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Nash D, Ellmen I, Knapp JJ, Menon R, Overton AK, Cheng J, Lynch MDJ, Nissimov JI, Charles TC. A Novel Tiled Amplicon Sequencing Assay Targeting the Tomato Brown Rugose Fruit Virus (ToBRFV) Genome Reveals Widespread Distribution in Municipal Wastewater Treatment Systems in the Province of Ontario, Canada. Viruses 2024; 16:460. [PMID: 38543825 PMCID: PMC10974707 DOI: 10.3390/v16030460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/13/2024] [Accepted: 03/15/2024] [Indexed: 05/23/2024] Open
Abstract
Tomato Brown Rugose Fruit Virus (ToBRFV) is a plant pathogen that infects important Solanaceae crop species and can dramatically reduce tomato crop yields. The ToBRFV has rapidly spread around the globe due to its ability to escape detection by antiviral host genes which confer resistance to other tobamoviruses in tomato plants. The development of robust and reproducible methods for detecting viruses in the environment aids in the tracking and reduction of pathogen transmission. We detected ToBRFV in municipal wastewater influent (WWI) samples, likely due to its presence in human waste, demonstrating a widespread distribution of ToBRFV in WWI throughout Ontario, Canada. To aid in global ToBRFV surveillance efforts, we developed a tiled amplicon approach to sequence and track the evolution of ToBRFV genomes in municipal WWI. Our assay recovers 95.7% of the 6393 bp ToBRFV RefSeq genome, omitting the terminal 5' and 3' ends. We demonstrate that our sequencing assay is a robust, sensitive, and highly specific method for recovering ToBRFV genomes. Our ToBRFV assay was developed using existing ARTIC Network resources, including primer design, sequencing library prep, and read analysis. Additionally, we adapted our lineage abundance estimation tool, Alcov, to estimate the abundance of ToBRFV clades in samples.
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Affiliation(s)
- Delaney Nash
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
- Metagenom Bio Life Science Inc., Waterloo, ON N2L 5V4, Canada
| | - Isaac Ellmen
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
- Metagenom Bio Life Science Inc., Waterloo, ON N2L 5V4, Canada
| | - Jennifer J. Knapp
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
| | - Ria Menon
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
| | - Alyssa K. Overton
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
| | - Jiujun Cheng
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
- Metagenom Bio Life Science Inc., Waterloo, ON N2L 5V4, Canada
| | - Michael D. J. Lynch
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
- Metagenom Bio Life Science Inc., Waterloo, ON N2L 5V4, Canada
| | - Jozef I. Nissimov
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
| | - Trevor C. Charles
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
- Metagenom Bio Life Science Inc., Waterloo, ON N2L 5V4, Canada
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Köndgen S, Oh DY, Thürmer A, Sedaghatjoo S, Patrono LV, Calvignac-Spencer S, Biere B, Wolff T, Dürrwald R, Fuchs S, Reiche J. A robust, scalable, and cost-efficient approach to whole genome sequencing of RSV directly from clinical samples. J Clin Microbiol 2024; 62:e0111123. [PMID: 38407068 PMCID: PMC10935636 DOI: 10.1128/jcm.01111-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 02/01/2024] [Indexed: 02/27/2024] Open
Abstract
Respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory tract infections causing significant morbidity and mortality among children and the elderly; two RSV vaccines and a monoclonal antibody have recently been approved. Thus, there is an increasing need for a detailed and continuous genomic surveillance of RSV circulating in resource-rich and resource-limited settings worldwide. However, robust, cost-effective methods for whole genome sequencing of RSV from clinical samples that are amenable to high-throughput are still scarce. We developed Next-RSV-SEQ, an experimental and computational pipeline to generate whole genome sequences of historic and current RSV genotypes by in-solution hybridization capture-based next generation sequencing. We optimized this workflow by automating library preparation and pooling libraries prior to enrichment in order to reduce hands-on time and cost, thereby augmenting scalability. Next-RSV-SEQ yielded near-complete to complete genome sequences for 98% of specimens with Cp values ≤31, at median on-target reads >93%, and mean coverage depths between ~1,000 and >5,000, depending on viral load. Whole genomes were successfully recovered from samples with viral loads as low as 230 copies per microliter RNA. We demonstrate that the method can be expanded to other respiratory viruses like parainfluenza virus and human metapneumovirus. Next-RSV-SEQ produces high-quality RSV genomes directly from culture isolates and, more importantly, clinical specimens of all genotypes in circulation. It is cost-efficient, scalable, and can be extended to other respiratory viruses, thereby opening new perspectives for a future effective and broad genomic surveillance of respiratory viruses. IMPORTANCE Respiratory syncytial virus (RSV) is a leading cause of severe acute respiratory tract infections in children and the elderly, and its prevention has become an increasing priority. Recently, vaccines and a long-acting monoclonal antibody to protect effectively against severe disease have been approved for the first time. Hence, there is an urgent need for genomic surveillance of RSV at the global scale to monitor virus evolution, especially with an eye toward immune evasion. However, robust, cost-effective methods for RSV whole genome sequencing that are suitable for high-throughput of clinical samples are currently scarce. Therefore, we have developed Next-RSV-SEQ, an experimental and computational pipeline that produces reliably high-quality RSV genomes directly from clinical specimens and isolates.
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Affiliation(s)
- Sophie Köndgen
- Influenza and Other Respiratory Viruses, Consultant Laboratory for RSV, PIV and HMPV, Robert Koch-Institute, Berlin, Germany
| | - Djin-Ye Oh
- Influenza and Other Respiratory Viruses, Consultant Laboratory for RSV, PIV and HMPV, Robert Koch-Institute, Berlin, Germany
| | - Andrea Thürmer
- Genome Competence Center, Robert Koch-Institute, Berlin, Germany
| | | | - Livia V. Patrono
- Epidemiology of highly pathogenic microorganisms, Robert Koch-Institute, Berlin, Germany
| | | | - Barbara Biere
- Influenza and Other Respiratory Viruses, Consultant Laboratory for RSV, PIV and HMPV, Robert Koch-Institute, Berlin, Germany
| | - Thorsten Wolff
- Influenza and Other Respiratory Viruses, Consultant Laboratory for RSV, PIV and HMPV, Robert Koch-Institute, Berlin, Germany
| | - Ralf Dürrwald
- Influenza and Other Respiratory Viruses, Consultant Laboratory for RSV, PIV and HMPV, Robert Koch-Institute, Berlin, Germany
| | - Stephan Fuchs
- Genome Competence Center, Robert Koch-Institute, Berlin, Germany
| | - Janine Reiche
- Influenza and Other Respiratory Viruses, Consultant Laboratory for RSV, PIV and HMPV, Robert Koch-Institute, Berlin, Germany
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3
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Faridl M, Mellyani K, Khoirunnisa K, Septiani P, Giri-Rachman EA, Nugrahapraja H, Rahmawati E, Alamanda CNC, Ristandi RB, Rachman RW, Robiani R, Fibriani A. RNA sequence analysis of nasopharyngeal swabs from asymptomatic and mildly symptomatic patients with COVID-19. Int J Infect Dis 2022; 122:449-460. [PMID: 35760384 PMCID: PMC9233886 DOI: 10.1016/j.ijid.2022.06.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 05/24/2022] [Accepted: 06/21/2022] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVES The characterization of asymptomatic and mildly symptomatic patients with COVID-19 by observing changes in gene expression profile and possible bacterial coinfection is relevant to be investigated. We aimed to identify transcriptomic and coinfection profiles in both groups of patients. METHODS A ribonucleic acid (RNA) sequence analysis on nasopharyngeal swabs were performed using a shotgun sequencing pipeline. Differential gene analysis, viral genome assembly, and metagenomics analysis were further performed using the retrieved data. RESULTS Both groups of patients underwent a cilia modification and mRNA splicing. Modulations in macroautophagy, epigenetics, and cell cycle processes were observed specifically in the asymptomatic group. Modulation in the RNA transport was found specifically in the mildly symptomatic group. The mildly symptomatic group showed modulation in the RNA transport and upregulation of autophagy regulator genes and genes in the complement system. No link between viral variants and disease severity was found. Microbiome analysis revealed the elevation of Streptococcus pneumoniae and Veillonella parvula proportion in symptomatic patients. CONCLUSION A reduction in the autophagy influx and modification in the epigenetic profile might be involved in halting the disease progression. A global dysregulation of RNA processing and translation might cause more severe outcomes in symptomatic individuals. Coinfection by opportunistic microflora should be taken into account when assessing the possible outcome of SARS-CoV-2 infection.
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Affiliation(s)
- Miftahul Faridl
- School of Life Sciences and Technology, Bandung Institute of Technology, Bandung, West Java, Indonesia
| | - Karlina Mellyani
- School of Life Sciences and Technology, Bandung Institute of Technology, Bandung, West Java, Indonesia
| | - Karimatu Khoirunnisa
- School of Life Sciences and Technology, Bandung Institute of Technology, Bandung, West Java, Indonesia
| | - Popi Septiani
- School of Life Sciences and Technology, Bandung Institute of Technology, Bandung, West Java, Indonesia
| | | | - Husna Nugrahapraja
- School of Life Sciences and Technology, Bandung Institute of Technology, Bandung, West Java, Indonesia
| | - Ema Rahmawati
- West Java Health Laboratory, Bandung, West Java, Indonesia
| | | | | | | | - Rini Robiani
- West Java Health Laboratory, Bandung, West Java, Indonesia
| | - Azzania Fibriani
- School of Life Sciences and Technology, Bandung Institute of Technology, Bandung, West Java, Indonesia,Corresponding author at: School of Life Sciences and Technology, Bandung Institute of Technology, Bandung, West Java, Indonesia
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4
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Maljkovic Berry I, Melendrez MC, Bishop-Lilly KA, Rutvisuttinunt W, Pollett S, Talundzic E, Morton L, Jarman RG. Next Generation Sequencing and Bioinformatics Methodologies for Infectious Disease Research and Public Health: Approaches, Applications, and Considerations for Development of Laboratory Capacity. J Infect Dis 2021; 221:S292-S307. [PMID: 31612214 DOI: 10.1093/infdis/jiz286] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Next generation sequencing (NGS) combined with bioinformatics has successfully been used in a vast array of analyses for infectious disease research of public health relevance. For instance, NGS and bioinformatics approaches have been used to identify outbreak origins, track transmissions, investigate epidemic dynamics, determine etiological agents of a disease, and discover novel human pathogens. However, implementation of high-quality NGS and bioinformatics in research and public health laboratories can be challenging. These challenges mainly include the choice of the sequencing platform and the sequencing approach, the choice of bioinformatics methodologies, access to the appropriate computation and information technology infrastructure, and recruiting and retaining personnel with the specialized skills and experience in this field. In this review, we summarize the most common NGS and bioinformatics workflows in the context of infectious disease genomic surveillance and pathogen discovery, and highlight the main challenges and considerations for setting up an NGS and bioinformatics-focused infectious disease research public health laboratory. We describe the most commonly used sequencing platforms and review their strengths and weaknesses. We review sequencing approaches that have been used for various pathogens and study questions, as well as the most common difficulties associated with these approaches that should be considered when implementing in a public health or research setting. In addition, we provide a review of some common bioinformatics tools and procedures used for pathogen discovery and genome assembly, along with the most common challenges and solutions. Finally, we summarize the bioinformatics of advanced viral, bacterial, and parasite pathogen characterization, including types of study questions that can be answered when utilizing NGS and bioinformatics.
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Affiliation(s)
- Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | | | - Kimberly A Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Maryland
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Simon Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland.,Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Eldin Talundzic
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Lindsay Morton
- Global Emerging Infections Surveillance, Armed Forces Health Surveillance Branch, Silver Spring, Maryland
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
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Anis E, Ilha MRS, Engiles JB, Wilkes RP. Evaluation of targeted next-generation sequencing for detection of equine pathogens in clinical samples. J Vet Diagn Invest 2020; 33:227-234. [PMID: 33305693 DOI: 10.1177/1040638720978381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Equine infectious disease outbreaks may have profound economic impact, resulting in losses of millions of dollars of revenue as a result of horse loss, quarantine, and cancelled events. Early and accurate diagnosis is essential to limit the spread of infectious diseases. However, laboratory detection of infectious agents, especially the simultaneous detection of multiple agents, can be challenging to the clinician and diagnostic laboratory. Next-generation sequencing (NGS), which allows millions of DNA templates to be sequenced simultaneously in a single reaction, is an ideal technology for comprehensive testing. We conducted a proof-of-concept study of targeted NGS to detect 62 common equine bacterial, viral, and parasitic pathogens in clinical samples. We designed 264 primers and constructed a bioinformatics tool for the detection of targeted pathogens. The designed primers were able to specifically detect the intended pathogens. Results of testing 27 clinical samples with our targeted NGS assay compared with results of routine tests (assessed as a group) yielded positive percent agreement of 81% and negative percent agreement of 83%, overall agreement of 81%, and kappa of 0.56 (moderate agreement). This moderate agreement was likely the result of low sensitivity of some primers. However, our NGS assay successfully detected multiple pathogens in the clinical samples, including some pathogens missed by routine techniques.
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Affiliation(s)
- Eman Anis
- Department of Pathobiology, New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA.,Department of Virology, Faculty of Veterinary Medicine, University of Sadat, El Beheira Governorate, Sadat City, Egypt
| | - Marcia R S Ilha
- Tifton Veterinary Diagnostic and Investigational Laboratory, College of Veterinary Medicine, University of Georgia, Tifton, GA
| | - Julie B Engiles
- Department of Pathobiology, New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA
| | - Rebecca P Wilkes
- Tifton Veterinary Diagnostic and Investigational Laboratory, College of Veterinary Medicine, University of Georgia, Tifton, GA.,Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN
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Sabatier M, Bal A, Destras G, Regue H, Quéromès G, Cheynet V, Lina B, Bardel C, Brengel-Pesce K, Navratil V, Josset L. Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses. Microorganisms 2020; 8:E1539. [PMID: 33036303 PMCID: PMC7601816 DOI: 10.3390/microorganisms8101539] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 12/25/2022] Open
Abstract
Viral metagenomics next-generation sequencing (mNGS) is increasingly being used to characterize the human virome. The impact of viral nucleic extraction on virome profiling has been poorly studied. Here, we aimed to compare the sensitivity and sample and reagent contamination of three extraction methods used for viral mNGS: two automated platforms (eMAG; MagNA Pure 24, MP24) and the manual QIAamp Viral RNA Mini Kit (QIAamp). Clinical respiratory samples (positive for Respiratory Syncytial Virus or Herpes Simplex Virus), one mock sample (including five viruses isolated from respiratory samples), and a no-template control (NTC) were extracted and processed through an mNGS workflow. QIAamp yielded a lower proportion of viral reads for both clinical and mock samples. The sample cross-contamination was higher when using MP24, with up to 36.09% of the viral reads mapping to mock viruses in the NTC (vs. 1.53% and 1.45% for eMAG and QIAamp, respectively). The highest number of viral reads mapping to bacteriophages in the NTC was found with QIAamp, suggesting reagent contamination. Our results highlight the importance of the extraction method choice for accurate virome characterization.
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Affiliation(s)
- Marina Sabatier
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Antonin Bal
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Grégory Destras
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Hadrien Regue
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
| | - Grégory Quéromès
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
| | - Valérie Cheynet
- Laboratoire Commun de Recherche Hospices Civils de Lyon—bioMérieux, Centre Hospitalier Lyon Sud, F-69310 Pierre-Bénite, France; (V.C.); (K.B.-P.)
| | - Bruno Lina
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Claire Bardel
- Université Lyon 1, Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, F-69100 Villeurbanne, France;
| | - Karen Brengel-Pesce
- Laboratoire Commun de Recherche Hospices Civils de Lyon—bioMérieux, Centre Hospitalier Lyon Sud, F-69310 Pierre-Bénite, France; (V.C.); (K.B.-P.)
| | - Vincent Navratil
- PRABI, Rhône Alpes Bioinformatics Center, UCBL, Université Claude Bernard Lyon 1, F-69000 Lyon, France;
- European Virus Bioinformatics Center, Leutragraben 1, D-07743 Jena, Germany
| | - Laurence Josset
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
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Carbo EC, Buddingh EP, Karelioti E, Sidorov IA, Feltkamp MC, Borne PAVD, Verschuuren JJ, Kroes AC, Claas EC, de Vries JJ. Improved diagnosis of viral encephalitis in adult and pediatric hematological patients using viral metagenomics. J Clin Virol 2020; 130:104566. [DOI: 10.1016/j.jcv.2020.104566] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 07/23/2020] [Accepted: 07/28/2020] [Indexed: 02/06/2023]
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Paskey AC, Frey KG, Schroth G, Gross S, Hamilton T, Bishop-Lilly KA. Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples. BMC Genomics 2019; 20:155. [PMID: 30808306 PMCID: PMC6390631 DOI: 10.1186/s12864-019-5543-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/18/2019] [Indexed: 01/23/2023] Open
Abstract
Background Sequencing-based detection and characterization of viruses in complex samples can suffer from lack of sensitivity due to a variety of factors including, but not limited to, low titer, small genome size, and contribution of host or environmental nucleic acids. Hybridization-based target enrichment is one potential method for increasing the sensitivity of viral detection via high-throughput sequencing. Results This study expands upon two previously developed panels of virus enrichment probes (for filoviruses and for respiratory viruses) to include other viruses of biodefense and/or biosurveillance concern to the U.S. Department of Defense and various international public health agencies. The newly expanded and combined panel is tested using carefully constructed synthetic metagenomic samples that contain clinically relevant amounts of viral genetic material. Target enrichment results in a dramatic increase in sensitivity for virus detection as compared to shotgun sequencing, yielding full, deeply covered viral genomes from materials with Ct values suggesting that amplicon sequencing would be likely to fail. Increased pooling to improve cost- and time-effectiveness does not negatively affect the ability to obtain full-length viral genomes, even in the case of co-infections, although as expected, it does decrease depth of coverage. Conclusions Hybridization-based target enrichment is an effective solution to obtain full-length viral genomes for samples from which virus detection would fail via unbiased, shotgun sequencing or even via amplicon sequencing. As the development and testing of probe sets for viral target enrichment expands and continues, the application of this technique, in conjunction with deeper pooling strategies, could make high-throughput sequencing more economical for routine use in biosurveillance, biodefense and outbreak investigations. Electronic supplementary material The online version of this article (10.1186/s12864-019-5543-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adrian C Paskey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center - Frederick, Fort Detrick, Frederick, MD, 21702, USA.,Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA.,Leidos, Reston, VA, 20190, USA
| | - Kenneth G Frey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center - Frederick, Fort Detrick, Frederick, MD, 21702, USA
| | | | | | - Theron Hamilton
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center - Frederick, Fort Detrick, Frederick, MD, 21702, USA
| | - Kimberly A Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center - Frederick, Fort Detrick, Frederick, MD, 21702, USA.
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