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Santos JD, Sobral D, Pinheiro M, Isidro J, Bogaardt C, Pinto M, Eusébio R, Santos A, Mamede R, Horton DL, Gomes JP, Borges V. INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance. Genome Med 2024; 16:61. [PMID: 38659008 PMCID: PMC11044337 DOI: 10.1186/s13073-024-01334-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Implementation of clinical metagenomics and pathogen genomic surveillance can be particularly challenging due to the lack of bioinformatics tools and/or expertise. In order to face this challenge, we have previously developed INSaFLU, a free web-based bioinformatics platform for virus next-generation sequencing data analysis. Here, we considerably expanded its genomic surveillance component and developed a new module (TELEVIR) for metagenomic virus identification. RESULTS The routine genomic surveillance component was strengthened with new workflows and functionalities, including (i) a reference-based genome assembly pipeline for Oxford Nanopore technologies (ONT) data; (ii) automated SARS-CoV-2 lineage classification; (iii) Nextclade analysis; (iv) Nextstrain phylogeographic and temporal analysis (SARS-CoV-2, human and avian influenza, monkeypox, respiratory syncytial virus (RSV A/B), as well as a "generic" build for other viruses); and (v) algn2pheno for screening mutations of interest. Both INSaFLU pipelines for reference-based consensus generation (Illumina and ONT) were benchmarked against commonly used command line bioinformatics workflows for SARS-CoV-2, and an INSaFLU snakemake version was released. In parallel, a new module (TELEVIR) for virus detection was developed, after extensive benchmarking of state-of-the-art metagenomics software and following up-to-date recommendations and practices in the field. TELEVIR allows running complex workflows, covering several combinations of steps (e.g., with/without viral enrichment or host depletion), classification software (e.g., Kaiju, Kraken2, Centrifuge, FastViromeExplorer), and databases (RefSeq viral genome, Virosaurus, etc.), while culminating in user- and diagnosis-oriented reports. Finally, to potentiate real-time virus detection during ONT runs, we developed findONTime, a tool aimed at reducing costs and the time between sample reception and diagnosis. CONCLUSIONS The accessibility, versatility, and functionality of INSaFLU-TELEVIR are expected to supply public and animal health laboratories and researchers with a user-oriented and pan-viral bioinformatics framework that promotes a strengthened and timely viral metagenomic detection and routine genomics surveillance. INSaFLU-TELEVIR is compatible with Illumina, Ion Torrent, and ONT data and is freely available at https://insaflu.insa.pt/ (online tool) and https://github.com/INSaFLU (code).
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Affiliation(s)
- João Dourado Santos
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniel Sobral
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Miguel Pinheiro
- Institute of Biomedicine-iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Joana Isidro
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Carlijn Bogaardt
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Surrey, UK
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Rodrigo Eusébio
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - André Santos
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Rafael Mamede
- Faculdade de Medicina, Instituto de Microbiologia, Instituto de Medicina Molecular, Universidade de Lisboa, Lisbon, Portugal
| | - Daniel L Horton
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Surrey, UK
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Veterinary and Animal Research Centre (CECAV), Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal.
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Roach MJ, Beecroft SJ, Mihindukulasuriya KA, Wang L, Paredes A, Cárdenas LAC, Henry-Cocks K, Lima LFO, Dinsdale EA, Edwards RA, Handley SA. Hecatomb: an integrated software platform for viral metagenomics. Gigascience 2024; 13:giae020. [PMID: 38832467 PMCID: PMC11148595 DOI: 10.1093/gigascience/giae020] [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: 07/17/2023] [Revised: 01/18/2024] [Accepted: 04/08/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND Modern sequencing technologies offer extraordinary opportunities for virus discovery and virome analysis. Annotation of viral sequences from metagenomic data requires a complex series of steps to ensure accurate annotation of individual reads and assembled contigs. In addition, varying study designs will require project-specific statistical analyses. FINDINGS Here we introduce Hecatomb, a bioinformatic platform coordinating commonly used tasks required for virome analysis. Hecatomb means "a great sacrifice." In this setting, Hecatomb is "sacrificing" false-positive viral annotations using extensive quality control and tiered-database searches. Hecatomb processes metagenomic data obtained from both short- and long-read sequencing technologies, providing annotations to individual sequences and assembled contigs. Results are provided in commonly used data formats useful for downstream analysis. Here we demonstrate the functionality of Hecatomb through the reanalysis of a primate enteric and a novel coral reef virome. CONCLUSION Hecatomb provides an integrated platform to manage many commonly used steps for virome characterization, including rigorous quality control, host removal, and both read- and contig-based analysis. Each step is managed using the Snakemake workflow manager with dependency management using Conda. Hecatomb outputs several tables properly formatted for immediate use within popular data analysis and visualization tools, enabling effective data interpretation for a variety of study designs. Hecatomb is hosted on GitHub (github.com/shandley/hecatomb) and is available for installation from Bioconda and PyPI.
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Affiliation(s)
- Michael J Roach
- Flinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, SA, Australia
- Adelaide Centre for Epigenetics, University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Immunogenomics Cancer Institute, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Sarah J Beecroft
- Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia
| | - Kathie A Mihindukulasuriya
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Leran Wang
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Anne Paredes
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Luis Alberto Chica Cárdenas
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Kara Henry-Cocks
- Flinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, SA, Australia
| | | | - Elizabeth A Dinsdale
- Flinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, SA, Australia
| | - Robert A Edwards
- Flinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, SA, Australia
| | - Scott A Handley
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
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3
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Afonso CL, Afonso AM. Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples. Vet Sci 2023; 10:690. [PMID: 38133241 PMCID: PMC10747646 DOI: 10.3390/vetsci10120690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/24/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023] Open
Abstract
Direct-targeted next-generation sequencing (tNGS), with its undoubtedly superior diagnostic capacity over real-time PCR (RT-PCR), and direct-non-targeted NGS (ntNGS), with its higher capacity to identify and characterize multiple agents, are both likely to become diagnostic methods of choice in the future. tNGS is a rapid and sensitive method for precise characterization of suspected agents. ntNGS, also known as agnostic diagnosis, does not require a hypothesis and has been used to identify unsuspected infections in clinical samples. Implemented in the form of multiplexed total DNA metagenomics or as total RNA sequencing, the approach produces comprehensive and actionable reports that allow semi-quantitative identification of most of the agents present in respiratory, cloacal, and tissue samples. The diagnostic benefits of the use of direct tNGS and ntNGS are high specificity, compatibility with different types of clinical samples (fresh, frozen, FTA cards, and paraffin-embedded), production of nearly complete infection profiles (viruses, bacteria, fungus, and parasites), production of "semi-quantitative" information, direct agent genotyping, and infectious agent mutational information. The achievements of NGS in terms of diagnosing poultry problems are described here, along with future applications. Multiplexing, development of standard operating procedures, robotics, sequencing kits, automated bioinformatics, cloud computing, and artificial intelligence (AI) are disciplines converging toward the use of this technology for active surveillance in poultry farms. Other advances in human and veterinary NGS sequencing are likely to be adaptable to avian species in the future.
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Lee E, Vansia R, Phelan J, Lofano A, Smith A, Wang A, Bilodeau GJ, Pernal SF, Guarna MM, Rott M, Griffiths JS. Area Wide Monitoring of Plant and Honey Bee ( Apis mellifera) Viruses in Blueberry ( Vaccinium corymbosum) Agroecosystems Facilitated by Honey Bee Pollination. Viruses 2023; 15:v15051209. [PMID: 37243295 DOI: 10.3390/v15051209] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/11/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Healthy agroecosystems are dependent on a complex web of factors and inter-species interactions. Flowers are hubs for pathogen transmission, including the horizontal or vertical transmission of plant-viruses and the horizontal transmission of bee-viruses. Pollination by the European honey bee (Apis mellifera) is critical for industrial fruit production, but bees can also vector viruses and other pathogens between individuals. Here, we utilized commercial honey bee pollination services in blueberry (Vaccinium corymbosum) farms for a metagenomics-based bee and plant virus monitoring system. Following RNA sequencing, viruses were identified by mapping reads to a reference sequence database through the bioinformatics portal Virtool. In total, 29 unique plant viral species were found at two blueberry farms in British Columbia (BC). Nine viruses were identified at one site in Ontario (ON), five of which were not identified in BC. Ilarviruses blueberry shock virus (BlShV) and prune dwarf virus (PDV) were the most frequently detected viruses in BC but absent in ON, while nepoviruses tomato ringspot virus and tobacco ringspot virus were common in ON but absent in BC. BlShV coat protein (CP) nucleotide sequences were nearly identical in all samples, while PDV CP sequences were more diverse, suggesting multiple strains of PDV circulating at this site. Ten bee-infecting viruses were identified, with black queen cell virus frequently detected in ON and BC. Area-wide bee-mediated pathogen monitoring can provide new insights into the diversity of viruses present in, and the health of, bee-pollination ecosystems. This approach can be limited by a short sampling season, biased towards pollen-transmitted viruses, and the plant material collected by bees can be very diverse. This can obscure the origin of some viruses, but bee-mediated virus monitoring can be an effective preliminary monitoring approach.
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Affiliation(s)
- Eunseo Lee
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
- London Research and Development Centre, Agriculture and Agri-Food Canada, 4902 Victoria Ave N, Vineland Station, ON L0R 2E0, Canada
| | - Raj Vansia
- London Research and Development Centre, Agriculture and Agri-Food Canada, 4902 Victoria Ave N, Vineland Station, ON L0R 2E0, Canada
- Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada
| | - James Phelan
- Sidney Laboratory, Centre for Plant Health, Canadian Food Inspection Agency, 8801 East Saanich Rd., North Saanich, BC V8L 1H3, Canada
| | - Andrea Lofano
- London Research and Development Centre, Agriculture and Agri-Food Canada, 4902 Victoria Ave N, Vineland Station, ON L0R 2E0, Canada
| | - Adam Smith
- Sidney Laboratory, Centre for Plant Health, Canadian Food Inspection Agency, 8801 East Saanich Rd., North Saanich, BC V8L 1H3, Canada
| | - Aiming Wang
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
| | - Guillaume J Bilodeau
- Ottawa Plant Laboratory, Canadian Food Inspection Agency, 3851 Fallowfield Rd., Ottawa, ON K2J 4S1, Canada
| | - Stephen F Pernal
- Beaverlodge Research Farm, Agriculture and Agri-Food Canada, P.O. Box 29, Beaverlodge, AB T0H 0C0, Canada
| | - M Marta Guarna
- Beaverlodge Research Farm, Agriculture and Agri-Food Canada, P.O. Box 29, Beaverlodge, AB T0H 0C0, Canada
| | - Michael Rott
- Sidney Laboratory, Centre for Plant Health, Canadian Food Inspection Agency, 8801 East Saanich Rd., North Saanich, BC V8L 1H3, Canada
| | - Jonathan S Griffiths
- London Research and Development Centre, Agriculture and Agri-Food Canada, 4902 Victoria Ave N, Vineland Station, ON L0R 2E0, Canada
- Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada
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Elimination of Foreign Sequences in Eukaryotic Viral Reference Genomes Improves the Accuracy of Virome Analysis. mSystems 2022; 7:e0090722. [PMID: 36286492 PMCID: PMC9765019 DOI: 10.1128/msystems.00907-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Widespread in public databases, foreign contaminant sequences pose a substantial obstacle in genomic analyses. Such contamination in viral genome databases is also notorious but more complicated and often causes questionable results in various applications, particularly in virome-based virus detection. Here, we conducted comprehensive screening and identification of the foreign sequences hidden in the largest eukaryotic viral genome collections of GenBank and UniProt using a scrutiny pipeline, which enables us to rigorously detect those problematic viral sequences (PVSs) with origins in hosts, vectors, and laboratory components. As a result, a total of 766 nucleotide PVSs and 276 amino acid PVSs with lengths up to 6,605 bp were determined, which were widely distributed in 39 families with many involving highly public health-concerning viruses, such as hepatitis C virus, Crimean-Congo hemorrhagic fever virus, and filovirus. The majority of these PVSs are genomic fragments of hosts including humans and bacteria. However, they cannot simply be regarded as foreign contaminants, since parts of them are results of natural occurrence or artificial engineering of viruses. Nevertheless, they severely disturb such sequence-based analyses as genome annotation, taxonomic assignment, and virome profiling. Therefore, we provide a clean version of the eukaryotic viral reference data set by the removal of these PVSs, which allows more accurate virome analysis with less time consumed than with other comprehensive databases. IMPORTANCE High-throughput sequencing-based viromics highly depends on reference databases, but foreign contamination is widespread in public databases and often leads to confusing and even wrong conclusions in genomic analysis and viromic profiling. To address this issue, we systematically detected and identified the contamination in the largest viral sequence collections of GenBank and UniProt based on a stringent scrutiny pipeline. We found hundreds of PVSs that are related to hosts, vectors, and laboratory components. By the removal of them, the resulting data set greatly improves the accuracy and efficiency of eukaryotic virome profiling. These results refresh our knowledge of the type and origin of PVSs and also have warning implications for viromic analysis. Viromic practitioners should be aware of these problems caused by PVSs and need to realize that a careful review of bioinformatic results is necessary for a reliable conclusion.
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Viral Metagenome-Based Precision Surveillance of Pig Population at Large Scale Reveals Viromic Signatures of Sample Types and Influence of Farming Management on Pig Virome. mSystems 2021; 6:e0042021. [PMID: 34100634 PMCID: PMC8269232 DOI: 10.1128/msystems.00420-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pigs are a major meat source worldwide and a pillar of Chinese animal husbandry; hence, their health and safety are a prioritized concern of the national economy. Although pig viruses have been continuously investigated, the full extent of the pig virome has remained unknown and emerging viruses are still a major threat to the pig industry. Here, we report a comprehensive study to delineate the pig virome of 1,841 healthy weaned pigs from 45 commercial farms collected from 25 major pig-producing regions across China. A viromic sequence data set, named Pigs_VIRES, which matched 96,586 viral genes from at least 249 genera within 66 families and which almost tripled the number of previously published pig viromic genes, was established. The majority of the mammalian viruses were closely related to currently known ones. A comparison with previously published viromes of bovines, avians, and humans has revealed the distinct composition of Pigs_VIRES, which has provided characteristic viromic signatures of serum, pharyngeal, and anal samples that were significantly influenced by farming management and disease control measures. Taken together, Pigs_VIRES has revealed the most complete viromic data set of healthy pigs to date. The compiled data also provide useful guidance to pig viral disease control and prevention and the biosafety management of pig farms. Especially, the established viromic protocol has created a precision surveillance strategy to potentially innovate currently used surveillance methods of animal infectious diseases, particularly by making precision surveillance available to other animal species on a large scale or even during a nationwide surveillance campaign. IMPORTANCE Pigs are deeply involved in human lives; hence, their viruses are associated with public health. Here, we established the most comprehensive virome of healthy piglets to date, which provides a viromic baseline of weaned pigs for disease prevention and control, highlighting that longitudinal viromic monitoring is needed to better understand the dynamics of the virome in pig development and disease occurrence. The present study also shows how high standards of animal farm management with strict biosafety measures can significantly minimize the risk of introduction of pathogenic viruses into pig farms. Particularly, the viromic strategy established, i.e., high-throughput detection and analyses of various known and unknown pathogenic viruses in a single test at large scale, has completely innovated current surveillance measures in provision of timely and precise detection of all potentially existing pathogenic viruses and can be widely applied in other animal species.
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7
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The virome of German bats: comparing virus discovery approaches. Sci Rep 2021; 11:7430. [PMID: 33795699 PMCID: PMC8016945 DOI: 10.1038/s41598-021-86435-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/15/2021] [Indexed: 12/14/2022] Open
Abstract
Bats are known to be reservoirs of several highly pathogenic viruses. Hence, the interest in bat virus discovery has been increasing rapidly over the last decade. So far, most studies have focused on a single type of virus detection method, either PCR, virus isolation or virome sequencing. Here we present a comprehensive approach in virus discovery, using all three discovery methods on samples from the same bats. By family-specific PCR screening we found sequences of paramyxoviruses, adenoviruses, herpesviruses and one coronavirus. By cell culture we isolated a novel bat adenovirus and bat orthoreovirus. Virome sequencing revealed viral sequences of ten different virus families and orders: three bat nairoviruses, three phenuiviruses, one orbivirus, one rotavirus, one orthoreovirus, one mononegavirus, five parvoviruses, seven picornaviruses, three retroviruses, one totivirus and two thymoviruses were discovered. Of all viruses identified by family-specific PCR in the original samples, none was found by metagenomic sequencing. Vice versa, none of the viruses found by the metagenomic virome approach was detected by family-specific PCRs targeting the same family. The discrepancy of detected viruses by different detection approaches suggests that a combined approach using different detection methods is necessary for virus discovery studies.
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8
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Deep viral blood metagenomics reveals extensive anellovirus diversity in healthy humans. Sci Rep 2021; 11:6921. [PMID: 33767340 PMCID: PMC7994813 DOI: 10.1038/s41598-021-86427-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/15/2021] [Indexed: 02/08/2023] Open
Abstract
Human blood metagenomics has revealed the presence of different types of viruses in apparently healthy subjects. By far, anelloviruses constitute the viral family that is more frequently found in human blood, although amplification biases and contaminations pose a major challenge in this field. To investigate this further, we subjected pooled plasma samples from 120 healthy donors in Spain to high-speed centrifugation, RNA and DNA extraction, random amplification, and massive parallel sequencing. Our results confirm the extensive presence of anelloviruses in such samples, which represented nearly 97% of the total viral sequence reads obtained. We assembled 114 different viral genomes belonging to this family, revealing remarkable diversity. Phylogenetic analysis of ORF1 suggested 28 potentially novel anellovirus species, 24 of which were validated by Sanger sequencing to discard artifacts. These findings underscore the importance of implementing more efficient purification procedures that enrich the viral fraction as an essential step in virome studies and question the suggested pathological role of anelloviruses.
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9
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Khan AS, Blümel J, Deforce D, Gruber MF, Jungbäck C, Knezevic I, Mallet L, Mackay D, Matthijnssens J, O'Leary M, Theuns S, Victoria J, Neels P. Report of the second international conference on next generation sequencing for adventitious virus detection in biologics for humans and animals. Biologicals 2020; 67:94-111. [PMID: 32660862 PMCID: PMC7351673 DOI: 10.1016/j.biologicals.2020.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 06/01/2020] [Indexed: 11/20/2022] Open
Abstract
The IABS-EU, in association with PROVAXS and Ghent University, hosted the "2nd Conference on Next Generation Sequencing (NGS) for Adventitious Virus Detection in Human and Veterinary Biologics" held on November 13th and 14th 2019, in Ghent, Belgium. The meeting brought together international experts from regulatory agencies, the biotherapeutics and biologics industries, contract research organizations, and academia, with the goal to develop a scientific consensus on the readiness of NGS for detecting adventitious viruses, and on the use of this technology to supplement or replace/substitute the currently used assays. Participants discussed the progress on the standardization and validation of the technical and bioinformatics steps in NGS for characterization and safety evaluation of biologics, including human and animal vaccines. It was concluded that NGS can be used for the detection of a broad range of viruses, including novel viruses, and therefore can complement, supplement or even replace some of the conventional adventitious virus detection assays. Furthermore, the development of reference viral standards, complete and correctly annotated viral databases, and protocols for the validation and follow-up investigations of NGS signals is necessary to enable broader use of NGS. An international collaborative effort, involving regulatory authorities, industry, academia, and other stakeholders is ongoing toward this goal.
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Affiliation(s)
- Arifa S Khan
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA.
| | | | | | - Marion F Gruber
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Carmen Jungbäck
- International Association for Biological Standardization for Europe, Lyon, France
| | | | | | | | | | - Maureen O'Leary
- P95 Pharmacovigilance and Epidemiology Services, Leuven, Belgium
| | | | | | - Pieter Neels
- International Association for Biological Standardization for Europe, Lyon, France
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Van Borm S, Fu Q, Winand R, Vanneste K, Hakhverdyan M, Höper D, Vandenbussche F. Evaluation of a commercial exogenous internal process control for diagnostic RNA virus metagenomics from different animal clinical samples. J Virol Methods 2020; 283:113916. [PMID: 32574649 DOI: 10.1016/j.jviromet.2020.113916] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/09/2020] [Accepted: 06/09/2020] [Indexed: 12/20/2022]
Abstract
Metagenomic next generation sequencing (mNGS) is increasingly recognized as an important complementary tool to targeted human and animal infectious disease diagnostics. It is, however, sensitive to biases and errors that are currently not systematically evaluated by the implementation of quality controls (QC) for the diagnostic use of mNGS. We evaluated a commercial reagent (Mengovirus extraction control kit, CeraamTools, bioMérieux) as an exogenous internal control for mNGS. It validates the integrity of reagents and workflow, the efficient isolation of viral nucleic acids and the absence of inhibitors in individual samples (verified using a specific qRT-PCR). Moreover, it validates the efficient generation of viral sequence data in individual samples (verified by normalized mengoviral read counts in the metagenomic analysis). We show that when using a completely random metagenomics workflow: (1) Mengovirus RNA can be reproducibly detected in different animal sample types (swine feces and sera, wild bird cloacal swabs), except for tissue samples (swine lung); (2) the Mengovirus control kit does not contain other contaminating viruses that may affect metagenomic experiments (using a cutoff of minimum 1 Kraken classified read per million (RPM)); (3) the addition of 2.17 × 106Mengovirus copies/mL of sample does not affect the virome composition of pig fecal samples or wild bird cloacal swab samples; (4) Mengovirus Cq values (using as cutoff the upper limit of the 99 % confidence interval of Cq values for a given sample matrix) allow the identification of samples with poor viral RNA extraction or high inhibitor load; (5) Mengovirus normalized read counts (cutoff RPM > 1) allow the identification of samples where the viral sequences are outcompeted by host or bacterial target sequences in the random metagenomic workflow. The implementation of two QC testing points, a first one after RNA extraction (Mengoviral qRT-PCR) and a second one after metagenomic data analysis provide valuable information for the validation of individual samples and results. Their implementation in addition to external controls validating runs or experiments should be carefully considered for a given sample type and workflow.
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Affiliation(s)
- Steven Van Borm
- Department of Animal Infectious Diseases, Sciensano, Groeselenbergstraat 99, 1180, Brussels, Belgium.
| | - Qiang Fu
- Transversal Activities in Applied Genomics, Sciensano, Rue Juliette Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Raf Winand
- Transversal Activities in Applied Genomics, Sciensano, Rue Juliette Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Rue Juliette Wytsmanstraat 14, 1050, Brussels, Belgium
| | | | - Dirk Höper
- FLI, Friedrich Löffler Institut, Südufer 10, 17493 Greifswald, Germany
| | - Frank Vandenbussche
- Department of Animal Infectious Diseases, Sciensano, Groeselenbergstraat 99, 1180, Brussels, Belgium
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Wang H, Kjellberg I, Sikora P, Rydberg H, Lindh M, Bergstedt O, Norder H. Hepatitis E virus genotype 3 strains and a plethora of other viruses detected in raw and still in tap water. WATER RESEARCH 2020; 168:115141. [PMID: 31590036 DOI: 10.1016/j.watres.2019.115141] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/24/2019] [Accepted: 09/29/2019] [Indexed: 06/10/2023]
Abstract
In this study, next generation sequencing was used to explore the virome in 20L up to 10,000L water from different purification steps at two Swedish drinking water treatment plants (DWTPs), and in tap water. One DWTP used ultrafiltration (UF) with 20 nm pores, the other UV light treatment after conventional treatment of the water. Viruses belonging to 26 different families were detected in raw water, in which 6-9 times more sequence reads were found for phages than for known environmental, plant or vertebrate viruses. The total number of viral reads was reduced more than 4-log10 after UF and 3-log10 over UV treatment. However, for some viruses the reduction was 3.5-log10 after UF, as for hepatitis E virus (HEV), which was also detected in tap water, with sequences similar to those in raw water and after treatment. This indicates that HEV had passed through the treatment and entered into the supply network. However, the viability of the viruses is unknown. In tap water 10-130 International Units of HEV RNA/mL were identified, which is a comparable low amount of virus. The risk of getting infected through consumption of tap water is probably negligible, but needs to be investigated. The HEV strains in the waters belonged to subtypes HEV3a and HEV3c/i, which is associated with unknown source of infection in humans infected in Sweden. None of these subtypes are common among pigs or wild boar, the major reservoirs for HEV, indicating that water may play a role in transmitting this virus. The results indicate that monitoring small fecal/oral transmitted viruses in DWTPs may be considered, especially during community outbreaks, to prevent potential transmission by tap water.
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Affiliation(s)
- Hao Wang
- Department of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sweden
| | | | - Per Sikora
- Department of Pathology and Genetics, Institute of Biomedicine at Sahlgrenska Academy, University of Gothenburg, 41345, Gothenburg, Sweden; Clinical Genomics Gothenburg, SciLife Labs, Gothenburg, Sweden
| | | | - Magnus Lindh
- Department of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sweden; Region Västra Götaland, Sahlgrenska University Hospital, Department of Infectious Diseases, Gothenburg, Sweden
| | - Olof Bergstedt
- Göteborgs Stad Kretslopp och vatten, Gothenburg, Sweden; City of Gothenburg and DRICKS Chalmers University of Technology, Gothenburg, Sweden
| | - Heléne Norder
- Department of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sweden; Region Västra Götaland, Sahlgrenska University Hospital, Department of Infectious Diseases, Gothenburg, Sweden.
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12
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Cholleti H, Berg M, Hayer J, Blomström AL. Vector-borne viruses and their detection by viral metagenomics. Infect Ecol Epidemiol 2018. [DOI: 10.1080/20008686.2018.1553465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Harindranath Cholleti
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mikael Berg
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Juliette Hayer
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anne-Lie Blomström
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
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13
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MahmoudAl-Atiyat R. Dynamic of Bacterial Diversity in Ileum Digesta Under Water Supplements of Antibiotics and Probiotics. Pak J Biol Sci 2017; 20:372-381. [PMID: 29023057 DOI: 10.3923/pjbs.2017.372.381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND OBJECTIVE Intestinal bacteria plays an important role in the physiological and immunological status of birds. The present study investigated the diversity of intestinal bacterial of broilers that were fed corn-soy diet and supplements of antibiotics and probiotics. MATERIALS AND METHODS The supplemented treatments were water, water with antibiotics, water with probiotic and water with antibiotics and probiotic. Eight randomly sampled broilers were slaughtered and their ileum digesta taken. The total of 32 samples was then subjected for DNA extraction. Subsequently, bacterial tag-encoded 16 FLX ampliconpyro sequencing (bTEFAP) procedures were performed. RESULTS Nearly all treatments samples contained Lactobacillus, with the majority related to water with probiotic treatment. In contrast, different pathogenic bacteria along with Lactobacillus observed for other three treatments. CONCLUSION The probiotics supplements made a shift towards useful bacterial species; Lactobacillus salivarius and Lactobacillus aviarius. This study promoted for replacing the probiotics as a prophylaxis in gastrointestinal infection and diseases instead of antibiotics.
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14
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Complete Coding Sequence of Usutu Virus Strain Gracula religiosa/U1609393/Belgium/2016 Obtained from the Brain Tissue of an Infected Captive Common Hill Myna ( Gracula religiosa). GENOME ANNOUNCEMENTS 2017; 5:5/12/e00042-17. [PMID: 28336592 PMCID: PMC5364217 DOI: 10.1128/genomea.00042-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The complete and annotated coding sequence and partial noncoding sequence of an Usutu virus genome were sequenced from RNA extracted from a clinical brain tissue sample obtained from a common hill myna (Gracula religiosa), demonstrating close homology with Usutu viruses circulating in Europe.
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15
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Moustafa A, Xie C, Kirkness E, Biggs W, Wong E, Turpaz Y, Bloom K, Delwart E, Nelson KE, Venter JC, Telenti A. The blood DNA virome in 8,000 humans. PLoS Pathog 2017; 13:e1006292. [PMID: 28328962 PMCID: PMC5378407 DOI: 10.1371/journal.ppat.1006292] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 04/03/2017] [Accepted: 03/14/2017] [Indexed: 02/06/2023] Open
Abstract
The characterization of the blood virome is important for the safety of blood-derived transfusion products, and for the identification of emerging pathogens. We explored non-human sequence data from whole-genome sequencing of blood from 8,240 individuals, none of whom were ascertained for any infectious disease. Viral sequences were extracted from the pool of sequence reads that did not map to the human reference genome. Analyses sifted through close to 1 Petabyte of sequence data and performed 0.5 trillion similarity searches. With a lower bound for identification of 2 viral genomes/100,000 cells, we mapped sequences to 94 different viruses, including sequences from 19 human DNA viruses, proviruses and RNA viruses (herpesviruses, anelloviruses, papillomaviruses, three polyomaviruses, adenovirus, HIV, HTLV, hepatitis B, hepatitis C, parvovirus B19, and influenza virus) in 42% of the study participants. Of possible relevance to transfusion medicine, we identified Merkel cell polyomavirus in 49 individuals, papillomavirus in blood of 13 individuals, parvovirus B19 in 6 individuals, and the presence of herpesvirus 8 in 3 individuals. The presence of DNA sequences from two RNA viruses was unexpected: Hepatitis C virus is revealing of an integration event, while the influenza virus sequence resulted from immunization with a DNA vaccine. Age, sex and ancestry contributed significantly to the prevalence of infection. The remaining 75 viruses mostly reflect extensive contamination of commercial reagents and from the environment. These technical problems represent a major challenge for the identification of novel human pathogens. Increasing availability of human whole-genome sequences will contribute substantial amounts of data on the composition of the normal and pathogenic human blood virome. Distinguishing contaminants from real human viruses is challenging. Novel sequencing technologies offer insight into the virome in human samples. Here, we identify the viral DNA sequences in blood of over 8,000 individuals undergoing whole genome sequencing. This approach serves to identify 94 viruses; however, many are shown to reflect widespread DNA contamination of commercial reagents or of environmental origin. While this represents a significant limitation to reliably identify novel viruses infecting humans, we could confidently detect sequences and quantify abundance of 19 human viruses in 42% of individuals. Ancestry, sex, and age were important determinants of viral prevalence. This large study calls attention on the challenge of interpreting next generation sequencing data for the identification of novel viruses. However, it serves to categorize the abundance of human DNA viruses using an unbiased technique.
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Affiliation(s)
- Ahmed Moustafa
- Human Longevity Inc., San Diego, California, United States of America
| | - Chao Xie
- Human Longevity Singapore Pte. Ltd., Singapore
| | - Ewen Kirkness
- Human Longevity Inc., San Diego, California, United States of America
| | - William Biggs
- Human Longevity Inc., San Diego, California, United States of America
| | - Emily Wong
- Human Longevity Inc., San Diego, California, United States of America
| | | | - Kenneth Bloom
- Human Longevity Inc., San Diego, California, United States of America
| | - Eric Delwart
- Blood Systems Research Institute, Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Karen E. Nelson
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - J. Craig Venter
- Human Longevity Inc., San Diego, California, United States of America
- J. Craig Venter Institute, La Jolla, California, United States of America
- * E-mail: (JCV); (AT)
| | - Amalio Telenti
- Human Longevity Inc., San Diego, California, United States of America
- J. Craig Venter Institute, La Jolla, California, United States of America
- * E-mail: (JCV); (AT)
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16
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Abstract
Whole-genome sequencing (WGS) of pathogens is becoming increasingly important not only for basic research but also for clinical science and practice. In virology, WGS is important for the development of novel treatments and vaccines, and for increasing the power of molecular epidemiology and evolutionary genomics. In this Opinion article, we suggest that WGS of viruses in a clinical setting will become increasingly important for patient care. We give an overview of different WGS methods that are used in virology and summarize their advantages and disadvantages. Although there are only partially addressed technical, financial and ethical issues in regard to the clinical application of viral WGS, this technique provides important insights into virus transmission, evolution and pathogenesis.
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Affiliation(s)
- Charlotte J. Houldcroft
- Department of Infection, UK; and the Division of Biological Anthropology, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, University of Cambridge, Cambridge CB2 3QG, UK.,
- and the Division of Biological Anthropology, University of Cambridge, Cambridge CB2 3QG, UK.,
| | - Mathew A. Beale
- Division of Infection and Immunity, University College London, London, WC1E 6BT UK
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK; and at Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK.,
- and at Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK.,
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17
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van Aerle R, Santos EM. Advances in the application of high-throughput sequencing in invertebrate virology. J Invertebr Pathol 2017; 147:145-156. [PMID: 28249815 DOI: 10.1016/j.jip.2017.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 02/22/2017] [Accepted: 02/24/2017] [Indexed: 10/20/2022]
Abstract
Over the last decade, advances in high-throughput sequencing technologies have revolutionised biological research, making it possible for DNA/RNA sequencing of any organism of interest to be undertaken. Sequencing approaches are now routinely used in the detection and characterisation of (novel) viruses, investigation of host-pathogen interactions, and effective development of disease treatment strategies. For the sequencing and identification of viruses of interest, metagenomics approaches using infected host tissue are frequently used, as it is not always possible to culture and isolate these pathogens. High-throughput sequencing can also be used to investigate host-pathogen interactions by investigating (temporal) transcriptomic responses of both the host and virus, potentially leading to the discovery of novel opportunities for treatment and drug targets. In addition, viruses in environmental samples (e.g. water or soil samples) can be identified using eDNA/metagenomics approaches. The promise that recent developments in sequencing brings to the field of invertebrate virology are not devoid of technical challenges, including the need for better laboratory and bioinformatics strategies to sequence and assemble virus genomes within complex tissue or environmental samples, and the difficulties associated with the annotation of the large number of novel viruses being discovered.
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Affiliation(s)
- R van Aerle
- Centre for Environment, Fisheries, and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, UK.
| | - E M Santos
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK.
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18
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Maciel-Vergara G, Ros VID. Viruses of insects reared for food and feed. J Invertebr Pathol 2017; 147:60-75. [PMID: 28189501 DOI: 10.1016/j.jip.2017.01.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 01/26/2017] [Accepted: 01/31/2017] [Indexed: 02/07/2023]
Abstract
The use of insects as food for humans or as feed for animals is an alternative for the increasing high demand for meat and has various environmental and social advantages over the traditional intensive production of livestock. Mass rearing of insects, under insect farming conditions or even in industrial settings, can be the key for a change in the way natural resources are utilized in order to produce meat, animal protein and a list of other valuable animal products. However, because insect mass rearing technology is relatively new, little is known about the different factors that determine the quality and yield of the production process. Obtaining such knowledge is crucial for the success of insect-based product development. One of the issues that is likely to compromise the success of insect rearing is the outbreak of insect diseases. In particular, viral diseases can be devastating for the productivity and the quality of mass rearing systems. Prevention and management of viral diseases imply the understanding of the different factors that interact in insect mass rearing. This publication provides an overview of the known viruses in insects most commonly reared for food and feed. Nowadays with large-scale sequencing techniques, new viruses are rapidly being discovered. We discuss factors affecting the emergence of viruses in mass rearing systems, along with virus transmission routes. Finally we provide an overview of the wide range of measures available to prevent and manage virus outbreaks in mass rearing systems, ranging from simple sanitation methods to highly sophisticated methods including RNAi and transgenics.
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Affiliation(s)
- Gabriela Maciel-Vergara
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark.
| | - Vera I D Ros
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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19
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Schlaberg R, Chiu CY, Miller S, Procop GW, Weinstock G. Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection. Arch Pathol Lab Med 2017; 141:776-786. [PMID: 28169558 DOI: 10.5858/arpa.2016-0539-ra] [Citation(s) in RCA: 325] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - Metagenomic sequencing can be used for detection of any pathogens using unbiased, shotgun next-generation sequencing (NGS), without the need for sequence-specific amplification. Proof-of-concept has been demonstrated in infectious disease outbreaks of unknown causes and in patients with suspected infections but negative results for conventional tests. Metagenomic NGS tests hold great promise to improve infectious disease diagnostics, especially in immunocompromised and critically ill patients. OBJECTIVE - To discuss challenges and provide example solutions for validating metagenomic pathogen detection tests in clinical laboratories. A summary of current regulatory requirements, largely based on prior guidance for NGS testing in constitutional genetics and oncology, is provided. DATA SOURCES - Examples from 2 separate validation studies are provided for steps from assay design, and validation of wet bench and bioinformatics protocols, to quality control and assurance. CONCLUSIONS - Although laboratory and data analysis workflows are still complex, metagenomic NGS tests for infectious diseases are increasingly being validated in clinical laboratories. Many parallels exist to NGS tests in other fields. Nevertheless, specimen preparation, rapidly evolving data analysis algorithms, and incomplete reference sequence databases are idiosyncratic to the field of microbiology and often overlooked.
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Affiliation(s)
- Robert Schlaberg
- From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock)
| | - Charles Y Chiu
- From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock)
| | - Steve Miller
- From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock)
| | - Gary W Procop
- From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock)
| | - George Weinstock
- From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock)
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- From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock)
| | -
- From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock)
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20
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Moreira ASD, Raabis SM, Graham ME, Dreyfus JM, Sibley SD, Godhardt-Cooper JA, Toohey-Kurth KL, Goldberg TL, Peek SF. Identification by next-generation sequencing of Aichivirus B in a calf with enterocolitis and neurologic signs. J Vet Diagn Invest 2017; 29:208-211. [PMID: 28176615 DOI: 10.1177/1040638716685597] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
An 11-d-old Holstein bull calf was presented to the Veterinary Medical Teaching Hospital at the University of Wisconsin-Madison because of a 4-d history of diarrhea and persistent low-grade fever. Initial diagnosis was enteritis caused by Cryptosporidium and rotavirus. During hospitalization, the calf became stuporous and was only responsive to noxious stimuli, with hypotonia of all 4 limbs, tail, head, and neck. A cerebrospinal fluid analysis revealed xanthochromia, with marked lymphocytic pleocytosis, which was suggestive of viral meningitis and/or encephalitis. Aichivirus B, which belongs to the Kobuvirus genus, was tentatively identified in spinal fluid by next-generation DNA sequencing. This virus can affect a multitude of species, including humans and cattle, and has been isolated from both healthy and diarrheic individuals. However, to date, a possible connection with neurologic disease has not been described, to our knowledge.
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Affiliation(s)
- Ana S D Moreira
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Sarah M Raabis
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Melissa E Graham
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Jennifer M Dreyfus
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Samuel D Sibley
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Jennifer A Godhardt-Cooper
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Kathy L Toohey-Kurth
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Tony L Goldberg
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Simon F Peek
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
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21
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Hjelmsø MH, Hellmér M, Fernandez-Cassi X, Timoneda N, Lukjancenko O, Seidel M, Elsässer D, Aarestrup FM, Löfström C, Bofill-Mas S, Abril JF, Girones R, Schultz AC. Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing. PLoS One 2017; 12:e0170199. [PMID: 28099518 PMCID: PMC5242460 DOI: 10.1371/journal.pone.0170199] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/02/2017] [Indexed: 01/18/2023] Open
Abstract
Viral sewage metagenomics is a novel field of study used for surveillance, epidemiological studies, and evaluation of waste water treatment efficiency. In raw sewage human waste is mixed with household, industrial and drainage water, and virus particles are, therefore, only found in low concentrations. This necessitates a step of sample concentration to allow for sensitive virus detection. Additionally, viruses harbor a large diversity of both surface and genome structures, which makes universal viral genomic extraction difficult. Current studies have tackled these challenges in many different ways employing a wide range of viral concentration and extraction procedures. However, there is limited knowledge of the efficacy and inherent biases associated with these methods in respect to viral sewage metagenomics, hampering the development of this field. By the use of next generation sequencing this study aimed to evaluate the efficiency of four commonly applied viral concentrations techniques (precipitation with polyethylene glycol, organic flocculation with skim milk, monolithic adsorption filtration and glass wool filtration) and extraction methods (Nucleospin RNA XS, QIAamp Viral RNA Mini Kit, NucliSENS® miniMAG®, or PowerViral® Environmental RNA/DNA Isolation Kit) to determine the viriome in a sewage sample. We found a significant influence of concentration and extraction protocols on the detected viriome. The viral richness was largest in samples extracted with QIAamp Viral RNA Mini Kit or PowerViral® Environmental RNA/DNA Isolation Kit. Highest viral specificity were found in samples concentrated by precipitation with polyethylene glycol or extracted with Nucleospin RNA XS. Detection of viral pathogens depended on the method used. These results contribute to the understanding of method associated biases, within the field of viral sewage metagenomics, making evaluation of the current literature easier and helping with the design of future studies.
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Affiliation(s)
- Mathis Hjort Hjelmsø
- Research Group for Genomic Epidemiology, The National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
- * E-mail:
| | - Maria Hellmér
- Division of Microbiology and Production, The National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Xavier Fernandez-Cassi
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology, and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - Natàlia Timoneda
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology, and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
- Institute of Biomedicine of the University of Barcelona, University of Barcelona, Barcelona, Catalonia, Spain
| | - Oksana Lukjancenko
- Research Group for Genomic Epidemiology, The National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Michael Seidel
- Institute of Hydrochemistry, Chair of Analytical Chemistry, Technical University of Munich, Munich, Germany
| | - Dennis Elsässer
- Institute of Hydrochemistry, Chair of Analytical Chemistry, Technical University of Munich, Munich, Germany
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, The National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Charlotta Löfström
- Division of Microbiology and Production, The National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Sílvia Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology, and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - Josep F. Abril
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology, and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
- Institute of Biomedicine of the University of Barcelona, University of Barcelona, Barcelona, Catalonia, Spain
| | - Rosina Girones
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology, and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - Anna Charlotte Schultz
- Division of Microbiology and Production, The National Food Institute, Technical University of Denmark, Søborg, Denmark
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Complete Genome Sequences of Three African Foot-and-Mouth Disease Viruses from Clinical Samples Isolated in 2009 and 2010. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00326-16. [PMID: 27151795 PMCID: PMC4859177 DOI: 10.1128/genomea.00326-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The complete genome sequences of three foot-and-mouth disease viruses (one virus of each serotype SAT1, SAT2 and O) were directly sequenced from RNA extracted from clinical bovine samples, demonstrating the feasibility of full-genome sequencing from strong positive samples taken from symptomatic animals.
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23
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Schlottau K, Schulze C, Bilk S, Hanke D, Höper D, Beer M, Hoffmann B. Detection of a Novel Bovine Astrovirus in a Cow with Encephalitis. Transbound Emerg Dis 2016; 63:253-9. [PMID: 26948516 DOI: 10.1111/tbed.12493] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Indexed: 02/06/2023]
Abstract
Encephalitis can be caused by several infectious agents, including bacteria, fungi, parasites and viruses. In many cases, the causative agent cannot be identified, because the pathogens are unknown or detection methods are not routinely available. In our case, a 15-month-old cow developed central nervous disorders and died within 6 days after the onset of clinical signs. The histopathology revealed an acute encephalitis, predominantly in the brain stem, and a ganglionitis of the trigeminal ganglion with massive neuronal necroses in both the brain and the ganglion. However, a relevant panel of bacterial and viral infections of cattle could be routinely excluded. Therefore, a brain sample from the cow was analysed using a metagenomics approach with next-generation sequencing. A novel bovine astrovirus (BoAstV-BH89/14) could be identified using the analysis pipeline RIEMS, and the finding could be confirmed with a specific BoAstV RT-qPCR. The genome of the bovine astrovirus (BoAstV), belonging to the family Astroviridae in the genus Mamastrovirus, has a length of 6478 bp. Sequence identities between 71% to a sheep astrovirus and 69% to two recently described bovine astroviruses from the USA and Switzerland were ascertained. The latter were also connected to encephalitis cases in cattle. Like these, the new virus described here was detected in different brain sections using the specific BoAstV RT-qPCR and fluorescent in situ hybridization. In conclusion, while astroviruses so far were mainly found in relation to gastroenteritis in animals and humans, recently detected astrovirus infections were also related to encephalitis.
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Affiliation(s)
- K Schlottau
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - C Schulze
- Berlin-Brandenburg State Laboratory, Frankfurt (Oder), Germany
| | - S Bilk
- Berlin-Brandenburg State Laboratory, Frankfurt (Oder), Germany
| | - D Hanke
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - D Höper
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - M Beer
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - B Hoffmann
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
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24
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Complete Genome Sequence of Bovine Polyomavirus Type 1 from Aborted Cattle, Isolated in Belgium in 2014. GENOME ANNOUNCEMENTS 2016; 4:4/2/e01646-15. [PMID: 26941154 PMCID: PMC4777765 DOI: 10.1128/genomea.01646-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The complete and fully annotated genome sequence of a bovine polyomavirus type 1 (BPyV/BEL/1/2014) from aborted cattle was assembled from a metagenomics data set. The 4,697-bp circular dsDNA genome contains 6 protein-coding genes. Bovine polyomavirus is unlikely to be causally related to the abortion cases.
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25
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Friis-Nielsen J, Kjartansdóttir KR, Mollerup S, Asplund M, Mourier T, Jensen RH, Hansen TA, Rey-Iglesia A, Richter SR, Nielsen IB, Alquezar-Planas DE, Olsen PVS, Vinner L, Fridholm H, Nielsen LP, Willerslev E, Sicheritz-Pontén T, Lund O, Hansen AJ, Izarzugaza JMG, Brunak S. Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers. Viruses 2016; 8:E53. [PMID: 26907326 PMCID: PMC4776208 DOI: 10.3390/v8020053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/29/2016] [Accepted: 02/05/2016] [Indexed: 12/17/2022] Open
Abstract
Virus discovery from high throughput sequencing data often follows a bottom-up approach where taxonomic annotation takes place prior to association to disease. Albeit effective in some cases, the approach fails to detect novel pathogens and remote variants not present in reference databases. We have developed a species independent pipeline that utilises sequence clustering for the identification of nucleotide sequences that co-occur across multiple sequencing data instances. We applied the workflow to 686 sequencing libraries from 252 cancer samples of different cancer and tissue types, 32 non-template controls, and 24 test samples. Recurrent sequences were statistically associated to biological, methodological or technical features with the aim to identify novel pathogens or plausible contaminants that may associate to a particular kit or method. We provide examples of identified inhabitants of the healthy tissue flora as well as experimental contaminants. Unmapped sequences that co-occur with high statistical significance potentially represent the unknown sequence space where novel pathogens can be identified.
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Affiliation(s)
- Jens Friis-Nielsen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Kristín Rós Kjartansdóttir
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Sarah Mollerup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Maria Asplund
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Randi Holm Jensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Thomas Arn Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Alba Rey-Iglesia
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Stine Raith Richter
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Ida Broman Nielsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - David E Alquezar-Planas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Pernille V S Olsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Helena Fridholm
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Lars Peter Nielsen
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, DK-2300 Copenhagen S, Denmark.
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Thomas Sicheritz-Pontén
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Ole Lund
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Anders Johannes Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Jose M G Izarzugaza
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Søren Brunak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
- NNF Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark.
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26
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Rosseel T, Ozhelvaci O, Freimanis G, Van Borm S. Evaluation of convenient pretreatment protocols for RNA virus metagenomics in serum and tissue samples. J Virol Methods 2015; 222:72-80. [PMID: 26025457 DOI: 10.1016/j.jviromet.2015.05.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 04/28/2015] [Accepted: 05/22/2015] [Indexed: 12/27/2022]
Abstract
Viral metagenomic approaches are increasingly being used for viral discovery. Various strategies are applied to enrich viral sequences, but there is often a lack of knowledge about their effective influence on the viral discovery sensitivity. We evaluate some convenient and widely used approaches for RNA virus discovery in clinical samples in order to reveal their sensitivity and potential bias introduced by the enrichment or amplifications steps. An RNA virus was artificially spiked at a fixed titer in serum and lung tissue, respectively, low and high nucleic acid content matrices. For serum, a simple DNase treatment on the RNA extract gave the maximum gain in proportion of viral sequences (83×), and a subsequent ribosomal RNA removal nearly doubled once more the proportion of viral sequences. For lung tissue, a ribosomal RNA depletion step on the RNA extract had the biggest gain in proportion of viral sequences (32×). We show also that direct sequencing of cDNA is recommended above an extra random PCR amplification step, and a that the virion enrichment strategy (filtration and nuclease treatment) has a beneficial effect for sequencing-based virus discovery. Our findings provide sample-dependent guidelines for targeted virus discovery strategies.
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Affiliation(s)
- Toon Rosseel
- Veterinary and Agrochemical Research Centre CODA/CERVA, Groeselenberg 99, Brussels Belgium
| | - Orkun Ozhelvaci
- Veterinary and Agrochemical Research Centre CODA/CERVA, Groeselenberg 99, Brussels Belgium
| | - Graham Freimanis
- The Pirbright Institute, Ash Rd, Woking GU24 0NF, United Kingdom
| | - Steven Van Borm
- Veterinary and Agrochemical Research Centre CODA/CERVA, Groeselenberg 99, Brussels Belgium.
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27
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Wang J, Moore NE, Murray ZL, McInnes K, White DJ, Tompkins DM, Hall RJ. Discovery of novel virus sequences in an isolated and threatened bat species, the New Zealand lesser short-tailed bat (Mystacina tuberculata). J Gen Virol 2015; 96:2442-2452. [PMID: 25900137 PMCID: PMC4681071 DOI: 10.1099/vir.0.000158] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Bats harbour a diverse array of viruses, including significant human pathogens. Extensive metagenomic studies of material from bats, in particular guano, have revealed a large number of novel or divergent viral taxa that were previously unknown. New Zealand has only two extant indigenous terrestrial mammals, which are both bats, Mystacina tuberculata (the lesser short-tailed bat) and Chalinolobus tuberculatus (the long-tailed bat). Until the human introduction of exotic mammals, these species had been isolated from all other terrestrial mammals for over 1 million years (potentially over 16 million years for M. tuberculata). Four bat guano samples were collected from M. tuberculata roosts on the isolated offshore island of Whenua hou (Codfish Island) in New Zealand. Metagenomic analysis revealed that this species still hosts a plethora of divergent viruses. Whilst the majority of viruses detected were likely to be of dietary origin, some putative vertebrate virus sequences were identified. Papillomavirus, polyomavirus, calicivirus and hepevirus were found in the metagenomic data and subsequently confirmed using independent PCR assays and sequencing. The new hepevirus and calicivirus sequences may represent new genera within these viral families. Our findings may provide an insight into the origins of viral families, given their detection in an isolated host species.
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Affiliation(s)
- Jing Wang
- Institute of Environmental Science & Research (ESR), at the National Centre for Biosecurity & Infectious Disease, PO Box 40158, Upper Hutt 5140, New Zealand
| | - Nicole E Moore
- Institute of Environmental Science & Research (ESR), at the National Centre for Biosecurity & Infectious Disease, PO Box 40158, Upper Hutt 5140, New Zealand
| | - Zak L Murray
- Institute of Environmental Science & Research (ESR), at the National Centre for Biosecurity & Infectious Disease, PO Box 40158, Upper Hutt 5140, New Zealand
| | - Kate McInnes
- Department of Conservation, , 18-32 Manners Street, PO Box 6011, Wellington, New Zealand
| | - Daniel J White
- Landcare Research, Private Bag 1930, Dunedin, New Zealand
| | | | - Richard J Hall
- Institute of Environmental Science & Research (ESR), at the National Centre for Biosecurity & Infectious Disease, PO Box 40158, Upper Hutt 5140, New Zealand
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28
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Carrillo-Tripp J, Bonning BC, Miller WA. Challenges associated with research on RNA viruses of insects. CURRENT OPINION IN INSECT SCIENCE 2015; 8:62-68. [PMID: 32846681 DOI: 10.1016/j.cois.2014.11.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 11/14/2014] [Indexed: 06/11/2023]
Abstract
Dicistroviridae and Iflaviridae (part of the group formerly identified as picorna-like viruses) are rapidly growing families within the order Picornavirales. Work on these emerging groups of arthropod viruses offers a unique and exciting opportunity for virologist, but this task comes with particular challenges. The lack of cell culture systems and infectious clones has imposed limitations on the advancement of study of these viruses. Here we discuss the goals and challenges regarding the establishment of controlled systems as well as some issues associated with insect RNA virology at the organismal level. These concerns apply to RNA viruses affecting other organisms for which basic research tools are limited. A list of pitfalls associated with RNA virus research along with recommendations is provided.
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Affiliation(s)
- Jimena Carrillo-Tripp
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, United States.
| | - Bryony C Bonning
- Department of Entomology, Iowa State University, Ames, IA 50011, United States
| | - W Allen Miller
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, United States
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29
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Hall RJ, Draper JL, Nielsen FGG, Dutilh BE. Beyond research: a primer for considerations on using viral metagenomics in the field and clinic. Front Microbiol 2015; 6:224. [PMID: 25859244 PMCID: PMC4373370 DOI: 10.3389/fmicb.2015.00224] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/06/2015] [Indexed: 11/23/2022] Open
Abstract
Powered by recent advances in next-generation sequencing technologies, metagenomics has already unveiled vast microbial biodiversity in a range of environments, and is increasingly being applied in clinics for difficult-to-diagnose cases. It can be tempting to suggest that metagenomics could be used as a “universal test” for all pathogens without the need to conduct lengthy serial testing using specific assays. While this is an exciting prospect, there are issues that need to be addressed before metagenomic methods can be applied with rigor as a diagnostic tool, including the potential for incidental findings, unforeseen consequences for trade and regulatory authorities, privacy and cultural issues, data sharing, and appropriate reporting of results to end-users. These issues will require consideration and discussion across a range of disciplines, with inclusion of scientists, ethicists, clinicians, diagnosticians, health practitioners, and ultimately the public. Here, we provide a primer for consideration on some of these issues.
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Affiliation(s)
- Richard J Hall
- Institute of Environmental Science and Research, National Centre for Biosecurity and Infectious Disease, Upper Hutt New Zealand
| | - Jenny L Draper
- Ministry for Primary Industries Animal Health Laboratory, National Centre for Biosecurity and Infectious Disease, Upper Hutt New Zealand
| | | | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht Netherlands ; Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen Netherlands ; Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro Brazil
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30
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Houldcroft CJ, Breuer J. Tales from the crypt and coral reef: the successes and challenges of identifying new herpesviruses using metagenomics. Front Microbiol 2015; 6:188. [PMID: 25821447 PMCID: PMC4358218 DOI: 10.3389/fmicb.2015.00188] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/20/2015] [Indexed: 12/14/2022] Open
Abstract
Herpesviruses are ubiquitous double-stranded DNA viruses infecting many animals, with the capacity to cause disease in both immunocompetent and immunocompromised hosts. Different herpesviruses have different cell tropisms, and have been detected in a diverse range of tissues and sample types. Metagenomics—encompassing viromics—analyses the nucleic acid of a tissue or other sample in an unbiased manner, making few or no prior assumptions about which viruses may be present in a sample. This approach has successfully discovered a number of novel herpesviruses. Furthermore, metagenomic analysis can identify herpesviruses with high degrees of sequence divergence from known herpesviruses and does not rely upon culturing large quantities of viral material. Metagenomics has had success in two areas of herpesvirus sequencing: firstly, the discovery of novel exogenous and endogenous herpesviruses in primates, bats and cnidarians; and secondly, in characterizing large areas of the genomes of herpesviruses previously only known from small fragments, revealing unexpected diversity. This review will discuss the successes and challenges of using metagenomics to identify novel herpesviruses, and future directions within the field.
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Affiliation(s)
- Charlotte J Houldcroft
- Infection, Inflammation and Rheumatology, Institute of Child Health, University College London , London, UK
| | - Judith Breuer
- Infection, Inflammation and Rheumatology, Institute of Child Health, University College London , London, UK ; Division of Infection and Immunity, University College London , London, UK
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31
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Sauvage V, Livartowski A, Boizeau L, Servant-Delmas A, Lionnet F, Lefrere JJ, Laperche S. No Evidence of Marseillevirus-like Virus Presence in Blood Donors and Recipients of Multiple Blood Transfusions. J Infect Dis 2014; 210:2017-8. [DOI: 10.1093/infdis/jiu443] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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