative & Molecular Biosciences Graduate Program, College of Veterinary Medicine, University of Minnesota, Twin Cities
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2
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Tarim EA, Karakuzu B, Oksuz C, Sarigil O, Kizilkaya M, Al-Ruweidi MKAA, Yalcin HC, Ozcivici E, Tekin HC. Microfluidic-based virus detection methods for respiratory diseases. EMERGENT MATERIALS 2021; 4:143-168. [PMID: 33786415 PMCID: PMC7992628 DOI: 10.1007/s42247-021-00169-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 01/19/2021] [Indexed: 05/04/2023]
Abstract
With the recent SARS-CoV-2 outbreak, the importance of rapid and direct detection of respiratory disease viruses has been well recognized. The detection of these viruses with novel technologies is vital in timely prevention and treatment strategies for epidemics and pandemics. Respiratory viruses can be detected from saliva, swab samples, nasal fluid, and blood, and collected samples can be analyzed by various techniques. Conventional methods for virus detection are based on techniques relying on cell culture, antigen-antibody interactions, and nucleic acids. However, these methods require trained personnel as well as expensive equipment. Microfluidic technologies, on the other hand, are one of the most accurate and specific methods to directly detect respiratory tract viruses. During viral infections, the production of detectable amounts of relevant antibodies takes a few days to weeks, hampering the aim of prevention. Alternatively, nucleic acid-based methods can directly detect the virus-specific RNA or DNA region, even before the immune response. There are numerous methods to detect respiratory viruses, but direct detection techniques have higher specificity and sensitivity than other techniques. This review aims to summarize the methods and technologies developed for microfluidic-based direct detection of viruses that cause respiratory infection using different detection techniques. Microfluidics enables the use of minimal sample volumes and thereby leading to a time, cost, and labor effective operation. Microfluidic-based detection technologies provide affordable, portable, rapid, and sensitive analysis of intact virus or virus genetic material, which is very important in pandemic and epidemic events to control outbreaks with an effective diagnosis.
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Affiliation(s)
- E. Alperay Tarim
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Betul Karakuzu
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Cemre Oksuz
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Oyku Sarigil
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Melike Kizilkaya
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | | | | | - Engin Ozcivici
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - H. Cumhur Tekin
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
- METU MEMS Center, Ankara, Turkey
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3
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Lipkin WI, Mishra N, Briese T. Screening for Viral Infections. ENCYCLOPEDIA OF VIROLOGY 2021. [PMCID: PMC7836304 DOI: 10.1016/b978-0-12-814515-9.00052-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This article reviews methods for diagnosis of viral infections including histopathology, culture, nucleic acid tests, and serology. We discuss the principles that underlie individual assays as well as their strengths and limitations. Our intent is to provide insights into selecting strategies for viral diagnosis and discovery that can be pursued by accessing more detailed and granular protocols.
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Zenhausern R, Chen CH, Yoon JY. Microfluidic sample preparation for respiratory virus detection: A review. BIOMICROFLUIDICS 2021; 15:011503. [PMID: 33643510 PMCID: PMC7889292 DOI: 10.1063/5.0041089] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 01/28/2021] [Indexed: 05/05/2023]
Abstract
Techniques used to prepare clinical samples have been perfected for use in diagnostic testing in a variety of clinical situations, e.g., to extract, concentrate, and purify respiratory virus particles. These techniques offer a high level of purity and concentration of target samples but require significant equipment and highly trained personnel to conduct, which is difficult to achieve in resource-limited environments where rapid testing and diagnostics are crucial for proper handling of respiratory viruses. Microfluidics has popularly been utilized toward rapid virus detection in resource-limited environments, where most devices focused on detection rather than sample preparation. Initial microfluidic prototypes have been hindered by their reliance on several off-chip preprocessing steps and external laboratory equipment. Recently, sample preparation methods have also been incorporated into microfluidics to conduct the virus detection in an all-in-one, automated manner. Extraction, concentration, and purification of viruses have been demonstrated in smaller volumes of samples and reagents, with no need for specialized training or complex machinery. Recent devices show the ability to function independently and efficiently to provide rapid, automated sample preparation as well as the detection of viral samples with high efficiency. In this review, methods of microfluidic sample preparation for the isolation and purification of viral samples are discussed, limitations of current systems are summarized, and potential advances are identified.
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Affiliation(s)
- Ryan Zenhausern
- Department of Biomedical Engineering, The University of Arizona, Tucson, Arizona 85721, USA
| | - Chia-Hung Chen
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong 999077, China
| | - Jeong-Yeol Yoon
- Department of Biomedical Engineering, The University of Arizona, Tucson, Arizona 85721, USA
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5
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Azevedo MLV, Malaquias MAS, de Paula CBV, de Souza CM, Júnior VHC, Raboni SM, Halila R, Rosendo G, Gozzo P, do Carmo LAP, Neto PC, Nagashima S, de Noronha L. The role of IL-17A/IL-17RA and lung injuries in children with lethal non-pandemic acute viral pneumonia. Immunobiology 2020; 225:151981. [PMID: 32747026 DOI: 10.1016/j.imbio.2020.151981] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/14/2020] [Accepted: 07/04/2020] [Indexed: 01/12/2023]
Abstract
This study aimed to evaluate IL-17A (interleukin 17A) and IL-17RA (IL-17A receptor) in a pediatric population that died with non-pandemic acute viral pneumonia compared to the non-viral pneumonia group. Necropsy lung samples (n = 193) from children that died after severe acute infection pneumonia were selected and processed for viral antigen detection by immunohistochemistry. After this, they were separated into two groups: virus-positive (n = 68) and virus-negative lung samples (n = 125). Immunohistochemistry was performed to assess the presence of IL-17A and IL-17RA in the lung tissue. The virus-positive group showed stronger immunolabeling for IL-17A and IL-17RA (p = 0.020 and p < 0.001, respectively). The result of this study may suggest that IL-17A and IL-17RA plays an essential role in the maintenance of viral infection and lung injuries. These aspects may increase the severity of the inflammatory response leading to lethal lung injuries in these patients. Children with community-acquired non-pandemic pneumonia that requiring hospitalization could benefit from using IL-17RA/IL-17A monoclonal antibodies to block their injurious effects.
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Affiliation(s)
- Marina Luise Viola Azevedo
- Laboratory of Experimental Pathology, School of Medicine, Pontifical Catholic University of Parana - PUCPR, R. Imaculada Conceição, 1155 - Prado Velho, Curitiba, PR, Brazil.
| | - Mineia Alessandra Scaranello Malaquias
- Laboratory of Experimental Pathology, School of Medicine, Pontifical Catholic University of Parana - PUCPR, R. Imaculada Conceição, 1155 - Prado Velho, Curitiba, PR, Brazil.
| | - Caroline Busatta Vaz de Paula
- Laboratory of Experimental Pathology, School of Medicine, Pontifical Catholic University of Parana - PUCPR, R. Imaculada Conceição, 1155 - Prado Velho, Curitiba, PR, Brazil.
| | - Cleber Machado de Souza
- Laboratory of Experimental Pathology, School of Medicine, Pontifical Catholic University of Parana - PUCPR, R. Imaculada Conceição, 1155 - Prado Velho, Curitiba, PR, Brazil.
| | - Victor Horácio Costa Júnior
- Laboratory of Experimental Pathology, School of Medicine, Pontifical Catholic University of Parana - PUCPR, R. Imaculada Conceição, 1155 - Prado Velho, Curitiba, PR, Brazil.
| | - Sonia Mara Raboni
- Virology Laboratory, Infectious Diseases Division, Federal University of Parana - UFPR, R. Padre Camargo, 280 - Alto da Gloria, Curitiba, PR, Brazil.
| | - Renata Halila
- Laboratory of Experimental Pathology, School of Medicine, Pontifical Catholic University of Parana - PUCPR, R. Imaculada Conceição, 1155 - Prado Velho, Curitiba, PR, Brazil.
| | - Giuliana Rosendo
- Laboratory of Experimental Pathology, School of Medicine, Pontifical Catholic University of Parana - PUCPR, R. Imaculada Conceição, 1155 - Prado Velho, Curitiba, PR, Brazil.
| | - Priscilla Gozzo
- Laboratory of Experimental Pathology, School of Medicine, Pontifical Catholic University of Parana - PUCPR, R. Imaculada Conceição, 1155 - Prado Velho, Curitiba, PR, Brazil.
| | - Leticia Arianne Panini do Carmo
- Laboratory of Experimental Pathology, School of Medicine, Pontifical Catholic University of Parana - PUCPR, R. Imaculada Conceição, 1155 - Prado Velho, Curitiba, PR, Brazil.
| | - Plínio Cézar Neto
- Laboratory of Experimental Pathology, School of Medicine, Pontifical Catholic University of Parana - PUCPR, R. Imaculada Conceição, 1155 - Prado Velho, Curitiba, PR, Brazil.
| | - Seigo Nagashima
- Laboratory of Experimental Pathology, School of Medicine, Pontifical Catholic University of Parana - PUCPR, R. Imaculada Conceição, 1155 - Prado Velho, Curitiba, PR, Brazil.
| | - Lucia de Noronha
- Laboratory of Experimental Pathology, School of Medicine, Pontifical Catholic University of Parana - PUCPR, R. Imaculada Conceição, 1155 - Prado Velho, Curitiba, PR, Brazil; Department of Medical Pathology, Federal University of Parana - UFPR, R. Padre Camargo, 280 - Alto da Glória, Curitiba, PR, Brazil.
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6
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Antarctic Penguins as Reservoirs of Diversity for Avian Avulaviruses. J Virol 2019; 93:JVI.00271-19. [PMID: 30894472 PMCID: PMC6532105 DOI: 10.1128/jvi.00271-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 03/05/2019] [Indexed: 02/06/2023] Open
Abstract
Approximately 99% of all viruses are still to be described, and in our changing world, any one of these unknown viruses could potentially expand their host range and cause epidemic disease in wildlife, agricultural animals, or humans. Avian avulavirus 1 causes outbreaks in wild birds and poultry and is thus well described. However, for many avulavirus species, only a single specimen has been described, and their viral ecology and epidemiology are unknown. Through the detection of avian avulaviruses in penguins from Antarctica, we have been able to expand upon our understanding of three avian avulavirus species (avian avulaviruses 17 to 19) and report a potentially novel avulavirus species. Importantly, we show that penguins appear to play a key role in the epidemiology of avian avulaviruses, and we encourage additional sampling of this avian group. Wild birds harbor a huge diversity of avian avulaviruses (formerly avian paramyxoviruses). Antarctic penguin species have been screened for avian avulaviruses since the 1980s and, as such, are known hosts of these viruses. In this study, we screened three penguin species from the South Shetland Islands and the Antarctic Peninsula for avian avulaviruses. We show that Adelie penguins (Pygoscelis adeliae) are hosts for four different avian avulavirus species, the recently described avian avulaviruses 17 to 19 and avian avulavirus 10-like, never before isolated in Antarctica. A total of 24 viruses were isolated and sequenced; avian avulavirus 17 was the most common, and phylogenetic analysis demonstrated patterns of occurrence, with different genetic clusters corresponding to penguin age and location. Following infection in specific-pathogen-free (SPF) chickens, all four avian avulavirus species were shed from the oral cavity for up to 7 days postinfection. There was limited shedding from the cloaca in a proportion of infected chickens, and all but one bird seroconverted by day 21. No clinical signs were observed. Taken together, we propose that penguin species, including Antarctic penguins, may be the central reservoir for a diversity of avian avulavirus species and that these viruses have the potential to infect other avian hosts. IMPORTANCE Approximately 99% of all viruses are still to be described, and in our changing world, any one of these unknown viruses could potentially expand their host range and cause epidemic disease in wildlife, agricultural animals, or humans. Avian avulavirus 1 causes outbreaks in wild birds and poultry and is thus well described. However, for many avulavirus species, only a single specimen has been described, and their viral ecology and epidemiology are unknown. Through the detection of avian avulaviruses in penguins from Antarctica, we have been able to expand upon our understanding of three avian avulavirus species (avian avulaviruses 17 to 19) and report a potentially novel avulavirus species. Importantly, we show that penguins appear to play a key role in the epidemiology of avian avulaviruses, and we encourage additional sampling of this avian group.
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Bioinformatics and Microarray-Based Technologies to Viral Genome Sequence Analysis. MICROBIAL GENOMICS IN SUSTAINABLE AGROECOSYSTEMS 2019. [PMCID: PMC7121691 DOI: 10.1007/978-981-13-8739-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Identification of microbial pathogen is an important event which lead to diagnosis, treatment, and control of infections produce by them. The high-throughput technology like microarray and new-generation sequencing machine are able to generate huge amount of nucleotide sequences of viral and bacterial genome of both known and unknown pathogens. Few years ago it was the DNA microarrays which had great potential to screen all the known pathogens and yet to be identified pathogen simultaneously. But after the development of a new generation sequencing, technologies and advance computational approach researchers are looking forward for a complete understanding of microbes and host interactions. The powerful sequencing platform is rapidly transforming the landscape of microbial identification and characterization. As bioinformatics analysis tools and databases are easily available to researchers, the enormous amount of data generated can be meaningfully handled for better understanding of the microbial world. Here in this chapter, we present commentary on how the computational method incorporated with sequencing technique made easy for microbial detection and characterization.
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8
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Bortz E, Wu TT, Patel P, Whitelegge JP, Sun R. Proteomics of Bronchoalveolar Lavage Fluid Reveals a Lung Oxidative Stress Response in Murine Herpesvirus-68 Infection. Viruses 2018; 10:v10120670. [PMID: 30486363 PMCID: PMC6316452 DOI: 10.3390/v10120670] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 11/15/2018] [Accepted: 11/20/2018] [Indexed: 12/25/2022] Open
Abstract
Murine herpesvirus-68 (MHV-68) productively infects mouse lungs, exhibiting a complex pathology characteristic of both acute viral infections and chronic respiratory diseases. We sought to discover proteins differentially expressed in bronchoalveolar lavage (BAL) from mice infected with MHV-68. Mice were infected intranasally with MHV-68. After nine days, as the lytic phase of infection resolved, differential BAL proteins were identified by two-dimensional (2D) electrophoresis and mass spectrometry. Of 23 unique proteins, acute phase proteins, vitamin A transport, and oxidative stress response factors Pdx6 and EC-SOD (Sod3) were enriched. Correspondingly, iNOS2 was induced in lung tissue by seven days post-infection. Oxidative stress was partly a direct result of MHV-68 infection, as reactive oxygen species (ROS) were induced in cultured murine NIH3T3 fibroblasts and human lung A549 cells infected with MHV-68. Finally, mice infected with a recombinant MHV-68 co-expressing inflammatory cytokine murine interleukin 6 (IL6) showed exacerbated oxidative stress and soluble type I collagen characteristic of tissue recovery. Thus, oxidative stress appears to be a salient feature of MHV-68 pathogenesis, in part caused by lytic replication of the virus and IL6. Proteins and small molecules in lung oxidative stress networks therefore may provide new therapeutic targets to ameliorate respiratory virus infections.
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Affiliation(s)
- Eric Bortz
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK 99508, USA.
| | - Ting-Ting Wu
- Department of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
| | - Parthive Patel
- Center for Molecular Biology and German Cancer Research Center (DKFZ), University of Heidelberg (ZMBH), 69120 Heidelberg, Germany.
| | - Julian P Whitelegge
- The Pasarow Mass Spectrometry Laboratory & the Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
| | - Ren Sun
- Department of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
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Sposito AJ, Kurdekar A, Zhao J, Hewlett I. Application of nanotechnology in biosensors for enhancing pathogen detection. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2018. [PMID: 29528198 DOI: 10.1002/wnan.1512] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Rapid detection and identification of pathogenic microorganisms is fundamental to minimizing the spread of infectious disease, and informing clinicians on patient treatment strategies. This need has led to the development of enhanced biosensors that utilize state of the art nanomaterials and nanotechnology, and represent the next generation of diagnostics. A primer on nanoscale biorecognition elements such as, nucleic acids, antibodies, and their synthetic analogs (molecular imprinted polymers), will be presented first. Next the application of various nanotechnologies for biosensor transduction will be discussed, along with the inherent nanoscale phenomenon that leads to their improved performance and capabilities in biosensor systems. A future outlook on characterization and quality assurance, nanotoxicity, and nanomaterial integration into lab-on-a-chip systems will provide the closing thoughts. This article is categorized under: Diagnostic Tools > Diagnostic Nanodevices Diagnostic Tools > Biosensing.
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Affiliation(s)
- Alex J Sposito
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Aditya Kurdekar
- Laboratories for Nanoscience and Nanotechnology Research, Sri Sathya Sai Institute of Higher Learning, Anantapur, India
| | - Jiangqin Zhao
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Indira Hewlett
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
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Gregianini TS, Seadi CF, Menegolla I, Martins LG, Ikuta N, Wolf JM, Lunge VR. Human metapneumovirus in Southern Brazil. Rev Soc Bras Med Trop 2018. [DOI: 10.1590/0037-8682-0435-2017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Briese T, Williams DT, Kapoor V, Diviney SM, Certoma A, Wang J, Johansen CA, Chowdhary R, Mackenzie JS, Lipkin WI. Analysis of Arbovirus Isolates from Australia Identifies Novel Bunyaviruses Including a Mapputta Group Virus from Western Australia That Links Gan Gan and Maprik Viruses. PLoS One 2016; 11:e0164868. [PMID: 27764175 PMCID: PMC5072647 DOI: 10.1371/journal.pone.0164868] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 10/03/2016] [Indexed: 01/01/2023] Open
Abstract
The Mapputta group comprises antigenically related viruses indigenous to Australia and Papua New Guinea that are included in the family Bunyaviridae but not currently assigned to a specific genus. We determined and analyzed the genome sequences of five Australian viruses isolated from mosquitoes collected during routine arbovirus surveillance in Western Australia (K10441, SW27571, K13190, and K42904) and New South Wales (12005). Based on matching sequences of all three genome segments to prototype MRM3630 of Trubanaman virus (TRUV), NB6057 of Gan Gan virus (GGV), and MK7532 of Maprik virus (MPKV), isolates K13190 and SW27571 were identified as TRUV, 12005 as GGV, and K42904 as a Mapputta group virus from Western Australia linking GGV and MPKV. The results confirmed serum neutralization data that had linked SW27571 to TRUV. The fifth virus, K10441 from Willare, was most closely related to Batai orthobunyavirus, presumably representing an Australian variant of the virus. Phylogenetic analysis also confirmed the close relationship of our TRUV and GGV isolates to two other recently described Australian viruses, Murrumbidgee virus and Salt Ash virus, respectively. Our findings indicate that TRUV has a wide circulation throughout the Australian continent, demonstrating for the first time its presence in Western Australia. Similarly, the presence of a virus related to GGV, which had been linked to human disease and previously known only from the Australian southeast, was demonstrated in Western Australia. Finally, a Batai virus isolate was identified in Western Australia. The expanding availability of genomic sequence for novel Australian bunyavirus variants supports the identification of suitably conserved or diverse primer-binding target regions to establish group-wide as well as virus-specific nucleic acid tests in support of specific diagnostic and surveillance efforts throughout Australasia.
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Affiliation(s)
- Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, United States of America
- * E-mail: (TB); (DTW)
| | - David T. Williams
- CSIRO, Australian Animal Health Laboratory, Geelong, Victoria, Australia
- School of Biomedical Sciences, Curtin University, Perth, Western Australia, Australia
- * E-mail: (TB); (DTW)
| | - Vishal Kapoor
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Sinead M. Diviney
- School of Biomedical Sciences, Curtin University, Perth, Western Australia, Australia
| | - Andrea Certoma
- CSIRO, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Jianning Wang
- CSIRO, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Cheryl A. Johansen
- The Arbovirus Surveillance and Research Laboratory, University of Western Australia, Nedlands, Western Australia, Australia
| | - Rashmi Chowdhary
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - John S. Mackenzie
- Faculty of Health Sciences, Curtin University, Perth, Western Australia, Australia
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, United States of America
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Wilson WC, Daniels P, Ostlund EN, Johnson DE, Oberst RD, Hairgrove TB, Mediger J, McIntosh MT. Diagnostic Tools for Bluetongue and Epizootic Hemorrhagic Disease Viruses Applicable to North American Veterinary Diagnosticians. Vector Borne Zoonotic Dis 2016; 15:364-73. [PMID: 26086557 DOI: 10.1089/vbz.2014.1702] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This review provides an overview of current and potential new diagnostic tests for bluetongue (BT) and epizootic hemorrhagic disease (EHD) viruses compiled from international participants of the Orbivirus Gap Analysis Workshop, Diagnostic Group. The emphasis of this review is on diagnostic tools available to North American veterinary diagnosticians. Standard diagnostic tests are readily available for BT/EHD viruses, and there are described tests that are published in the World Organization for Animal Health (OIE) Terrestrial Manual. There is however considerable variation in the diagnostic approach to these viruses. Serological assays are well established, and many laboratories are experienced in running these assays. Numerous nucleic acid amplification assays are also available for BT virus (BTV) and EHD virus (EHDV). Although there is considerable experience with BTV reverse-transcriptase PCR (RT-PCR), there are no standards or comparisons of the protocols used by various state and federal veterinary diagnostic laboratories. Methods for genotyping BTV and EHDV isolates are available and are valuable tools for monitoring and analyzing circulating viruses. These methods include RT-PCR panels or arrays, RT-PCR and sequencing of specific genome segments, or the use of next-generation sequencing. In addition to enabling virus characterization, use of advanced molecular detection methods, including DNA microarrays and next-generation sequencing, significantly enhance the ability to detect unique virus strains that may arise through genetic drift, recombination, or viral genome segment reassortment, as well as incursions of new virus strains from other geographical areas.
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Affiliation(s)
- William C Wilson
- 1 Arthropod-Borne Animal Diseases Research Unit, Center for Grain and Animal Health Research , USDA, ARS, Manhattan, Kansas
| | - Peter Daniels
- 2 CSIRO Australian Animal Health Laboratory , Geelong, Australia
| | - Eileen N Ostlund
- 3 National Veterinary Services Laboratories, USDA, APHIS, VS, Science, Technology and Analysis Services , Ames, Iowa
| | - Donna E Johnson
- 3 National Veterinary Services Laboratories, USDA, APHIS, VS, Science, Technology and Analysis Services , Ames, Iowa
| | - Richard D Oberst
- 4 Kansas Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University , Manhattan, Kansas
| | | | - Jessica Mediger
- 6 Department of Veterinary and Biomedical Sciences, South Dakota State University , Brookings, South Dakota
| | - Michael T McIntosh
- 7 Foreign Animal Disease Diagnostic Laboratory, USDA, APHIS, VS, STAS, NVSL, Plum Island Disease Center , Greenport, New York
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Multiplex Technologies. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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Pathogen Discovery. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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15
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Yadav BS, Pokhriyal M, Ratta B, Kumar A, Saxena M, Sharma B. Viral diagnosis in Indian livestock using customized microarray chips. Bioinformation 2015; 11:489-92. [PMID: 26912948 PMCID: PMC4748017 DOI: 10.6026/97320630011489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 10/09/2015] [Indexed: 01/18/2023] Open
Abstract
Viral diagnosis in Indian livestock using customized microarray chips is gaining momentum in recent years. Hence, it is possible to design customized microarray chip for viruses infecting livestock in India. Customized microarray chips identified Bovine herpes virus-1 (BHV-1), Canine Adeno Virus-1 (CAV-1), and Canine Parvo Virus-2 (CPV-2) in clinical samples. Microarray identified specific probes were further confirmed using RT-PCR in all clinical and known samples. Therefore, the application of microarray chips during viral disease outbreaks in Indian livestock is possible where conventional methods are unsuitable. It should be noted that customized application requires a detailed cost efficiency calculation.
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Affiliation(s)
- Brijesh S Yadav
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, India - 243122
| | - Mayank Pokhriyal
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, India - 243122
| | - Barkha Ratta
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, India - 243122
| | - Ajay Kumar
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, India - 243122
| | - Meeta Saxena
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, India - 243122
| | - Bhaskar Sharma
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, India - 243122
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Hamidi SV, Ghourchian H. Colorimetric monitoring of rolling circle amplification for detection of H5N1 influenza virus using metal indicator. Biosens Bioelectron 2015; 72:121-6. [PMID: 25974174 DOI: 10.1016/j.bios.2015.04.078] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 04/22/2015] [Accepted: 04/23/2015] [Indexed: 11/24/2022]
Abstract
A new colorimetric method for monitoring of rolling circle amplification was developed. At first H5N1 target hybrids with padlock probe (PLP) and then PLP is circularized upon the action of T4 ligase enzyme. Subsequently, the circular probe is served as a template for hyperbranched rolling circle amplification (HRCA) by utilizing Bst DNA polymerase enzyme. By improving the reaction, pyrophosphate is produced via DNA polymerization and chelates the Mg(2+) in the buffer solution. This causes change in solution color in the presence of hydroxy naphthol blue (HNB) as a metal indicator. By using pH shock instead of heat shock and isothermal RCA reaction not only the procedure becomes easier, but also application of HNB for colorimetric detection of RCA reaction further simplifies the assay. The responses of the biosensor toward H5N1 were linear in the concentration range from 0.16 to 1.20 pM with a detection limit of 28 fM.
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Affiliation(s)
- Seyed Vahid Hamidi
- Laboratory of Microanalysis, Institute of Bioc hemistry and Biophysics, University of Tehran, P.O. Box 131451384, Tehran, Iran; Nanobiomedicine Center of Excellence,g Nanoscience and Nanotechnology Research Center, University of Tehran, P.O. Box 131451384, Tehran, Iran
| | - Hedayatollah Ghourchian
- Laboratory of Microanalysis, Institute of Bioc hemistry and Biophysics, University of Tehran, P.O. Box 131451384, Tehran, Iran; Nanobiomedicine Center of Excellence,g Nanoscience and Nanotechnology Research Center, University of Tehran, P.O. Box 131451384, Tehran, Iran.
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Sultankulova KT, Chervyakova OV, Kozhabergenov NS, Shorayeva KA, Strochkov VM, Orynbayev MB, Sandybayev NT, Sansyzbay AR, Vasin AV. Comparative evaluation of effectiveness of IAVchip DNA microarray in influenza A diagnosis. ScientificWorldJournal 2014; 2014:620580. [PMID: 25548788 PMCID: PMC4274914 DOI: 10.1155/2014/620580] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/22/2014] [Accepted: 09/28/2014] [Indexed: 01/30/2023] Open
Abstract
The paper describes comparative evaluation of IAVchip DNA microarray, reverse transcription PCR (RT-PCR), and real-time RT-PCR versus virus isolation in chicken embryos and shows their diagnostic effectiveness in detection and subtyping of influenza A virus. The tests were evaluated with use of 185 specimens from humans, animals, and birds. IAVchip DNA microarray demonstrates higher diagnostic effectiveness (99.45%) in early influenza A diagnosis as compared to the real-time PCR (98.38%) and RT-PCR (96.22%), thus showing its clear superiority. Diagnostic sensitivity of IAVchip DNA microarray (100%) exceeds the same of RT-PCR (95.95%) and real-time RT-PCR (97.96%) in the range of estimated confidence intervals. IAVchip DNA microarray and real-time RT-PCR displayed equal diagnostic specificity (98.85%), while diagnostic specificity of RT-PCR was 96.40%. IAVchip DNA microarray has an advantage over the other tests for influenza A diagnosis and virus identification as a more rapid method that allows performing simultaneous detection and subtyping of about tens of specimens within one experiment during 8-10 hours. The developed IAVchip DNA microarray is a general test tool that enables identifying simultaneously 16 hemagglutinin (HA) and 9 neuraminidase (NA) subtypes of influenza A virus and also to screen the influenza A viruses from humans, animals, and birds by M and NP genes.
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Affiliation(s)
- K. T. Sultankulova
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of Ministry of Education and Science of Republic of Kazakhstan, Gvardeiskiy, Kordaiskiy Rayon, Zhambylskaya Oblast 080409, Kazakhstan
| | - O. V. Chervyakova
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of Ministry of Education and Science of Republic of Kazakhstan, Gvardeiskiy, Kordaiskiy Rayon, Zhambylskaya Oblast 080409, Kazakhstan
| | - N. S. Kozhabergenov
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of Ministry of Education and Science of Republic of Kazakhstan, Gvardeiskiy, Kordaiskiy Rayon, Zhambylskaya Oblast 080409, Kazakhstan
| | - K. A. Shorayeva
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of Ministry of Education and Science of Republic of Kazakhstan, Gvardeiskiy, Kordaiskiy Rayon, Zhambylskaya Oblast 080409, Kazakhstan
| | - V. M. Strochkov
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of Ministry of Education and Science of Republic of Kazakhstan, Gvardeiskiy, Kordaiskiy Rayon, Zhambylskaya Oblast 080409, Kazakhstan
| | - M. B. Orynbayev
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of Ministry of Education and Science of Republic of Kazakhstan, Gvardeiskiy, Kordaiskiy Rayon, Zhambylskaya Oblast 080409, Kazakhstan
| | - N. T. Sandybayev
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of Ministry of Education and Science of Republic of Kazakhstan, Gvardeiskiy, Kordaiskiy Rayon, Zhambylskaya Oblast 080409, Kazakhstan
| | - A. R. Sansyzbay
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of Ministry of Education and Science of Republic of Kazakhstan, Gvardeiskiy, Kordaiskiy Rayon, Zhambylskaya Oblast 080409, Kazakhstan
| | - A. V. Vasin
- Research Institute of Influenza, Ministry of Healthcare of the Russian Federation, Prof. Popov Street 15/17, Saint Petersburg 197376, Russia
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Chandler DP, Griesemer SB, Knickerbocker C, Golova JB, Lambarqui A, Perov AN, Zimmerman C, Wiles C, Rudy GB, St George K. Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. J Virol Methods 2014; 208:152-9. [PMID: 25066276 PMCID: PMC4175443 DOI: 10.1016/j.jviromet.2014.07.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 07/09/2014] [Accepted: 07/15/2014] [Indexed: 11/22/2022]
Abstract
The objectives of this study were to develop a user-friendly, gel element microarray test for influenza virus detection, subtyping, and neuraminidase inhibitor resistance detection, assess the performance characteristics of the assay, and perform a clinical evaluation on retrospective nasopharyngeal swab specimens. A streamlined microarray workflow enabled a single user to run up to 24 tests in an 8h shift. The most sensitive components of the test were the primers and probes targeting the A/H1 pdm09 HA gene with an analytical limit of detection (LoD) <100 gene copies (gc) per reaction. LoDs for all targets in nasopharyngeal swab samples were ≤1000 gc, with the exception of one target in the seasonal A/H1N1 subtype. Seasonal H275Y variants were detectable in a mixed population when present at >5% with wild type virus, while the 2009 pandemic H1N1 H275Y variant was detectable at ≤1% in a mixture with pandemic wild type virus. Influenza typing and subtyping results concurred with those obtained with real-time RT-PCR assays on more than 97% of the samples tested. The results demonstrate that a large panel of single-plex, real-time RT-PCR tests can be translated to an easy-to-use, sensitive, and specific microarray test for potential diagnostic use.
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Affiliation(s)
- Darrell P Chandler
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, United States.
| | - Sara B Griesemer
- Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY 12208, United States
| | | | - Julia B Golova
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, United States
| | - Amine Lambarqui
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, United States
| | - Alexander N Perov
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, United States
| | - Cynthia Zimmerman
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, United States
| | - Cory Wiles
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, United States
| | - George B Rudy
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, United States
| | - Kirsten St George
- Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY 12208, United States
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Abstract
Gastroenteritis is a clinical illness of humans and other animals that is characterized by vomiting and diarrhea and caused by a variety of pathogens, including viruses. An increasing number of viral species have been associated with gastroenteritis or have been found in stool samples as new molecular tools have been developed. In this work, a DNA microarray capable in theory of parallel detection of more than 100 viral species was developed and tested. Initial validation was done with 10 different virus species, and an additional 5 species were validated using clinical samples. Detection limits of 1 × 10(3) virus particles of Human adenovirus C (HAdV), Human astrovirus (HAstV), and group A Rotavirus (RV-A) were established. Furthermore, when exogenous RNA was added, the limit for RV-A detection decreased by one log. In a small group of clinical samples from children with gastroenteritis (n = 76), the microarray detected at least one viral species in 92% of the samples. Single infection was identified in 63 samples (83%), and coinfection with more than one virus was identified in 7 samples (9%). The most abundant virus species were RV-A (58%), followed by Anellovirus (15.8%), HAstV (6.6%), HAdV (5.3%), Norwalk virus (6.6%), Human enterovirus (HEV) (9.2%), Human parechovirus (1.3%), Sapporo virus (1.3%), and Human bocavirus (1.3%). To further test the specificity and sensitivity of the microarray, the results were verified by reverse transcription-PCR (RT-PCR) detection of 5 gastrointestinal viruses. The RT-PCR assay detected a virus in 59 samples (78%). The microarray showed good performance for detection of RV-A, HAstV, and calicivirus, while the sensitivity for HAdV and HEV was low. Furthermore, some discrepancies in detection of mixed infections were observed and were addressed by reverse transcription-quantitative PCR (RT-qPCR) of the viruses involved. It was observed that differences in the amount of genetic material favored the detection of the most abundant virus. The microarray described in this work should help in understanding the etiology of gastroenteritis in humans and animals.
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Baurakiades E, Costa VH, Raboni SM, de Almeida VRT, Larsen KSK, Kohler JN, Gozzo PDC, Klassen G, Manica GCM, de Noronha L. The roles of ADAM33, ADAM28, IL-13 and IL-4 in the development of lung injuries in children with lethal non-pandemic acute infectious pneumonia. J Clin Virol 2014; 61:585-9. [PMID: 25453333 DOI: 10.1016/j.jcv.2014.10.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 10/11/2014] [Indexed: 11/16/2022]
Abstract
BACKGROUND ADAM28, ADAM33, IL-13, IL-4 and other cytokines (IL-6 and IL-10) seem to play important roles in the persistence and maintenance of acute inflammatory processes that ultimately lead to lung remodeling and pulmonary fibrosis, which may be responsible for the high morbidity and mortality rates associated with non-pandemic acute viral pneumonias in childhood. OBJECTIVES The aim of this study was to evaluate the roles of ADAM33, ADAM28, IL4, IL6, IL10 and IL13 in the development of inflammation and alveolar fibrosis due to lethal acute respiratory infections of the lower airway in a pediatric population, especially in those with viral etiology. STUDY DESIGN For this study, 193 cases were selected, and samples from the cases were processed for viral antigen detection by immunohistochemistry and then separated into two groups: virus-positive (n=68) and virus-negative (n=125). Immunohistochemistry was performed to assess the presence of metalloproteinases (ADAM33 and ADAM28) and inflammatory cytokines (IL-4, IL-13, IL-6, IL-10) in the alveolar septa. RESULTS The virus-positive group showed stronger immunolabeling for ADAM33, ADAM28, IL-4 and IL-13 (p<0.0001 for all variables). The staining intensities for ADAM33 and ADAM28 were directly proportional to the intensities for IL-4 and IL-13 (p<0.0001). CONCLUSIONS The results of this study suggest that these proteins play important roles in pulmonary inflammatory reactions elicited against etiological viral agents. In addition, these mediators may affect the process of lung remodeling and the development of pulmonary fibrosis.
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Affiliation(s)
- Emanuele Baurakiades
- Pontifical Catholic University of Paraná, Rua Imaculada Conceição, 1155, Prado Velho, Curitiba, Paraná, Brazil.
| | - Victor Horácio Costa
- Pontifical Catholic University of Paraná, Rua Imaculada Conceição, 1155, Prado Velho, Curitiba, Paraná, Brazil.
| | - Sonia Mara Raboni
- Hospital de Clínicas of Federal University of Paraná, Rua General Carneiro, 181, Centro, Curitiba, Paraná, Brazil.
| | | | - Kelly Susana Kunze Larsen
- Pontifical Catholic University of Paraná, Rua Imaculada Conceição, 1155, Prado Velho, Curitiba, Paraná, Brazil.
| | - Juliana Nemetz Kohler
- Pontifical Catholic University of Paraná, Rua Imaculada Conceição, 1155, Prado Velho, Curitiba, Paraná, Brazil.
| | - Priscilla do Carmo Gozzo
- Pontifical Catholic University of Paraná, Rua Imaculada Conceição, 1155, Prado Velho, Curitiba, Paraná, Brazil.
| | - Giseli Klassen
- Federal University of Paraná, Rua General Carneiro, 181, Centro, Curitiba, Paraná, Brazil.
| | - Graciele C M Manica
- Federal University of Paraná, Rua General Carneiro, 181, Centro, Curitiba, Paraná, Brazil.
| | - Lucia de Noronha
- Pontifical Catholic University of Paraná, Rua Imaculada Conceição, 1155, Prado Velho, Curitiba, Paraná, Brazil.
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de Souza Costa VH, Baurakiades E, Viola Azevedo ML, Traiano G, Kowal Rosales J, Kunze Larsen KS, Raboni SM, de Noronha L. Immunohistochemistry analysis of pulmonary infiltrates in necropsy samples of children with non-pandemic lethal respiratory infections (RSV; ADV; PIV1; PIV2; PIV3; FLU A; FLU B). J Clin Virol 2014; 61:211-5. [PMID: 25052332 PMCID: PMC7173026 DOI: 10.1016/j.jcv.2014.06.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/18/2014] [Accepted: 06/25/2014] [Indexed: 11/30/2022]
Abstract
Respiratory infections represent a globally cause of mortality in childhood. Individuals with impaired cellular immunity have more severe diseases. The inflammatory response appears to play role in recovery from these diseases. TCD8+ count (immunohistochemistry) was higher in the viral pneumonias (p
= 0.04). Tissue TCD8+ lymphocytes play role in the viral pneumonia inflammatory response.
Background Acute viral respiratory infections represent a globally important cause of morbidity and mortality in childhood. An individual's cellular response appears to play a critical role in recovery from infections, given that individuals with impaired cellular immunity, congenital or acquired, have more severe diseases and secrete the virus for longer periods. Objectives The aim of this study was to immunohistochemically evaluate the expression of the cell surface antigens CD4, CD8, CD25, CD14 and CD74, in pneumonic infiltrates in the alveolar septa using paraffin-embedded lung samples from autopsies of immunocompetent children who died of lethal, non-pandemic, severe acute respiratory infections. Study design From 794 cases of pediatric autopsies of patients with severe respiratory disease (between 1960 and 2004), 193 cases were selected for this study. To identify subpopulations of inflammatory cells in the alveolar septa, cell surface antigen expression was assessed by immunohistochemistry using the following primary antibodies: anti-CD4, anti-CD8, anti-CD14, anti-CD25 and anti-CD74. Results The TCD8+ lymphocyte count was higher in the virus-positive group (p = 0.04) and was also much higher among cases that were positive for more than three viral types (p = 0.016). There were fewer CD14+ cells in cases of AdV (adenovirus) infection (p = 0.002), and there was a predominance of CD74+ cells in the histopathological pattern defined as interstitial pneumonitis (p = 0.037). Conclusions The results of this study demonstrate that TCD8+ lymphocytes present in the alveolar septa participate to a greater extent in the response toward viral pneumonia, while CD14+ cell numbers are often reduced in cases of AdV.
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Affiliation(s)
| | - Emanuele Baurakiades
- Pontifícia Universidade Católica do Paraná, Rua Imaculada Conceição, 1155 Prado Velho, Curitiba, Paraná, Brazil.
| | - Marina Louise Viola Azevedo
- Pontifícia Universidade Católica do Paraná, Rua Imaculada Conceição, 1155 Prado Velho, Curitiba, Paraná, Brazil.
| | - Gabriela Traiano
- Pontifícia Universidade Católica do Paraná, Rua Imaculada Conceição, 1155 Prado Velho, Curitiba, Paraná, Brazil.
| | - Jeana Kowal Rosales
- Pontifícia Universidade Católica do Paraná, Rua Imaculada Conceição, 1155 Prado Velho, Curitiba, Paraná, Brazil.
| | - Kelly Susana Kunze Larsen
- Pontifícia Universidade Católica do Paraná, Rua Imaculada Conceição, 1155 Prado Velho, Curitiba, Paraná, Brazil.
| | - Sonia Maria Raboni
- Universidade Federal do Paraná - Hospital de Clínicas, Rua General Carneiro, 181 Centro, Curitiba, Paraná, Brazil.
| | - Lucia de Noronha
- Pontifícia Universidade Católica do Paraná, Rua Imaculada Conceição, 1155 Prado Velho, Curitiba, Paraná, Brazil.
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Briese T, Chowdhary R, Travassos da Rosa A, Hutchison SK, Popov V, Street C, Tesh RB, Lipkin WI. Upolu virus and Aransas Bay virus, two presumptive bunyaviruses, are novel members of the family Orthomyxoviridae. J Virol 2014; 88:5298-309. [PMID: 24574415 PMCID: PMC4019087 DOI: 10.1128/jvi.03391-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 02/21/2014] [Indexed: 01/23/2023] Open
Abstract
UNLABELLED Emerging and zoonotic pathogens pose continuing threats to human health and ongoing challenges to diagnostics. As nucleic acid tests are playing increasingly prominent roles in diagnostics, the genetic characterization of molecularly uncharacterized agents is expected to significantly enhance detection and surveillance capabilities. We report the identification of two previously unrecognized members of the family Orthomyxoviridae, which includes the influenza viruses and the tick-transmitted Thogoto and Dhori viruses. We provide morphological, serologic, and genetic evidence that Upolu virus (UPOV) from Australia and Aransas Bay virus (ABV) from North America, both previously considered potential bunyaviruses based on electron microscopy and physicochemical features, are orthomyxoviruses instead. Their genomes show up to 68% nucleotide sequence identity to Thogoto virus (segment 2; ∼74% at the amino acid level) and a more distant relationship to Dhori virus, the two prototype viruses of the recognized species of the genus Thogotovirus. Despite sequence similarity, the coding potentials of UPOV and ABV differed from that of Thogoto virus, instead being like that of Dhori virus. Our findings suggest that the tick-transmitted viruses UPOV and ABV represent geographically distinct viruses in the genus Thogotovirus of the family Orthomyxoviridae that do not fit in the two currently recognized species of this genus. IMPORTANCE Upolu virus (UPOV) and Aransas Bay virus (ABV) are shown to be orthomyxoviruses instead of bunyaviruses, as previously thought. Genetic characterization and adequate classification of agents are paramount in this molecular age to devise appropriate surveillance and diagnostics. Although more closely related to Thogoto virus by sequence, UPOV and ABV differ in their coding potentials by lacking a proposed pathogenicity factor. In this respect, they are similar to Dhori virus, which, despite the lack of a pathogenicity factor, can cause disease. These findings enable further studies into the evolution and pathogenicity of orthomyxoviruses.
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Affiliation(s)
- Thomas Briese
- Center for Infection and Immunity, Columbia University, New York, New York, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Rashmi Chowdhary
- Center for Infection and Immunity, Columbia University, New York, New York, USA
| | | | | | - Vsevolod Popov
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Craig Street
- Center for Infection and Immunity, Columbia University, New York, New York, USA
| | - Robert B. Tesh
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - W. Ian Lipkin
- Center for Infection and Immunity, Columbia University, New York, New York, USA
- Department of Pathology and Neurology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
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Hsu CC, Tokarz R, Briese T, Tsai HC, Quan PL, Lipkin WI. Use of staged molecular analysis to determine causes of unexplained central nervous system infections. Emerg Infect Dis 2014; 19:1470-7. [PMID: 23965845 PMCID: PMC3810931 DOI: 10.3201/eid1909.130474] [Citation(s) in RCA: 15] [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] [Indexed: 01/17/2023] Open
Abstract
No agent is implicated in most central nervous system (CNS) infections. To investigate cerebrospinal fluid samples from patients with CNS infections of unknown cause in 1 hospital in Taiwan, we used a staged molecular approach, incorporating techniques including multiplex MassTag PCR, 16S rRNA PCR, DNA microarray, and high-throughput pyrosequencing. We determined the infectious agent for 31 (24%) of 131 previously negative samples. Candidate pathogens were identified for 25 (27%) of 94 unexplained meningitis cases and 6 (16%) of 37 unexplained encephalitis cases. Epstein-Barr virus (18 infections) accounted for most of the identified agents in unexplained meningitis cases, followed by Escherichia coli (5), enterovirus (2), human herpesvirus 2 (1), and Mycobacterium tuberculosis. Herpesviruses were identified in samples from patients with unexplained encephalitis cases, including varicella-zoster virus (3 infections), human herpesvirus 1 (2), and cytomegalovirus (1). Our study confirms the power of multiplex MassTag PCR as a rapid diagnostic tool for identifying pathogens causing unexplained CNS infections.
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Yadav BS, Pokhriyal M, Vasishtha DP, Sharma B. Animal Viruses Probe dataset (AVPDS) for microarray-based diagnosis and identification of viruses. Curr Microbiol 2013; 68:301-4. [PMID: 24129840 PMCID: PMC7079848 DOI: 10.1007/s00284-013-0477-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 09/02/2013] [Indexed: 11/28/2022]
Abstract
AVPDS (Animal Viruses Probe dataset) is a dataset of virus-specific and conserve oligonucleotides for identification and diagnosis of viruses infecting animals. The current dataset contain 20,619 virus specific probes for 833 viruses and their subtypes and 3,988 conserved probes for 146 viral genera. Dataset of virus specific probe has been divided into two fields namely virus name and probe sequence. Similarly conserved probes for virus genera table have genus, and subgroup within genus name and probe sequence. The subgroup within genus is artificially divided subgroups with no taxonomic significance and contains probes which identifies viruses in that specific subgroup of the genus. Using this dataset we have successfully diagnosed the first case of Newcastle disease virus in sheep and reported a mixed infection of Bovine viral diarrhea and Bovine herpesvirus in cattle. These dataset also contains probes which cross reacts across species experimentally though computationally they meet specifications. These probes have been marked. We hope that this dataset will be useful in microarray-based detection of viruses. The dataset can be accessed through the link https://dl.dropboxusercontent.com/u/94060831/avpds/HOME.html.
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Affiliation(s)
- Brijesh S Yadav
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, India,
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Huang W, Yang Y, Zhang X, Zhao C, Yin A, Zhang X, He Z, Jiang Y, Zhang L. An easy operating pathogen microarray (EOPM) platform for rapid screening of vertebrate pathogens. BMC Infect Dis 2013; 13:437. [PMID: 24053492 PMCID: PMC3848773 DOI: 10.1186/1471-2334-13-437] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 09/13/2013] [Indexed: 11/17/2022] Open
Abstract
Background Infectious diseases emerge frequently in China, partly because of its large and highly mobile population. Therefore, a rapid and cost-effective pathogen screening method with broad coverage is required for prevention and control of infectious diseases. The availability of a large number of microbial genome sequences generated by conventional Sanger sequencing and next generation sequencing has enabled the development of a high-throughput high-density microarray platform for rapid large-scale screening of vertebrate pathogens. Methods An easy operating pathogen microarray (EOPM) was designed to detect almost all known pathogens and related species based on their genomic sequences. For effective identification of pathogens from EOPM data, a statistical enrichment algorithm has been proposed, and further implemented in a user-friendly web-based interface. Results Using multiple probes designed to specifically detect a microbial genus or species, EOPM can correctly identify known pathogens at the species or genus level in blinded testing. Despite a lower sensitivity than PCR, EOPM is sufficiently sensitive to detect the predominant pathogens causing clinical symptoms. During application in two recent clinical infectious disease outbreaks in China, EOPM successfully identified the responsible pathogens. Conclusions EOPM is an effective surveillance platform for infectious diseases, and can play an important role in infectious disease control.
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Affiliation(s)
- Weiwei Huang
- BioChain (Beijing) Science & Technology Inc,, No,7A, Yongchang North Rd, Business Development Area, Beijing 100176, China.
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Ratta B, Yadav BS, Pokhriyal M, Saxena M, Sharma B. Microarray chip based identification of a mixed infection of bovine herpesvirus 1 and bovine viral diarrhea 2 from Indian cattle. Curr Microbiol 2013; 68:127-31. [PMID: 24026447 PMCID: PMC7080061 DOI: 10.1007/s00284-013-0448-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 07/22/2013] [Indexed: 11/08/2022]
Abstract
Bovine herpesvirus 1 (BHV1) and bovine viral diarrhea virus 2 (BVD2) are endemic in India although no mixed infection with these viruses has been reported from India. We report first mixed infection of these viruses in cattle during routine screening with a microarray chip. 62 of the 69 probes of BHV1 and 42 of the 57 BVD2 probes in the chip gave positive signals for the virus. The virus infections were subsequently confirmed by RT-PCR. We also discuss the implications of these findings.
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Affiliation(s)
- Barkha Ratta
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, 243122 India
| | - Brijesh Singh Yadav
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, 243122 India
| | - Mayank Pokhriyal
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, 243122 India
| | - Meeta Saxena
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, 243122 India
| | - Bhaskar Sharma
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, 243122 India
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27
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Lee HS, Briese T, Winkler C, Rewers M, Bonifacio E, Hyoty H, Pflueger M, Simell O, She JX, Hagopian W, Lernmark Å, Akolkar B, Krischer J, Ziegler AG. Next-generation sequencing for viruses in children with rapid-onset type 1 diabetes. Diabetologia 2013; 56:1705-1711. [PMID: 23657799 PMCID: PMC4019381 DOI: 10.1007/s00125-013-2924-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 04/05/2013] [Indexed: 02/02/2023]
Abstract
AIMS/HYPOTHESIS Viruses are candidate causative agents in the pathogenesis of autoimmune (type 1) diabetes. We hypothesised that children with a rapid onset of type 1 diabetes may have been exposed to such agents shortly before the initiation of islet autoimmunity, possibly at high dose, and thus study of these children could help identify viruses involved in the development of autoimmune diabetes. METHODS We used next-generation sequencing to search for viruses in plasma samples and examined the history of infection and fever in children enrolled in The Environmental Determinants of Diabetes in the Young (TEDDY) study who progressed to type 1 diabetes within 6 months from the appearance of islet autoimmunity, and in matched islet-autoantibody-negative controls. RESULTS Viruses were not detected more frequently in plasma from rapid-onset patients than in controls during the period surrounding seroconversion. In addition, infection histories were found to be similar between children with rapid-onset diabetes and control children, although episodes of fever were reported less frequently in children with rapid-onset diabetes. CONCLUSIONS/INTERPRETATION These findings do not support the presence of viraemia around the time of seroconversion in young children with rapid-onset type 1 diabetes.
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Affiliation(s)
- H-S. Lee
- Pediatric Epidemiology Center, Department of Pediatrics, University of South Florida, Tampa, FL, USA
| | - T. Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - C. Winkler
- Forschergruppe Diabetes e.V., Neuherberg, Germany
- Institute of Diabetes Research, Helmholtz Zentrum München and Forschergruppe Diabetes, Klinikum rechts der Isar, Technische Universität München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - M. Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO, USA
| | - E. Bonifacio
- Center for Regenerative Therapies-Dresden, Dresden University of Technology, Dresden, Germany
| | - H. Hyoty
- Department of Virology, University of Tampere, Finland
| | - M. Pflueger
- Institute of Diabetes Research, Helmholtz Zentrum München and Forschergruppe Diabetes, Klinikum rechts der Isar, Technische Universität München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - O. Simell
- Department of Pediatrics, Turku University Central Hospital, Turku, Finland
| | - J. X. She
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Georgia Regents University, Augusta, GA, USA
| | - W. Hagopian
- Pacific Northwest Diabetes Research Institute, Seattle, WA, USA
| | - Å. Lernmark
- Department of Clinical Sciences, Lund University, Skåne University Hospital SUS, Malmö, Sweden
| | - B. Akolkar
- National Institute of Diabetes & Digestive & Kidney Disorders, Bethesda, MD, USA
| | - J. Krischer
- Pediatric Epidemiology Center, Department of Pediatrics, University of South Florida, Tampa, FL, USA
| | - A. G. Ziegler
- Forschergruppe Diabetes e.V., Neuherberg, Germany
- Institute of Diabetes Research, Helmholtz Zentrum München and Forschergruppe Diabetes, Klinikum rechts der Isar, Technische Universität München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
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28
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Bousbia S, Raoult D, La Scola B. Pneumonia pathogen detection and microbial interactions in polymicrobial episodes. Future Microbiol 2013; 8:633-60. [DOI: 10.2217/fmb.13.26] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Recent reports show that microbial communities associated with respiratory infections, such as pneumonia and cystic fibrosis, are more complex than expected. Most of these communities are polymicrobial and might comprise microorganisms originating from several diverse biological and ecological sources. Moreover, unexpected bacteria in the etiology of these respiratory infections have been increasingly identified. These findings were established with the use of efficient microbiological diagnostic tools, particularly molecular tools based on common gene amplification, followed by cloning and sequencing approaches, which facilitated the identification of the polymicrobial flora. Similarly, recent investigations reported that microbial interactions might exist between species in polymicrobial communities, including typical pneumonia pathogens, such as Pseudomonas aeruginosa and Candida albicans. Here, we review recent tools for microbial diagnosis, in particular, of intensive care unit pneumonia and the reported interactions between microbial species that have primarily been identified in the etiology of these infections.
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Affiliation(s)
- Sabri Bousbia
- Aix-Marseille Université, URMITE, UM 63, CNRS 7278, IRD 198, INSERM U1095, Facultés de Médecine, Marseille, France
- IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique – Hôpitaux de Marseille, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, URMITE, UM 63, CNRS 7278, IRD 198, INSERM U1095, Facultés de Médecine, Marseille, France
- IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique – Hôpitaux de Marseille, Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique – Hôpitaux de Marseille, Marseille, France
- Aix-Marseille Université, URMITE, UM 63, CNRS 7278, IRD 198, INSERM U1095, Facultés de Médecine, Marseille, France.
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29
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Abstract
Determining the viral etiology of respiratory tract infections (RTI) has been limited for the most part to specific primer PCR-based methods due to their increased sensitivity and specificity compared to other methods, such as tissue culture. However, specific primer approaches have limited the ability to fully understand the diversity of infecting pathogens. A pathogen chip system (PathChip), developed at the Genome Institute of Singapore (GIS), using a random-tagged PCR coupled to a chip with over 170,000 probes, has the potential to recognize all known human viral pathogens. We tested 290 nasal wash specimens from Filipino children <2 years of age with respiratory tract infections using culture and 3 PCR methods-EraGen, Luminex, and the GIS PathChip. The PathChip had good diagnostic accuracy, ranging from 85.9% (95% confidence interval [CI], 81.3 to 89.7%) for rhinovirus/enteroviruses to 98.6% (95% CI, 96.5 to 99.6%) for PIV 2, compared to the other methods and additionally identified a number of viruses not detected by these methods.
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30
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Yadav BS, Ronda V, Vashista DP, Sharma B. Sequencing and computational approaches to identification and characterization of microbial organisms. Biomed Eng Comput Biol 2013; 5:43-9. [PMID: 25288901 PMCID: PMC4147756 DOI: 10.4137/becb.s10886] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The recent advances in sequencing technologies and computational approaches are propelling scientists ever closer towards complete understanding of human-microbial interactions. The powerful sequencing platforms are rapidly producing huge amounts of nucleotide sequence data which are compiled into huge databases. This sequence data can be retrieved, assembled, and analyzed for identification of microbial pathogens and diagnosis of diseases. In this article, we present a commentary on how the metagenomics incorporated with microarray and new sequencing techniques are helping microbial detection and characterization.
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Affiliation(s)
- Brijesh Singh Yadav
- Department of Botany and Microbiology, H.N.B. Garhwal University, Srinagar, India. ; Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, India
| | - Venkateswarlu Ronda
- Central Institute of Fisheries Technology, Cochin, India. ; Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, India
| | - Dinesh P Vashista
- Department of Botany and Microbiology, H.N.B. Garhwal University, Srinagar, India
| | - Bhaskar Sharma
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, India
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31
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Berthet N, Paulous S, Coffey LL, Frenkiel MP, Moltini I, Tran C, Matheus S, Ottone C, Ungeheuer MN, Renaudat C, Caro V, Dussart P, Gessain A, Desprès P. Resequencing microarray method for molecular diagnosis of human arboviral diseases. J Clin Virol 2012; 56:238-43. [PMID: 23219893 DOI: 10.1016/j.jcv.2012.10.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 10/31/2012] [Indexed: 12/29/2022]
Abstract
BACKGROUND Resequencing DNA microarray (RMA) technology uses probes designed to identify a panel of viral sequences. It can be used for detecting emerging viruses by revealing the nucleotide polymorphisms within the target of interest. OBJECTIVES/STUDY DESIGN As a new tool for molecular diagnosis of arbovirus infection, high density PathogenID v2.0 RMA (PID2-RMA) was assessed for the detection and genetic analysis of dengue, West Nile, and Chikungunya viruses in spiked blood samples or sera from individuals infected with dengue virus. Viral RNAs extracted from biological samples were retrotranscribed into cDNA and amplified using the Phi 29 polymerase-based method. This amplified cDNA was used for hybridization on PID2-RMA. RESULTS A good specificity of RMA-based detection was demonstrated using a panel of arboviruses including Dengue, West Nile and Chikungunya viruses. This technology was also efficient for the detection and genetic analysis of the different serotypes of dengue virus in sera of infected patients. Furthermore, the mixing of dengue, West Nile and Chikungunya prototype viruses within a single sample of human blood did not interfere with the sensitivity of PID2-RMA. CONCLUSIONS Our data show that high density PID2-RMA was suitable for the identification of medically important arboviruses. It appears to be particularly adapted to the genetic analysis of dengue, West Nile, and Chikungunya viruses in urgent clinical situations where the rapid identification and characterization of the pathogen is essential.
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Affiliation(s)
- N Berthet
- Institut Pasteur, Epidemiology and Physiopathology of Oncogenic Viruses Unit, 28 rue du Docteur Roux, F75015 Paris, France
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32
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Simultaneous detection of major enteric viruses using a combimatrix microarray. J Microbiol 2012; 50:970-7. [DOI: 10.1007/s12275-012-2228-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 07/05/2012] [Indexed: 01/02/2023]
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33
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Fancello L, Raoult D, Desnues C. Computational tools for viral metagenomics and their application in clinical research. Virology 2012; 434:162-74. [PMID: 23062738 PMCID: PMC7111993 DOI: 10.1016/j.virol.2012.09.025] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 09/15/2012] [Accepted: 09/23/2012] [Indexed: 02/06/2023]
Abstract
There are 100 times more virions than eukaryotic cells in a healthy human body. The characterization of human-associated viral communities in a non-pathological state and the detection of viral pathogens in cases of infection are essential for medical care and epidemic surveillance. Viral metagenomics, the sequenced-based analysis of the complete collection of viral genomes directly isolated from an organism or an ecosystem, bypasses the “single-organism-level” point of view of clinical diagnostics and thus the need to isolate and culture the targeted organism. The first part of this review is dedicated to a presentation of past research in viral metagenomics with an emphasis on human-associated viral communities (eukaryotic viruses and bacteriophages). In the second part, we review more precisely the computational challenges posed by the analysis of viral metagenomes, and we illustrate the problem of sequences that do not have homologs in public databases and the possible approaches to characterize them.
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Affiliation(s)
- L Fancello
- Aix Marseille University, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
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34
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Leski TA, Lin B, Malanoski AP, Stenger DA. Application of resequencing microarrays in microbial detection and characterization. Future Microbiol 2012; 7:625-37. [PMID: 22568717 DOI: 10.2217/fmb.12.30] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Microarrays are powerful, highly parallel assays that are transforming microbiological diagnostics and research. The adaptation of microarray-based resequencing technology for microbial detection and characterization resulted in the development of a number assays that have unique advantages over other existing technologies. This technological platform seems to be especially useful for sensitive and high-resolution multiplexed diagnostics for clinical syndromes with similar symptoms, screening environmental samples for biothreat agents, as well as genotyping and whole-genome analysis of single pathogens.
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Affiliation(s)
- Tomasz A Leski
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, SW, Washington, DC 20375, USA.
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35
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Bhat N, O'Brien KL, Karron RA, Driscoll AJ, Murdoch DR. Use and evaluation of molecular diagnostics for pneumonia etiology studies. Clin Infect Dis 2012; 54 Suppl 2:S153-8. [PMID: 22403230 PMCID: PMC3297547 DOI: 10.1093/cid/cir1060] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 12/21/2011] [Indexed: 01/16/2023] Open
Abstract
Comprehensive microbiological testing will be a core function of the Pneumonia Etiology Research for Child Health (PERCH) project. The development stage of PERCH provided the time and resources necessary for us to conduct a comprehensive review of the current state of respiratory diagnostics. These efforts allowed us to articulate the unique requirements of PERCH, establish that molecular methods would be central to our testing strategy, and focus on a short list of candidate platforms. This process also highlighted critical challenges in the general design and interpretation of diagnostic evaluation studies, particularly in the field of respiratory infections. Although our final molecular diagnostic platform was ultimately selected on the basis of operational and strategic considerations determined by the specific context of PERCH, our review highlighted several conceptual and practical challenges in respiratory diagnostics that have broader relevance for the performance and interpretation of pneumonia research studies.
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Affiliation(s)
- Niranjan Bhat
- Department of International Health, Johns Hopkins Bloomberg School of Public Health
- Division of Infectious Diseases, Department of Pediatrics, Johns Hopkins School of Medicine
| | | | - Ruth A. Karron
- Center for Immunization Research, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - David R. Murdoch
- Department of Pathology, University of Otago
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
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36
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Jokela P, Piiparinen H, Mannonen L, Auvinen E, Lappalainen M. Performance of the Luminex xTAG Respiratory Viral Panel Fast in a clinical laboratory setting. J Virol Methods 2012; 182:82-6. [PMID: 22465255 PMCID: PMC7119588 DOI: 10.1016/j.jviromet.2012.03.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 03/11/2012] [Accepted: 03/14/2012] [Indexed: 11/29/2022]
Abstract
The aim of the study was to develop a real-time RT-PCR for the detection of enteroviruses (EVs) and rhinoviruses (RVs) and to assess the performance of the xTAG RVP Fast assay in comparison to a direct fluorescent assay (DFA), a real-time RT-PCR assay for the detection of respiratory syncytial virus (RSV) and human metapneumovirus (hMPV), and the EV/RV RT-PCR assay developed in this study. The performance of the RVP Fast assay was assessed in the analysis of 373 nasopharyngeal samples. For the viruses of the DFA panel, detection rates of 27.6% and 23.8% were obtained by RVP and DFA, respectively, in analysis of a set of 297 samples collected in 2009–2010. These results show statistically significant superiority of the RVP Fast assay (P = 0.049). For RSV, hMPV, EV, and RV, detection rates of 48.0% and 45.2% were achieved by RVP and RT-PCR, respectively. For individual targets, increased detection of EV/RV (P = 0.043) and decreased detection of influenza A virus (P = 0.004) by RVP in comparison to real-time RT-PCR was observed. The results of the present study imply the need to adjust the InfA component of the RVP Fast assay to also cover the InfA(H1N1) 2009 virus.
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Affiliation(s)
- Pia Jokela
- Department of Virology, Haartman Institute, University of Helsinki, FIN-00014 Helsinki, Finland.
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37
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Chowdhary R, Street C, Travassos da Rosa A, Nunes MRT, Tee KK, Hutchison SK, Vasconcelos PFC, Tesh RB, Lipkin WI, Briese T. Genetic characterization of the Wyeomyia group of orthobunyaviruses and their phylogenetic relationships. J Gen Virol 2012; 93:1023-1034. [PMID: 22278828 DOI: 10.1099/vir.0.039479-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Phylogenetic analyses can give new insights into the evolutionary history of viruses, especially of viruses with segmented genomes. However, sequence information for many viral families or genera is still limited and phylogenies based on single or short genome fragments can be misleading. We report the first genetic analysis of all three genome segments of Wyeomyia group viruses Wyeomyia, Taiassui, Macaua, Sororoca, Anhembi and Cachoeira Porteira (BeAr328208) in the genus Orthobunyavirus of the family Bunyaviridae. In addition, Tucunduba and Iaco viruses were identified as members of the Wyeomyia group. Features of Wyeomyia group members that distinguish them from other viruses in the Bunyamwera serogroup and from other orthobunyaviruses, including truncated NSs sequences that may not counteract the host's interferon response, were characterized. Our findings also suggest genome reassortment within the Wyeomyia group, identifying Macaua and Tucunduba viruses as M-segment reassortants that, in the case of Tucunduba virus, may have altered pathogenicity, stressing the need for whole-genome sequence information to facilitate characterization of orthobunyaviruses and their phylogenetic relationships.
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Affiliation(s)
- Rashmi Chowdhary
- Center for Infection and Immunity, Columbia University, New York, NY, USA
| | - Craig Street
- Center for Infection and Immunity, Columbia University, New York, NY, USA
| | | | - Marcio R T Nunes
- Department of Arbovirology and Hemorrhagic Fevers, Instituto Evandro Chagas, Ananindeua, Pará, Brazil
| | - Kok Keng Tee
- Center for Infection and Immunity, Columbia University, New York, NY, USA
| | | | - Pedro F C Vasconcelos
- Center for Technological Innovation, Instituto Evandro Chagas, Ananindeua, Pará, Brazil
| | - Robert B Tesh
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - W Ian Lipkin
- Department of Pathology and Neurology, College of Physicians and Surgeons, Mailman School of Public Health, Columbia University, New York, NY, USA.,Center for Infection and Immunity, Columbia University, New York, NY, USA
| | - Thomas Briese
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA.,Center for Infection and Immunity, Columbia University, New York, NY, USA
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38
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Hasib L, Dilcher M, Hufert F, Meyer-König U, Weidmann M. Development of a flow-through [corrected] microarray based reverse transcriptase multiplex ligation-dependent probe amplification assay for the detection of European Bunyaviruses. [corrected]. Mol Biotechnol 2012; 49:176-86. [PMID: 21390485 PMCID: PMC3172416 DOI: 10.1007/s12033-011-9389-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
It is suspected that apart from tick-borne encephalitis virus several additional European Arboviruses such as the sandfly borne Toscana virus, sandfly fever Sicilian virus and sandfly fever Naples virus, mosquito-borne Tahyna virus, Inkoo virus, Batai virus and tick-borne Uukuniemi virus cause aseptic meningo-encephalitis or febrile disease in Europe. Currently, the microarray technology is developing rapidly and there are many efforts to apply it to infectious diseases diagnostics. In order to arrive at an assay system useful for high throughput analysis of samples from aseptic meningo-encephalitis cases the authors developed a combined multiplex ligation-dependent probe amplification and flow-through microarray assay for the detection of European Bunyaviruses. These results show that this combined assay indeed is highly sensitive, and specific for the accurate detection of multiple viruses.
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Affiliation(s)
- Lekbira Hasib
- Department of Virology, University Medical Center Göttingen, Kreuzbergring 57 37075, Göttingen, Germany.
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39
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Abstract
The laboratory diagnosis of influenza uses a wide range of techniques including rapid immunoassays, immunofluorescence techniques, virus culture methods, and increasingly sophisticated molecular assays. The potential utility of each of these methods has changed over the years, most dramatically perhaps with the emergence of the pandemic H1N1 2009 influenza virus. While rapid immunoassays had previously been widely used in clinics and emergency departments, their poor detection sensitivity for the 2009 subtype brought their application into question. Concerns were also raised about the detection sensitivities of antibody reagents used in immunofluorescence methods, and the safety of virus culture was initially questioned with regard to the newly emerged subtype. Early molecular detection techniques had been labor intensive, and required separate facilities in order to prevent contamination. Those techniques have largely been supplanted by more modern methods, most notably real-time reverse transcription PCR assays, which are currently the method of choice in many laboratories for the detection and subtyping of influenza viruses. Suspension and low-density array assays are also increasingly used, in an effort to detect larger numbers of viruses in a single assay, and microarrays have proven valuable for outbreak analysis and pathogen discovery. Each laboratory must assess the optimal methods for its situation and the best application of each technique, taking into account numerous factors including its budget, equipment, staff expertise, the patient population that it serves, the needs of its submitting clinicians, and its surveillance and public health responsibilities.
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Affiliation(s)
- Kirsten St George
- Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, USA.
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40
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Differentiation of the seven major lyssavirus species by oligonucleotide microarray. J Clin Microbiol 2011; 50:619-25. [PMID: 22189108 DOI: 10.1128/jcm.00848-11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
An oligonucleotide microarray, LyssaChip, has been developed and verified as a highly specific diagnostic tool for differentiation of the 7 major lyssavirus species. As with conventional typing microarray methods, the LyssaChip relies on sequence differences in the 371-nucleotide region coding for the nucleoprotein. This region was amplified using nested reverse transcription-PCR primers that bind to the 7 major lyssaviruses. The LyssaChip includes 57 pairs of species typing and corresponding control oligonucleotide probes (oligoprobes) immobilized on glass slides, and it can analyze 12 samples on a single slide within 8 h. Analysis of 111 clinical brain specimens (65 from animals with suspected rabies submitted to the laboratory and 46 of butchered dog brain tissues collected from restaurants) showed that the chip method was 100% sensitive and highly consistent with the "gold standard," a fluorescent antibody test (FAT). The chip method could detect rabies virus in highly decayed brain tissues, whereas the FAT did not, and therefore the chip test may be more applicable to highly decayed brain tissues than the FAT. LyssaChip may provide a convenient and inexpensive alternative for diagnosis and differentiation of rabies and rabies-related diseases.
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41
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Palacios G, Wellehan JFX, Raverty S, Bussetti AV, Hui J, Savji N, Nollens HH, Lambourn D, Celone C, Hutchison S, Calisher CH, Nielsen O, Lipkin WI. Discovery of an orthoreovirus in the aborted fetus of a Steller sea lion (Eumetopias jubatus). J Gen Virol 2011; 92:2558-2565. [PMID: 21795475 PMCID: PMC3352366 DOI: 10.1099/vir.0.032649-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 07/21/2011] [Indexed: 01/13/2023] Open
Abstract
An aborted mid-gestational male Steller sea lion fetus with an attached placenta was recovered on the floor of an open floating capture trap located off Norris Rock near Denman Island, British Columbia. Viral culture of the placenta demonstrated cytopathic effect. Although no specific signal was obtained in microarray experiments using RNA obtained from viral culture, elution and sequence analysis revealed the presence of a reovirus. Complete genome pyrosequencing led to the identification of an orthoreovirus that we have tentatively named Steller sea lion reovirus (SSRV). Phylogenetic analysis revealed similarities between SSRV and orthoreoviruses of birds, bats and other mammals that suggests potential for interspecies transmission.
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Affiliation(s)
- Gustavo Palacios
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - James F. X. Wellehan
- Marine Animal Disease Laboratory, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Stephen Raverty
- Animal Health Center, Abbotsford Agriculture Centre, Provincial Government of British Columbia, Abbotsford, British Columbia, Canada
| | - Ana V. Bussetti
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Jeffrey Hui
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Nazir Savji
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Hendrik H. Nollens
- Marine Animal Disease Laboratory, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Dyanna Lambourn
- Marine Mammal Investigations, Washington Department of Fish and Wildlife, Washington, USA
| | | | | | - Charles H. Calisher
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Ole Nielsen
- Department of Fisheries and Oceans Canada, Winnipeg, Manitoba, Canada
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
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Abstract
DNA microarrays have emerged as a viable platform for detection of pathogenic organisms in clinical and environmental samples. These microbial detection arrays occupy a middle ground between low cost, narrowly focused assays such as multiplex PCR and more expensive, broad-spectrum technologies like high-throughput sequencing. While pathogen detection arrays have been used primarily in a research context, several groups are aggressively working to develop arrays for clinical diagnostics, food safety testing, environmental monitoring and biodefense. Statistical algorithms that can analyze data from microbial detection arrays and provide easily interpretable results are absolutely required in order for these efforts to succeed. In this article, we will review the most promising array designs and analysis algorithms that have been developed to date, comparing their strengths and weaknesses for pathogen detection and discovery.
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Affiliation(s)
- Kevin S McLoughlin
- Global Security, Lawrence Livermore National Laboratory, Livermore, CA 94551 USA.
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Quan PL, Williams DT, Johansen CA, Jain K, Petrosov A, Diviney SM, Tashmukhamedova A, Hutchison SK, Tesh RB, Mackenzie JS, Briese T, Lipkin WI. Genetic characterization of K13965, a strain of Oak Vale virus from Western Australia. Virus Res 2011; 160:206-13. [PMID: 21740935 DOI: 10.1016/j.virusres.2011.06.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 06/17/2011] [Accepted: 06/21/2011] [Indexed: 10/18/2022]
Abstract
K13965, an uncharacterized virus, was isolated in 1993 from Anopheles annulipes mosquitoes collected in the Kimberley region of northern Western Australia. Here, we report its genomic sequence, identify it as a rhabdovirus, and characterize its phylogenetic relationships. The genome comprises a P' (C) and SH protein similar to the recently characterized Tupaia and Durham viruses, and shows overlap between G and L genes. Comparison of K13965 genome sequence to other rhabdoviruses identified K13965 as a strain of the unclassified Australian Oak Vale rhabdovirus, whose complete genome sequence we also determined. Phylogenetic analysis of N and L sequences indicated genetic relationship to a recently proposed Sandjima virus clade, although the Oak Vale virus sequences form a branch separate from the African members of that group.
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Affiliation(s)
- Phenix-Lan Quan
- Center for Infection and Immunity, Columbia University, New York, NY 10032, USA
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Berthet N, Deletoile A, Passet V, Kennedy GC, Manuguerra JC, Cole ST, Brisse S. Reconstructed ancestral sequences improve pathogen identification using resequencing DNA microarrays. PLoS One 2010; 5:e15243. [PMID: 21187950 PMCID: PMC3004854 DOI: 10.1371/journal.pone.0015243] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 11/09/2010] [Indexed: 11/19/2022] Open
Abstract
We describe the benefit of using reconstructed ancestral sequences (RAS) on resequencing microarrays for rapid pathogen identification, with Enterobacteriaceae rpoB sequences as a model. Our results demonstrate a sharp improvement of call rate and accuracy when using RASs as compared to extant sequences. This improvement was attributed to the lower sequence divergence of RASs, which also expanded the sequence space covered by the microarray. Extension of this novel microarray design strategy to viruses, antimicrobial resistance elements or toxins is straightforward.
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Affiliation(s)
- Nicolas Berthet
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
- Institut Pasteur, Epidemiology and Pathophysiology Oncogenic Virus Unit, CNRS URA3015, Paris, France
| | - Alexis Deletoile
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
| | - Virginie Passet
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
| | | | | | - Stewart T. Cole
- Global Health Institute, Laboratory of Microbial Pathogenesis, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sylvain Brisse
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
- * E-mail:
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46
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A microbial detection array (MDA) for viral and bacterial detection. BMC Genomics 2010; 11:668. [PMID: 21108826 PMCID: PMC3017867 DOI: 10.1186/1471-2164-11-668] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 11/25/2010] [Indexed: 12/21/2022] Open
Abstract
Background Identifying the bacteria and viruses present in a complex sample is useful in disease diagnostics, product safety, environmental characterization, and research. Array-based methods have proven utility to detect in a single assay at a reasonable cost any microbe from the thousands that have been sequenced. Methods We designed a pan-Microbial Detection Array (MDA) to detect all known viruses (including phages), bacteria and plasmids and developed a novel statistical analysis method to identify mixtures of organisms from complex samples hybridized to the array. The array has broader coverage of bacterial and viral targets and is based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection of divergent species with homology to sequenced organisms, and to have no significant matches to the human genome sequence. Results In blinded testing on spiked samples with single or multiple viruses, the MDA was able to correctly identify species or strains. In clinical fecal, serum, and respiratory samples, the MDA was able to detect and characterize multiple viruses, phage, and bacteria in a sample to the family and species level, as confirmed by PCR. Conclusions The MDA can be used to identify the suite of viruses and bacteria present in complex samples.
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Murdoch DR, Jennings LC, Bhat N, Anderson TP. Emerging advances in rapid diagnostics of respiratory infections. Infect Dis Clin North Am 2010; 24:791-807. [PMID: 20674804 PMCID: PMC7134633 DOI: 10.1016/j.idc.2010.04.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent developments in rapid diagnostics for respiratory infections have mostly occurred in the areas of antigen and nucleic acid detection. Nucleic acid amplification tests have improved the ability to identify respiratory viruses in clinical specimens and have played pivotal roles in the rapid characterization of new viral pathogens. Antigen-detection assays in immunochromatographic or similar formats are most easily developed as near-patient tests, although they have been developed commercially only for a limited range of respiratory pathogens. New approaches for respiratory pathogen detection are needed, and breath analysis is an exciting area with enormous potential.
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Affiliation(s)
- David R Murdoch
- Department of Pathology, University of Otago Christchurch, Christchurch 8140, New Zealand.
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Allred AF, Wu G, Wulan T, Fischer KF, Holbrook MR, Tesh RB, Wang D. VIPR: A probabilistic algorithm for analysis of microbial detection microarrays. BMC Bioinformatics 2010; 11:384. [PMID: 20646301 PMCID: PMC2921407 DOI: 10.1186/1471-2105-11-384] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 07/20/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND All infectious disease oriented clinical diagnostic assays in use today focus on detecting the presence of a single, well defined target agent or a set of agents. In recent years, microarray-based diagnostics have been developed that greatly facilitate the highly parallel detection of multiple microbes that may be present in a given clinical specimen. While several algorithms have been described for interpretation of diagnostic microarrays, none of the existing approaches is capable of incorporating training data generated from positive control samples to improve performance. RESULTS To specifically address this issue we have developed a novel interpretive algorithm, VIPR (Viral Identification using a PRobabilistic algorithm), which uses Bayesian inference to capitalize on empirical training data to optimize detection sensitivity. To illustrate this approach, we have focused on the detection of viruses that cause hemorrhagic fever (HF) using a custom HF-virus microarray. VIPR was used to analyze 110 empirical microarray hybridizations generated from 33 distinct virus species. An accuracy of 94% was achieved as measured by leave-one-out cross validation. CONCLUSIONS VIPR outperformed previously described algorithms for this dataset. The VIPR algorithm has potential to be broadly applicable to clinical diagnostic settings, wherein positive controls are typically readily available for generation of training data.
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Affiliation(s)
- Adam F Allred
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
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Application of broad-spectrum resequencing microarray for genotyping rhabdoviruses. J Virol 2010; 84:9557-74. [PMID: 20610710 DOI: 10.1128/jvi.00771-10] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The rapid and accurate identification of pathogens is critical in the control of infectious disease. To this end, we analyzed the capacity for viral detection and identification of a newly described high-density resequencing microarray (RMA), termed PathogenID, which was designed for multiple pathogen detection using database similarity searching. We focused on one of the largest and most diverse viral families described to date, the family Rhabdoviridae. We demonstrate that this approach has the potential to identify both known and related viruses for which precise sequence information is unavailable. In particular, we demonstrate that a strategy based on consensus sequence determination for analysis of RMA output data enabled successful detection of viruses exhibiting up to 26% nucleotide divergence with the closest sequence tiled on the array. Using clinical specimens obtained from rabid patients and animals, this method also shows a high species level concordance with standard reference assays, indicating that it is amenable for the development of diagnostic assays. Finally, 12 animal rhabdoviruses which were currently unclassified, unassigned, or assigned as tentative species within the family Rhabdoviridae were successfully detected. These new data allowed an unprecedented phylogenetic analysis of 106 rhabdoviruses and further suggest that the principles and methodology developed here may be used for the broad-spectrum surveillance and the broader-scale investigation of biodiversity in the viral world.
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50
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Epstein JH, Quan PL, Briese T, Street C, Jabado O, Conlan S, Ali Khan S, Verdugo D, Hossain MJ, Hutchison SK, Egholm M, Luby SP, Daszak P, Lipkin WI. Identification of GBV-D, a novel GB-like flavivirus from old world frugivorous bats (Pteropus giganteus) in Bangladesh. PLoS Pathog 2010; 6:e1000972. [PMID: 20617167 PMCID: PMC2895649 DOI: 10.1371/journal.ppat.1000972] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 05/27/2010] [Indexed: 11/19/2022] Open
Abstract
Bats are reservoirs for a wide range of zoonotic agents including lyssa-, henipah-, SARS-like corona-, Marburg-, Ebola-, and astroviruses. In an effort to survey for the presence of other infectious agents, known and unknown, we screened sera from 16 Pteropus giganteus bats from Faridpur, Bangladesh, using high-throughput pyrosequencing. Sequence analyses indicated the presence of a previously undescribed virus that has approximately 50% identity at the amino acid level to GB virus A and C (GBV-A and -C). Viral nucleic acid was present in 5 of 98 sera (5%) from a single colony of free-ranging bats. Infection was not associated with evidence of hepatitis or hepatic dysfunction. Phylogenetic analysis indicates that this first GBV-like flavivirus reported in bats constitutes a distinct species within the Flaviviridae family and is ancestral to the GBV-A and -C virus clades.
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Affiliation(s)
- Jonathan H. Epstein
- Conservation Medicine Program, Wildlife Trust, New York, New York, United States of America
| | - Phenix-Lan Quan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Craig Street
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Omar Jabado
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Sean Conlan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Shahneaz Ali Khan
- Conservation Medicine Program, Wildlife Trust, New York, New York, United States of America
- Chittagong Veterinary & Animal Sciences University, Chittagong, Bangladesh
| | - Dawn Verdugo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - M. Jahangir Hossain
- Programme on Infectious Disease and Vaccine Sciences, International Centre for Diarrheal Disease Research, Bangladesh (ICDDR,B), Dhaka, Bangladesh
| | | | - Michael Egholm
- 454 Life Sciences, Branford, Connecticut, United States of America
| | - Stephen P. Luby
- Programme on Infectious Disease and Vaccine Sciences, International Centre for Diarrheal Disease Research, Bangladesh (ICDDR,B), Dhaka, Bangladesh
| | - Peter Daszak
- Conservation Medicine Program, Wildlife Trust, New York, New York, United States of America
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
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