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Thapliyal P, Sah V, Rautela I, Joshi M, Tyagi S, Verma R, Sharma MD. Next Generation Sequencing: Latent applications in clinical diagnostics with the advent of bioinformatic frameworks. Pathol Res Pract 2024; 263:155606. [PMID: 39357183 DOI: 10.1016/j.prp.2024.155606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 09/03/2024] [Accepted: 09/24/2024] [Indexed: 10/04/2024]
Abstract
For the past 3-4 decades, the discovery of Sanger's method of pyrosequencing was the only method unparalleled till 2005 being employed as a method of whole genome sequencing (WGS). Following this, a revolutionary extensive parallel sequencing method, Next Generation Sequencing (NGS), was engineered. NGS supported a substantial number of bases under a high throughput metagenomic interrogation. Bioinformatics contributed notably to this advancement. It provided alignment tools, assembly algorithms, and protocols such as Illumina and hybridization capture which have metamorphosed clinical and translational diagnostics. With the extension in precision medicine and targeted therapy under NGS sectors such as epigenetics, transcriptomics, mutation detection, prognosis, therapeutics, and patient management have been gaining progress. Using NGS in real-time clinical settings has been proven to produce positive outcomes. The most recent instrumental benefaction of NGS has been decoding the SARS-CoV-2 virus epidemiology with the assistance of multiplex PCR. So far, it had been employed to inspect different levels of viral loads from low to mid. This has been executed by amplification and phylogenetic examination of the load to raise a connective link with the evolutionary history leading up to the period of origin. The depletion in the consumed time and extensive genome size under analysis was further coupled by a cutback in the cost of sequencing while executing NGS. With the aid of this review paper, we aspire to manifest how the above-mentioned elements have boosted, tissue, microbial, and molecular data interrogation. Along with this, promoting, and stimulating an extensive evaluation and expansion in the paradigm of morphological and phenotypic study, via bioinformatics can facilitate further advancement in personalized and concise clinical research.
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Affiliation(s)
- Priya Thapliyal
- Department of Biochemistry, H.N.B. Garhwal (A Central) University, Srinagar, Uttarakhand 246174, India
| | - Vijayalaxmi Sah
- Department of Biotechnology, School of Applied and Life Sciences (SALS), Uttaranchal University, Dehradun, Uttarakhand 248001, India
| | - Indra Rautela
- Department of Biotechnology, School of Applied and Life Sciences (SALS), Uttaranchal University, Dehradun, Uttarakhand 248001, India
| | - Mallika Joshi
- Department of Biotechnology, Chandigarh University, Gharaun, Mohali, Punjab 140413, India
| | - Sheetal Tyagi
- Department of Chemistry, School of Basic and Applied Sciences, Shri Guru Ram Rai University, Patel Nagar, Dehradun, Uttarakhand 248001, India
| | - Rashmi Verma
- Department of Biotechnology, School of Basic and Applied Sciences, Shri Guru Ram Rai University, Patel Nagar, Dehradun, Uttarakhand 248001, India
| | - Manish Dev Sharma
- Department of Biotechnology, School of Basic and Applied Sciences, Shri Guru Ram Rai University, Patel Nagar, Dehradun, Uttarakhand 248001, India.
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2
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Haddad G, Bellali S, Fontanini A, Francis R, La Scola B, Levasseur A, Bou Khalil J, Raoult D. Rapid Scanning Electron Microscopy Detection and Sequencing of Severe Acute Respiratory Syndrome Coronavirus 2 and Other Respiratory Viruses. Front Microbiol 2020; 11:596180. [PMID: 33329483 PMCID: PMC7711091 DOI: 10.3389/fmicb.2020.596180] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/23/2020] [Indexed: 12/23/2022] Open
Abstract
There is an urgent need for accurate and rapid testing methods to quickly identify infected patients as well as asymptomatic carriers, in order to prevent the spread of emerging viruses. Here, we developed a rapid testing strategy by scanning electron microscopy capable of detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses directly from patients. We evaluated our results by comparing them to real-time reverse transcription-polymerase chain reaction (RT-PCR) and metagenomic sequencing results. We correlated the presence of the SARS-CoV-2 to the viral load, where samples with Ct values lower than 18 were all detected by scanning electron microscopy (SEM). The sensitivity deacresed progressively with higher Ct values. In addition, we found a correlation with metagenomic sequencing, where all samples detected by SEM were sequenced and viral sequences were easily recovered. Following this study, SEM proved its efficiency as a frontline method for directly detecting previously unknown microorganisms that cannot be targeted by molecular methods and can cause potential outbreaks.
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Affiliation(s)
- Gabriel Haddad
- Aix-Marseille Université, Institut de Recherche pour le Développement(IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Sara Bellali
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Anthony Fontanini
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Rania Francis
- Aix-Marseille Université, Institut de Recherche pour le Développement(IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Bernard La Scola
- Aix-Marseille Université, Institut de Recherche pour le Développement(IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Anthony Levasseur
- Aix-Marseille Université, Institut de Recherche pour le Développement(IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Jacques Bou Khalil
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, Institut de Recherche pour le Développement(IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
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3
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Souza LDC, Blawid R, Silva JMF, Nagata T. Human virome in nasopharynx and tracheal secretion samples. Mem Inst Oswaldo Cruz 2019; 114:e190198. [PMID: 31596309 PMCID: PMC6779266 DOI: 10.1590/0074-02760190198] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/20/2019] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND In Brazil the implementation of the Sentinel Surveillance System of
Influenza began in 2000. Central public health laboratories use reverse
transcription-quantitative polymerase chain reaction (RT-qPCR) for diagnosis
of respiratory viruses, but this protocol identifies only specific targets,
resulted in inconclusive diagnosis for many samples. Thus, high-throughput
sequencing (HTS) would be complementary method in the identification of
pathogens in inconclusive samples for RT-qPCR or other specific detection
protocols. OBJECTIVES This study aimed to detect unidentified viruses using HTS approach in
negative samples of nasopharynx/tracheal secretions by the standard RT-qPCR
collected in the Federal District, Brazil. METHODS Nucleic acids were extracted from samples collected in winter period of 2016
and subjected to HTS. The results were confirmed by the multiplex PR21
RT-qPCR, which identifies 21 respiratory pathogens. FINDINGS The main viruses identified by HTS were of families
Herpesviridae, Coronaviridae,
Parvoviridae and Picornaviridae, with
the emphasis on rhinoviruses. The presence of respiratory viruses in the
samples was confirmed by the PR21 multiplex RT-qPCR. Coronavirus,
enterovirus, bocavirus and rhinovirus were found by multiplex RT-qPCR as
well as by HTS analyses. MAIN CONCLUSIONS Wide virus diversity was found by different methodologies and high frequency
of rhinovirus occurrence was confirmed in population in winter, showing its
relevance for public health.
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Affiliation(s)
- Larissa da Costa Souza
- Universidade de Brasília, Departamento de Biologia Celular, Pós-Graduação em Biologia Microbiana, Brasília, DF, Brasil.,Laboratório Central de Saúde Pública do Distrito Federal, Brasília, DF, Brasil
| | - Rosana Blawid
- Universidade Federal Rural de Pernambuco, Departamento de Agronomia, Recife, PE, Brasil
| | - João Marcos Fagundes Silva
- Universidade de Brasília, Departamento de Biologia Celular, Pós-Graduação em Biologia Molecular, Brasília, DF, Brasil
| | - Tatsuya Nagata
- Universidade de Brasília, Departamento de Biologia Celular, Pós-Graduação em Biologia Microbiana, Brasília, DF, Brasil.,Universidade de Brasília, Departamento de Biologia Celular, Pós-Graduação em Biologia Molecular, Brasília, DF, Brasil
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4
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Dahyot S, Lemee L, Pestel-Caron M. [Description and role of bacteriological techniques in the management of lung infections]. Rev Mal Respir 2017; 34:1098-1113. [PMID: 28688757 PMCID: PMC7134997 DOI: 10.1016/j.rmr.2016.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/28/2016] [Indexed: 01/07/2023]
Abstract
Les pneumopathies aiguës recouvrent des contextes cliniques variés et les étiologies bactériennes impliquées le sont tout autant. Aucun outil microbiologique n’est 100 % sensible ni 100 % spécifique et malgré les investigations, plus de 30 % des pneumopathies restent sans étiologie identifiée. Si aucun prélèvement n’est indiqué pour les patients traités en ambulatoire, les prélèvements respiratoires non invasifs sont à privilégier pour les pneumopathies aiguës hospitalisées (communautaires ou associées aux soins), tandis que les prélèvements invasifs sont indiqués en seconde ligne pour les pneumopathies aiguës communautaires en réanimation, et en première ligne pour les pneumopathies aiguës de l’immunodéprimé. La culture microbiologique garde une place importante, à condition que le malade soit prélevé avant instauration de l’antibiothérapie. Certains contextes peuvent justifier le recours aux hémocultures, à la recherche d’antigènes urinaires ou aux sérologies. Les PCR rendent déjà service au quotidien mais l’avenir à court terme appartient probablement aux panels moléculaires multiplex capables de détecter de nombreux micro-organismes en quelques heures, surtout dans les pneumopathies communautaires sévères de réanimation et les pneumopathies aiguës de l’immunodéprimé. Le séquençage nucléotidique haut débit révolutionnera bientôt le diagnostic microbiologique, en pneumologie comme dans les autres domaines de l’infectiologie.
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Affiliation(s)
- S Dahyot
- UNIROUEN, GRAM EA2656, laboratoire de bactériologie, CHU de Rouen, Normandie université, 76000 Rouen, France.
| | - L Lemee
- UNIROUEN, GRAM EA2656, laboratoire de bactériologie, CHU de Rouen, Normandie université, 76000 Rouen, France
| | - M Pestel-Caron
- UNIROUEN, GRAM EA2656, laboratoire de bactériologie, CHU de Rouen, Normandie université, 76000 Rouen, France
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5
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A metagenomics study for the identification of respiratory viruses in mixed clinical specimens: an application of the iterative mapping approach. Arch Virol 2017; 162:2003-2012. [PMID: 28424887 PMCID: PMC7087367 DOI: 10.1007/s00705-017-3367-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 03/09/2017] [Indexed: 12/14/2022]
Abstract
Metagenomic approaches to detect viral genomes and variants in clinical samples have various challenges, including low viral titers and bacterial and human genome contamination. To address these limitations, we examined a next-generation sequencing (NGS) and iterative mapping approach for virus detection in clinical samples. We analyzed 40 clinical specimens from hospitalized children diagnosed with acute bronchiolitis, croup, or respiratory tract infections in which virus identification by viral culture or polymerase chain reaction (PCR) was unsuccessful. For our NGS data analysis pipeline, clinical samples were pooled into two NGS groups to reduce sequencing costs, and the depth and coverage of assembled contigs were effectively increased using an iterative mapping approach. PCR was individually performed for each specimen according to the NGS-predicted viral type. We successfully detected previously unidentified respiratory viruses in 26 of 40 specimens using our proposed NGS pipeline. Two dominant populations within the detected viruses were human rhinoviruses (HRVs; n = 14) and human coronavirus NL63 (n = 8), followed by human parainfluenza virus (HPIV), human parechovirus, influenza A virus, respiratory syncytial virus (RSV), and human metapneumovirus. This is the first study reporting the complete genome sequences of HRV-A101, HRV-C3, HPIV-4a, and RSV, as well as an analysis of their genetic variants, in Taiwan. These results demonstrate that this NGS pipeline allows to detect viruses which were not identified by routine diagnostic assays, directly from clinical samples.
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6
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Munang'andu HM, Mugimba KK, Byarugaba DK, Mutoloki S, Evensen Ø. Current Advances on Virus Discovery and Diagnostic Role of Viral Metagenomics in Aquatic Organisms. Front Microbiol 2017; 8:406. [PMID: 28382024 PMCID: PMC5360701 DOI: 10.3389/fmicb.2017.00406] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 02/27/2017] [Indexed: 12/20/2022] Open
Abstract
The global expansion of the aquaculture industry has brought with it a corresponding increase of novel viruses infecting different aquatic organisms. These emerging viral pathogens have proved to be a challenge to the use of traditional cell-cultures and immunoassays for identification of new viruses especially in situations where the novel viruses are unculturable and no antibodies exist for their identification. Viral metagenomics has the potential to identify novel viruses without prior knowledge of their genomic sequence data and may provide a solution for the study of unculturable viruses. This review provides a synopsis on the contribution of viral metagenomics to the discovery of viruses infecting different aquatic organisms as well as its potential role in viral diagnostics. High throughput Next Generation sequencing (NGS) and library construction used in metagenomic projects have simplified the task of generating complete viral genomes unlike the challenge faced in traditional methods that use multiple primers targeted at different segments and VPs to generate the entire genome of a novel virus. In terms of diagnostics, studies carried out this far show that viral metagenomics has the potential to serve as a multifaceted tool able to study and identify etiological agents of single infections, co-infections, tissue tropism, profiling viral infections of different aquatic organisms, epidemiological monitoring of disease prevalence, evolutionary phylogenetic analyses, and the study of genomic diversity in quasispecies viruses. With sequencing technologies and bioinformatics analytical tools becoming cheaper and easier, we anticipate that metagenomics will soon become a routine tool for the discovery, study, and identification of novel pathogens including viruses to enable timely disease control for emerging diseases in aquaculture.
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Affiliation(s)
- Hetron M. Munang'andu
- Section of Aquatic Medicine and Nutrition, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life SciencesOslo, Norway
| | - Kizito K. Mugimba
- Section of Aquatic Medicine and Nutrition, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life SciencesOslo, Norway
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere UniversityKampala, Uganda
| | - Denis K. Byarugaba
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere UniversityKampala, Uganda
| | - Stephen Mutoloki
- Section of Aquatic Medicine and Nutrition, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life SciencesOslo, Norway
| | - Øystein Evensen
- Section of Aquatic Medicine and Nutrition, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life SciencesOslo, Norway
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7
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Lefterova MI, Suarez CJ, Banaei N, Pinsky BA. Next-Generation Sequencing for Infectious Disease Diagnosis and Management: A Report of the Association for Molecular Pathology. J Mol Diagn 2015; 17:623-34. [PMID: 26433313 DOI: 10.1016/j.jmoldx.2015.07.004] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 05/27/2015] [Accepted: 07/02/2015] [Indexed: 12/31/2022] Open
Abstract
Next-generation sequencing (NGS) technologies are increasingly being used for diagnosis and monitoring of infectious diseases. Herein, we review the application of NGS in clinical microbiology, focusing on genotypic resistance testing, direct detection of unknown disease-associated pathogens in clinical specimens, investigation of microbial population diversity in the human host, and strain typing. We have organized the review into three main sections: i) applications in clinical virology, ii) applications in clinical bacteriology, mycobacteriology, and mycology, and iii) validation, quality control, and maintenance of proficiency. Although NGS holds enormous promise for clinical infectious disease testing, many challenges remain, including automation, standardizing technical protocols and bioinformatics pipelines, improving reference databases, establishing proficiency testing and quality control measures, and reducing cost and turnaround time, all of which would be necessary for widespread adoption of NGS in clinical microbiology laboratories.
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Affiliation(s)
- Martina I Lefterova
- Association for Molecular Pathology Next-Generation Sequencing in Infectious Disease Work Group, Bethesda, Maryland; Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Carlos J Suarez
- Association for Molecular Pathology Next-Generation Sequencing in Infectious Disease Work Group, Bethesda, Maryland; Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Niaz Banaei
- Association for Molecular Pathology Next-Generation Sequencing in Infectious Disease Work Group, Bethesda, Maryland; Department of Pathology, Stanford University School of Medicine, Stanford, California; Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California
| | - Benjamin A Pinsky
- Association for Molecular Pathology Next-Generation Sequencing in Infectious Disease Work Group, Bethesda, Maryland; Department of Pathology, Stanford University School of Medicine, Stanford, California; Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California.
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8
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Dormitzer PR. Rapid Production of Synthetic Influenza Vaccines. Curr Top Microbiol Immunol 2014; 386:237-73. [DOI: 10.1007/82_2014_399] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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9
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Abstract
Pathogen discovery is critically important to infectious diseases and public health. Nearly all new outbreaks are caused by the emergence of novel viruses. Genomic tools for pathogen discovery include consensus PCR, microarrays, and deep sequencing. Downstream studies are often necessary to link a candidate novel virus to a disease.
Viral pathogen discovery is of critical importance to clinical microbiology, infectious diseases, and public health. Genomic approaches for pathogen discovery, including consensus polymerase chain reaction (PCR), microarrays, and unbiased next-generation sequencing (NGS), have the capacity to comprehensively identify novel microbes present in clinical samples. Although numerous challenges remain to be addressed, including the bioinformatics analysis and interpretation of large datasets, these technologies have been successful in rapidly identifying emerging outbreak threats, screening vaccines and other biological products for microbial contamination, and discovering novel viruses associated with both acute and chronic illnesses. Downstream studies such as genome assembly, epidemiologic screening, and a culture system or animal model of infection are necessary to establish an association of a candidate pathogen with disease.
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10
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Bibby K. Metagenomic identification of viral pathogens. Trends Biotechnol 2013; 31:275-9. [PMID: 23415279 DOI: 10.1016/j.tibtech.2013.01.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 01/21/2013] [Accepted: 01/22/2013] [Indexed: 11/19/2022]
Abstract
The target-independent identification of viral pathogens using 'shotgun' metagenomic sequencing is an emerging approach with potentially wide applications in clinical diagnostics, public health monitoring, and viral discovery. In this approach, all viral nucleic acids present in a sample are sequenced in a random, shotgun manner. Pathogens are then identified without the prerequisite of searching for a specific viral pathogen. In this opinion article, I discuss the current state and future research directions for this emerging and disruptive technology. With further technical developments, viral metagenomics has the potential to be deployed as a powerful and widely adopted tool, transforming the way that viral disease is researched, monitored, and treated.
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Affiliation(s)
- Kyle Bibby
- Department of Civil and Environmental Engineering, University of Pittsburgh, 709 Benedum Hall, 3700 O'Hara Street, Pittsburgh, PA 15261, USA.
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11
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Yang Z, Mao G, Liu Y, Chen YC, Liu C, Luo J, Li X, Zen K, Pang Y, Wu J, Liu F. Detection of the pandemic H1N1/2009 influenza A virus by a highly sensitive quantitative real-time reverse-transcription polymerase chain reaction assay. Virol Sin 2013; 28:24-35. [PMID: 23385352 DOI: 10.1007/s12250-013-3290-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 01/23/2013] [Indexed: 11/29/2022] Open
Abstract
A quantitative real time reverse-transcription polymerase chain reaction (qRT-PCR) assay with specific primers recommended by the World Health Organization (WHO) has been widely used successfully for detection and monitoring of the pandemic H1N1/2009 influenza A virus. In this study, we report the design and characterization of a novel set of primers to be used in a qRT-PCR assay for detecting the pandemic H1N1/2009 virus. The newly designed primers target three regions that are highly conserved among the hemagglutinin (HA) genes of the pandemic H1N1/2009 viruses and are different from those targeted by the WHO-recommended primers. The qRT-PCR assays with the newly designed primers are highly specific, and as specific as the WHO-recommended primers for detecting pandemic H1N1/2009 viruses and other influenza viruses including influenza B viruses and influenza A viruses of human, swine, and raccoon dog origin. Furthermore, the qRT-PCR assays with the newly designed primers appeared to be at least 10-fold more sensitive than those with the WHO-recommended primers as the detection limits of the assays with our primers and the WHO-recommended primers were 2.5 and 25 copies of target RNA per reaction, respectively. When tested with 83 clinical samples, 32 were detected to be positive using the qRT-PCR assays with our designed primers, while only 25 were positive by the assays with the WHO-recommended primers. These results suggest that the qRT-PCR system with the newly designed primers represent a highly sensitive assay for diagnosis of the pandemic H1N1/2009 virus infection.
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Affiliation(s)
- Zhu Yang
- Institute of Virology, School of Life Sciences, Nanjing University, Nanjing 210093, Jiangsu, China
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12
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Marusov G, Sweatt A, Pietrosimone K, Benson D, Geary SJ, Silbart LK, Challa S, Lagoy J, Lawrence DA, Lynes MA. A microarray biosensor for multiplexed detection of microbes using grating-coupled surface plasmon resonance imaging. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:348-59. [PMID: 22029256 PMCID: PMC3312245 DOI: 10.1021/es201239f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Grating-coupled surface plasmon resonance imaging (GCSPRI) utilizes an optical diffraction grating embossed on a gold-coated sensor chip to couple collimated incident light into surface plasmons. The angle at which this coupling occurs is sensitive to the capture of analyte at the chip surface. This approach permits the use of disposable biosensor chips that can be mass-produced at low cost and spotted in microarray format to greatly increase multiplexing capabilities. The current GCSPRI instrument has the capacity to simultaneously measure binding at over 1000 unique, discrete regions of interest (ROIs) by utilizing a compact microarray of antibodies or other specific capture molecules immobilized on the sensor chip. In this report, we describe the use of GCSPRI to directly detect multiple analytes over a large dynamic range, including soluble protein toxins, bacterial cells, and viruses, in near real-time. GCSPRI was used to detect a variety of agents that would be useful for diagnostic and environmental sensing purposes, including macromolecular antigens, a nontoxic form of Pseudomonas aeruginosa exotoxin A (ntPE), Bacillus globigii, Mycoplasma hyopneumoniae, Listeria monocytogenes, Escherichia coli, and M13 bacteriophage. These studies indicate that GCSPRI can be used to simultaneously assess the presence of toxins and pathogens, as well as quantify specific antibodies to environmental agents, in a rapid, label-free, and highly multiplexed assay requiring nanoliter amounts of capture reagents.
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Affiliation(s)
- Gregory Marusov
- Department of Molecular and Cell Biology, The University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269-3125
| | - Andrew Sweatt
- Department of Molecular and Cell Biology, The University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269-3125
| | - Kathryn Pietrosimone
- Department of Molecular and Cell Biology, The University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269-3125
| | - David Benson
- Department of Molecular and Cell Biology, The University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269-3125
| | - Steven J. Geary
- Department of Pathobiology, The University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269-3125
- The Center of Excellence For Vaccine Research, The University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269-3125
| | - Lawrence K. Silbart
- Department of Allied Health Sciences, The University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269-3125
- The Center of Excellence For Vaccine Research, The University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269-3125
| | - Sreerupa Challa
- Department of Allied Health Sciences, The University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269-3125
- The Center of Excellence For Vaccine Research, The University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269-3125
| | - Jacqueline Lagoy
- Department of Molecular and Cell Biology, The University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269-3125
| | | | - Michael A. Lynes
- Department of Molecular and Cell Biology, The University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269-3125
- The Center of Excellence For Vaccine Research, The University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269-3125
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13
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Applications of next-generation sequencing technologies to diagnostic virology. Int J Mol Sci 2011; 12:7861-84. [PMID: 22174638 PMCID: PMC3233444 DOI: 10.3390/ijms12117861] [Citation(s) in RCA: 177] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 10/20/2011] [Accepted: 11/07/2011] [Indexed: 02/07/2023] Open
Abstract
Novel DNA sequencing techniques, referred to as “next-generation” sequencing (NGS), provide high speed and throughput that can produce an enormous volume of sequences with many possible applications in research and diagnostic settings. In this article, we provide an overview of the many applications of NGS in diagnostic virology. NGS techniques have been used for high-throughput whole viral genome sequencing, such as sequencing of new influenza viruses, for detection of viral genome variability and evolution within the host, such as investigation of human immunodeficiency virus and human hepatitis C virus quasispecies, and monitoring of low-abundance antiviral drug-resistance mutations. NGS techniques have been applied to metagenomics-based strategies for the detection of unexpected disease-associated viruses and for the discovery of novel human viruses, including cancer-related viruses. Finally, the human virome in healthy and disease conditions has been described by NGS-based metagenomics.
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14
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Kim H, Bartsch MS, Renzi RF, He J, Van de Vreugde JL, Claudnic MR, Patel KD. Automated digital microfluidic sample preparation for next-generation DNA sequencing. ACTA ACUST UNITED AC 2011; 16:405-14. [PMID: 22093297 DOI: 10.1016/j.jala.2011.07.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Indexed: 10/17/2022]
Abstract
Next-generation sequencing (NGS) technology is a promising tool for identifying and characterizing unknown pathogens, but its usefulness in time-critical biodefense and public health applications is currently limited by the lack of fast, efficient, and reliable automated DNA sample preparation methods. To address this limitation, we are developing a digital microfluidic (DMF) platform to function as a fluid distribution hub, enabling the integration of multiple subsystem modules into an automated NGS library sample preparation system. A novel capillary interface enables highly repeatable transfer of liquid between the DMF device and the external fluidic modules, allowing both continuous-flow and droplet-based sample manipulations to be performed in one integrated system. Here, we highlight the utility of the DMF hub platform and capillary interface for automating two key operations in the NGS sample preparation workflow. Using an in-line contactless conductivity detector in conjunction with the capillary interface, we demonstrate closed-loop automated fraction collection of target analytes from a continuous-flow sample stream into droplets on the DMF device. Buffer exchange and sample cleanup, the most repeated steps in NGS library preparation, are also demonstrated on the DMF platform using a magnetic bead assay and achieving an average DNA recovery efficiency of 80%±4.8%.
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Affiliation(s)
- Hanyoup Kim
- Sandia National Laboratories, Livermore, CA 94550, USA
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Unbiased parallel detection of viral pathogens in clinical samples by use of a metagenomic approach. J Clin Microbiol 2011; 49:3463-9. [PMID: 21813714 DOI: 10.1128/jcm.00273-11] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viral infectious diseases represent a major threat to public health and are among the greatest disease burdens worldwide. Rapid and accurate identification of viral agents is crucial for both outbreak control and estimating regional disease burdens. Recently developed metagenomic methods have proven to be powerful tools for simultaneous pathogen detection. Here, we performed a systematic study of the capability of the short-read-based metagenomic approach in the molecular detection of viral pathogens in nasopharyngeal aspirate samples from patients with acute lower respiratory tract infections (n = 16). Using the high-throughput capacity of ultradeep sequencing and a dedicated data interpretation method, we successfully identified seven species of known respiratory viral agents from 15 samples, a result that was consistent with results of conventional PCR assays. We also detected a coinfected case that was missed by regular PCR testing. Using the metagenomic data, 11 draft genomes of the abundantly detected viruses in the samples were reconstructed with 21.84% to 98.53% coverage. Our results show the power of the short-read-based metagenomic approach for accurate and parallel screening of viral pathogens. Although there are some inherent difficulties in applying this approach to clinical samples, including a lack of controls, limited specimen quantity, and high contamination rate, our work will facilitate further application of this unprecedented high-throughput method to clinical samples.
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