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Zhao Y, Huang F, Wang W, Gao R, Fan L, Wang A, Gao SH. Application of high-throughput sequencing technologies and analytical tools for pathogen detection in urban water systems: Progress and future perspectives. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165867. [PMID: 37516185 DOI: 10.1016/j.scitotenv.2023.165867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 07/31/2023]
Abstract
The ubiquitous presence of pathogenic microorganisms, such as viruses, bacteria, fungi, and protozoa, in urban water systems poses a significant risk to public health. The emergence of infectious waterborne diseases mediated by urban water systems has become one of the leading global causes of mortality. However, the detection and monitoring of these pathogenic microorganisms have been limited by the complexity and diversity in the environmental samples. Conventional methods were restricted by long assay time, high benchmarks of identification, and narrow application sceneries. Novel technologies, such as high-throughput sequencing technologies, enable potentially full-spectrum detection of trace pathogenic microorganisms in complex environmental matrices. This review discusses the current state of high-throughput sequencing technologies for identifying pathogenic microorganisms in urban water systems with a concise summary. Furthermore, future perspectives in pathogen research emphasize the need for detection methods with high accuracy and sensitivity, the establishment of precise detection standards and procedures, and the significance of bioinformatics software and platforms. We have compiled a list of pathogens analysis software/platforms/databases that boast robust engines and high accuracy for preference. We highlight the significance of analyses by combining targeted and non-targeted sequencing technologies, short and long reads technologies, sequencing technologies, and bioinformatic tools in pursuing upgraded biosafety in urban water systems.
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Affiliation(s)
- Yanmei Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Fang Huang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Wenxiu Wang
- Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China.
| | - Rui Gao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Lu Fan
- Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Aijie Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Shu-Hong Gao
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China.
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VPipe: an Automated Bioinformatics Platform for Assembly and Management of Viral Next-Generation Sequencing Data. Microbiol Spectr 2022; 10:e0256421. [PMID: 35234489 PMCID: PMC8941893 DOI: 10.1128/spectrum.02564-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Next-generation sequencing (NGS) is a powerful tool for detecting and investigating viral pathogens; however, analysis and management of the enormous amounts of data generated from these technologies remains a challenge. Here, we present VPipe (the Viral NGS Analysis Pipeline and Data Management System), an automated bioinformatics pipeline optimized for whole-genome assembly of viral sequences and identification of diverse species. VPipe automates the data quality control, assembly, and contig identification steps typically performed when analyzing NGS data. Users access the pipeline through a secure web-based portal, which provides an easy-to-use interface with advanced search capabilities for reviewing results. In addition, VPipe provides a centralized system for storing and analyzing NGS data, eliminating common bottlenecks in bioinformatics analyses for public health laboratories with limited on-site computational infrastructure. The performance of VPipe was validated through the analysis of publicly available NGS data sets for viral pathogens, generating high-quality assemblies for 12 data sets. VPipe also generated assemblies with greater contiguity than similar pipelines for 41 human respiratory syncytial virus isolates and 23 SARS-CoV-2 specimens. IMPORTANCE Computational infrastructure and bioinformatics analysis are bottlenecks in the application of NGS to viral pathogens. As of September 2021, VPipe has been used by the U.S. Centers for Disease Control and Prevention (CDC) and 12 state public health laboratories to characterize >17,500 and 1,500 clinical specimens and isolates, respectively. VPipe automates genome assembly for a wide range of viruses, including high-consequence pathogens such as SARS-CoV-2. Such automated functionality expedites public health responses to viral outbreaks and pathogen surveillance.
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3
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Bajrai LH, Sohrab SS, Alandijany TA, Mobashir M, Reyaz M, Kamal MA, Firoz A, Parveen S, Azhar EI. Gene Expression Profiling of Early Acute Febrile Stage of Dengue Infection and Its Comparative Analysis With Streptococcus pneumoniae Infection. Front Cell Infect Microbiol 2021; 11:707905. [PMID: 34778101 PMCID: PMC8581568 DOI: 10.3389/fcimb.2021.707905] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 09/30/2021] [Indexed: 02/05/2023] Open
Abstract
Infectious diseases are the disorders caused by organisms such as bacteria, viruses, fungi, or parasites. Although many of them are permentantly hazardous, a number of them live in and on our bodies and they are normally harmless or even helpful. Under certain circumstances, some organisms may cause diseases and these infectious diseases may be passed directly from person to person or via intermediate vectors including insects and other animals. Dengue virus and Streptococcus pneumoniae are the critical and common sources of infectious diseases. So, it is critical to understand the gene expression profiling and their inferred functions in comparison to the normal and virus infected conditions. Here, we have analyzed the gene expression profiling for dengue hemorrhagic fever, dengue fever, and normal human dataset. Similar to it, streptococcus pneumoniae infectious data were analyzed and both the outcomes were compared. Our study leads to the conclusion that the dengue hemorrhagic fever arises in result to potential change in the gene expression pattern, and the inferred functions obviously belong to the immune system, but also there are some additional potential pathways which are critical signaling pathways. In the case of pneumoniae infection, 19 pathways were enriched, almost all these pathways are associated with the immune system and 17 of the enriched pathways were common with dengue infection except platelet activation and antigen processing and presentation. In terms of the comparative study between dengue virus and Streptococcus pneumoniae infection, we conclude that cell adhesion molecules (CAMs), MAPK signaling pathway, natural killer cell mediated cytotoxicity, regulation of actin cytoskeleton, and cytokine-cytokine receptor interaction are commonly enriched in all the three cases of dengue infection and Streptococcus pneumoniae infection, focal adhesion was enriched between classical dengue fever — dengue hemorrhagic fever, dengue hemorrhagic fever—normal samples, and SP, and antigen processing and presentation and Leukocyte transendothelial migration were enriched in classical dengue fever —normal samples, dengue hemorrhagic fever—normal samples, and Streptococcus pneumoniae infection.
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Affiliation(s)
- Leena H Bajrai
- Special Infectious Agents Unit - BSL-3, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia.,Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sayed S Sohrab
- Special Infectious Agents Unit - BSL-3, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Thamir A Alandijany
- Special Infectious Agents Unit - BSL-3, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad Mobashir
- SciLifeLab, Department of Oncology and Pathology Karolinska Institutet, Stockholm, Sweden
| | - Muddassir Reyaz
- Department of Healthcare Management, Jamia Hamdard Hamdard Nagar, New Delhi, India
| | - Mohammad A Kamal
- West China School of Nursing/Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.,King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Enzymoics, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | - Ahmad Firoz
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Shabana Parveen
- Department of Bioscience, Jamia Millia Islamia, New Delhi, India
| | - Esam I Azhar
- Special Infectious Agents Unit - BSL-3, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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4
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Tharakan R, Sawa A. Minireview: Novel Micropeptide Discovery by Proteomics and Deep Sequencing Methods. Front Genet 2021; 12:651485. [PMID: 34025718 PMCID: PMC8136307 DOI: 10.3389/fgene.2021.651485] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
A novel class of small proteins, called micropeptides, has recently been discovered in the genome. These proteins, which have been found to play important roles in many physiological and cellular systems, are shorter than 100 amino acids and were overlooked during previous genome annotations. Discovery and characterization of more micropeptides has been ongoing, often using -omics methods such as proteomics, RNA sequencing, and ribosome profiling. In this review, we survey the recent advances in the micropeptides field and describe the methodological and conceptual challenges facing future micropeptide endeavors.
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Affiliation(s)
- Ravi Tharakan
- National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Akira Sawa
- Departments of Psychiatry, Neuroscience, Biomedical Engineering, and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
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5
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Berg MG, Olivo A, Forberg K, Harris BJ, Yamaguchi J, Shirazi R, Gozlan Y, Sauleda S, Kaptue L, Rodgers MA, Mor O, Cloherty GA. Advanced molecular surveillance approaches for characterization of blood borne hepatitis viruses. PLoS One 2020; 15:e0236046. [PMID: 32678844 PMCID: PMC7367454 DOI: 10.1371/journal.pone.0236046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/26/2020] [Indexed: 12/27/2022] Open
Abstract
Defining genetic diversity of viral infections directly from patient specimens is the ultimate goal of surveillance. Simple tools that can provide full-length sequence information on blood borne viral hepatitis viruses: hepatitis C, hepatitis B and hepatitis D viruses (HCV, HBV and HDV) remain elusive. Here, an unbiased metagenomic next generation sequencing approach (mNGS) was used for molecular characterization of HCV infections (n = 99) from Israel which yielded full-length HCV sequences in 89% of samples, with 7 partial sequences sufficient for classification. HCV genotypes were primarily 1b (68%) and 1a (19%), with minor representation of genotypes 2c (1%) and 3a (8%). HBV/HDV coinfections were characterized by suppressed HBV viral loads, resulting in sparse mNGS coverage. A probe-based enrichment approach (xGen) aiming to increase HBV and HDV coverage was validated on a panel of diverse genotypes, geography and titers. The method extended HBV genome coverage a median 61% (range 8–84%) and provided orders of magnitude boosts in reads and sequence depth for both viruses. When HBV-xGen was applied to Israeli samples, coverage was improved by 28–73% in 4 samples and identified HBV genotype A1, A2, D1 specimens and a dual B/D infection. Abundant HDV reads in mNGS libraries yielded 18/26 (69%) full genomes and 8 partial sequences, with HDV-xGen only providing minimal extension (3–11%) of what were all genotype 1 genomes. Advanced molecular approaches coupled to virus-specific capture probes promise to enhance surveillance of viral infections and aid in monitoring the spread of local subtypes.
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Affiliation(s)
- Michael G. Berg
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, Illinois, United States of America
- * E-mail:
| | - Ana Olivo
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, Illinois, United States of America
| | - Kenn Forberg
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, Illinois, United States of America
| | - Barbara J. Harris
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, Illinois, United States of America
| | - Julie Yamaguchi
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, Illinois, United States of America
| | - Rachel Shirazi
- Central Virology Laboratory, National HIV and Viral Hepatitis Reference Center, Public Health Services, Ministry of Health, Tel-Hashomer, Ramat-Gan, Israel
| | - Yael Gozlan
- Central Virology Laboratory, National HIV and Viral Hepatitis Reference Center, Public Health Services, Ministry of Health, Tel-Hashomer, Ramat-Gan, Israel
| | - Silvia Sauleda
- Transfusion Safety Laboratory, Banc de Sang i Teixits, Servei Català de la Salut, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Mary A. Rodgers
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, Illinois, United States of America
| | - Orna Mor
- Central Virology Laboratory, National HIV and Viral Hepatitis Reference Center, Public Health Services, Ministry of Health, Tel-Hashomer, Ramat-Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Israel
| | - Gavin A. Cloherty
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, Illinois, United States of America
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Kamau E, Oketch JW, de Laurent ZR, Phan MVT, Agoti CN, Nokes DJ, Cotten M. Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia. BMC Genomics 2020; 21:5. [PMID: 31898474 PMCID: PMC6941262 DOI: 10.1186/s12864-019-6400-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 12/15/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Human metapneumovirus (HMPV) is an important cause of acute respiratory illness in young children. Whole genome sequencing enables better identification of transmission events and outbreaks, which is not always possible with sub-genomic sequences. RESULTS We report a 2-reaction amplicon-based next generation sequencing method to determine the complete genome sequences of five HMPV strains, representing three subgroups (A2, B1 and B2), directly from clinical samples. In addition to reporting five novel HMPV genomes from Africa we examined genetic diversity and sequence patterns of publicly available HMPV genomes. We found that the overall nucleotide sequence identity was 71.3 and 80% for HMPV group A and B, respectively, the diversity between HMPV groups was greater at amino acid level for SH and G surface protein genes, and multiple subgroups co-circulated in various countries. Comparison of sequences between HMPV groups revealed variability in G protein length (219 to 241 amino acids) due to changes in the stop codon position. Genome-wide phylogenetic analysis showed congruence with the individual gene sequence sets except for F and M2 genes. CONCLUSION This is the first genomic characterization of HMPV genomes from African patients.
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Affiliation(s)
- Everlyn Kamau
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
| | - John W Oketch
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - My V T Phan
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | | | - D James Nokes
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute, University of Warwick, Coventry, UK
| | - Matthew Cotten
- MRC/UVRI & LSHTM Uganda Research Unit, Entebbe, Uganda
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
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Thierry M, Gladieux P, Fournier E, Tharreau D, Ioos R. A Genomic Approach to Develop a New qPCR Test Enabling Detection of the Pyricularia oryzae Lineage Causing Wheat Blast. PLANT DISEASE 2020; 104:60-70. [PMID: 31647693 DOI: 10.1094/pdis-04-19-0685-re] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Rapid detection is key to managing emerging diseases because it allows their spread around the world to be monitored and limited. The first major wheat blast epidemics were reported in 1985 in the Brazilian state of Paraná. Following this outbreak, the disease quickly spread to neighboring regions and countries and, in 2016, the first report of wheat blast disease outside South America was released. This Asian outbreak was due to the trade of infected South American seed, demonstrating the importance of detection tests in order to avoid importing contaminated biological material into regions free from the pathogen. Genomic analysis has revealed that one particular lineage within the fungal species Pyricularia oryzae is associated with this disease: the Triticum lineage. A comparison of 81 Pyricularia genomes highlighted polymorphisms specific to the Triticum lineage, and this study developed a real-time PCR test targeting one of these polymorphisms. The test's performance was then evaluated in order to measure its analytical specificity, analytical sensitivity, and robustness. The C17 quantitative PCR test detected isolates belonging to the Triticum lineage with high sensitivity, down to 13 plasmid copies or 1 pg of genomic DNA per reaction tube. The blast-based approach developed here to study P. oryzae can be transposed to other emerging diseases.
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Affiliation(s)
- Maud Thierry
- UMR BGPI, Montpellier University, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR BGPI, F-34398 Montpellier, France
- ANSES Plant Health Laboratory, Mycology Unit, Domaine de Pixérécourt, Bâtiment E, F-54220 Malzéville, France
| | - Pierre Gladieux
- UMR BGPI, Montpellier University, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Elisabeth Fournier
- UMR BGPI, Montpellier University, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Didier Tharreau
- UMR BGPI, Montpellier University, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR BGPI, F-34398 Montpellier, France
| | - Renaud Ioos
- ANSES Plant Health Laboratory, Mycology Unit, Domaine de Pixérécourt, Bâtiment E, F-54220 Malzéville, France
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A rapid and label-free platform for virus capture and identification from clinical samples. Proc Natl Acad Sci U S A 2019; 117:895-901. [PMID: 31882450 PMCID: PMC6969489 DOI: 10.1073/pnas.1910113117] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Viruses evolve rapidly and unpredictably, challenging the effectiveness of disease diagnostics. To help control outbreaks and understand their origins, the first step is often isolating viruses from infected samples for characterization. We demonstrate that multiple emerging virus strains can be simultaneously enriched and optically detected in only a few minutes without using any labels. A portable platform that captures viruses by their size, coupled to Raman spectroscopy, resulted in successful virus identification with 90% accuracy in real time directly from clinical samples. Furthermore, this viable enrichment process enables further culturing and characterization by electron microscopy and deep sequencing. This microplatform is an effective disease-monitoring system and broadens virus surveillance by enabling real-time virus identification. Emerging and reemerging viruses are responsible for a number of recent epidemic outbreaks. A crucial step in predicting and controlling outbreaks is the timely and accurate characterization of emerging virus strains. We present a portable microfluidic platform containing carbon nanotube arrays with differential filtration porosity for the rapid enrichment and optical identification of viruses. Different emerging strains (or unknown viruses) can be enriched and identified in real time through a multivirus capture component in conjunction with surface-enhanced Raman spectroscopy. More importantly, after viral capture and detection on a chip, viruses remain viable and get purified in a microdevice that permits subsequent in-depth characterizations by various conventional methods. We validated this platform using different subtypes of avian influenza A viruses and human samples with respiratory infections. This technology successfully enriched rhinovirus, influenza virus, and parainfluenza viruses, and maintained the stoichiometric viral proportions when the samples contained more than one type of virus, thus emulating coinfection. Viral capture and detection took only a few minutes with a 70-fold enrichment enhancement; detection could be achieved with as little as 102 EID50/mL (50% egg infective dose per microliter), with a virus specificity of 90%. After enrichment using the device, we demonstrated by sequencing that the abundance of viral-specific reads significantly increased from 4.1 to 31.8% for parainfluenza and from 0.08 to 0.44% for influenza virus. This enrichment method coupled to Raman virus identification constitutes an innovative system that could be used to quickly track and monitor viral outbreaks in real time.
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9
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Jørgensen PS, Folke C, Carroll SP. Evolution in the Anthropocene: Informing Governance and Policy. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2019. [DOI: 10.1146/annurev-ecolsys-110218-024621] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Anthropocene biosphere constitutes an unprecedented phase in the evolution of life on Earth with one species, humans, exerting extensive control. The increasing intensity of anthropogenic forces in the twenty-first century has widespread implications for attempts to govern both human-dominated ecosystems and the last remaining wild ecosystems. Here, we review how evolutionary biology can inform governance and policies in the Anthropocene, focusing on five governance challenges that span biodiversity, environmental management, food and other biomass production, and human health. The five challenges are: ( a) evolutionary feedbacks, ( b) maintaining resilience, ( c) alleviating constraints, ( d) coevolutionary disruption, and ( e) biotechnology. Strategies for governing these dynamics will themselves have to be coevolutionary, as eco-evolutionary and social dynamics change in response to each other.
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Affiliation(s)
- Peter Søgaard Jørgensen
- Global Economic Dynamics and the Biosphere, Royal Swedish Academy of Sciences, SE104-05 Stockholm, Sweden;,
- Stockholm Resilience Centre, Stockholm University, SE106-91 Stockholm, Sweden
| | - Carl Folke
- Global Economic Dynamics and the Biosphere, Royal Swedish Academy of Sciences, SE104-05 Stockholm, Sweden;,
- Stockholm Resilience Centre, Stockholm University, SE106-91 Stockholm, Sweden
- Beijer Institute of Ecological Economics, Royal Swedish Academy of Sciences, SE104-05 Stockholm, Sweden
| | - Scott P. Carroll
- Institute for Contemporary Evolution, Davis, California 95616, USA
- Department of Entomology and Nematology, University of California, Davis, California 95616, USA
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Bouso JM, Planet PJ. Complete nontuberculous mycobacteria whole genomes using an optimized DNA extraction protocol for long-read sequencing. BMC Genomics 2019; 20:793. [PMID: 31666009 PMCID: PMC6822416 DOI: 10.1186/s12864-019-6134-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/23/2019] [Indexed: 12/15/2022] Open
Abstract
Background Nontuberculous mycobacteria (NTM) are a major cause of pulmonary and systemic disease in at-risk populations. Gaps in knowledge about transmission patterns, evolution, and pathogenicity during infection have prompted a recent surge in genomic NTM research. Increased availability and affordability of whole genome sequencing (WGS) techniques provide new opportunities to sequence and construct complete bacterial genomes faster and at a lower cost. However, extracting large quantities of pure genomic DNA is particularly challenging with NTM due to its slow growth and recalcitrant cell wall. Here we report a DNA extraction protocol that is optimized for long-read WGS of NTM, yielding large quantities of highly pure DNA with no additional clean-up steps. Results Our DNA extraction method was compared to 6 other methods with variations in timing of mechanical disruption and enzymatic digestion of the cell wall, quantity of matrix material, and reagents used in extraction and precipitation. We tested our optimized method on 38 clinical isolates from the M. avium and M. abscessus complexes, which yielded optimal quality and quantity measurements for Oxford Nanopore Technologies sequencing. We also present the efficient completion of circularized M. avium subspecies hominissuis genomes using our extraction technique and the long-read sequencing MinION platform, including the identification of a novel plasmid. Conclusions Our optimized extraction protocol and assembly pipeline was both sufficient and efficient for genome closure. We expect that our finely-tuned extraction method will prove to be a valuable tool in long-read sequencing and completion of mycobacterial genomes going forward. Utilization of comprehensive, long-read based approaches will advance the understanding evolution and pathogenicity of NTM infections.
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Affiliation(s)
- Jennifer M Bouso
- Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Paul J Planet
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.
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11
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Abstract
Although viruses comprise the most abundant genetic material in the biosphere, to date only several thousand virus species have been formally defined. Such a limited perspective on virus diversity has in part arisen because viruses were traditionally considered only as etiologic agents of overt disease in humans or economically important species and were often difficult to identify using cell culture. This view has dramatically changed with the rise of metagenomics, which is transforming virus discovery and revealing a remarkable diversity of viruses sampled from diverse cellular organisms. These newly discovered viruses help fill major gaps in the evolutionary history of viruses, revealing a near continuum of diversity among genera, families, and even orders of RNA viruses. Herein, we review some of the recent advances in our understanding of the RNA virosphere that have stemmed from metagenomics, note future directions, and highlight some of the remaining challenges to this rapidly developing field.
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Affiliation(s)
- Yong-Zhen Zhang
- Shanghai Public Health Clinical Center and School of Public Health, Fudan University, Shanghai 200433, China; .,Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China
| | - Yan-Mei Chen
- Shanghai Public Health Clinical Center and School of Public Health, Fudan University, Shanghai 200433, China; .,Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China
| | - Wen Wang
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China
| | - Xin-Chen Qin
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China
| | - Edward C Holmes
- Shanghai Public Health Clinical Center and School of Public Health, Fudan University, Shanghai 200433, China; .,Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China.,Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia
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12
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Ellwanger JH, Kaminski VDL, Chies JAB. Emerging infectious disease prevention: Where should we invest our resources and efforts? J Infect Public Health 2019; 12:313-316. [PMID: 30928239 DOI: 10.1016/j.jiph.2019.03.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 02/25/2019] [Accepted: 03/11/2019] [Indexed: 02/07/2023] Open
Abstract
Strategies focused on the prevention of emerging infectious disease outbreaks are currently in the spotlight of discussions among researchers committed to infectious disease control. In this mini-review, we provided a brief update on this discussion and characterized the three main targets for investments in emerging infectious disease prevention: animals, human sentinels for spillover events, and the general human population. Furthermore, the pros and cons of each target are highlighted. Despite the particularities of the proposed targets, each of them can fill different gaps in the surveillance of infectious diseases. When all three targets are focused on together, they create a powerful strategy of emerging infectious disease prevention.
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Affiliation(s)
- Joel H Ellwanger
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Valéria de Lima Kaminski
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - José A B Chies
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil.
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Abstract
Viruses, which are the most abundant biological entities on the planet, have been regarded as the "dark matter" of biology in the sense that despite their ubiquity and frequent presence in large numbers, their detection and analysis are not always straightforward. The majority of them are very small (falling under the limit of 0.5 μm), and collectively, they are extraordinarily diverse. In fact, the majority of the genetic diversity on the planet is found in the so-called virosphere, or the world of viruses. Furthermore, the most frequent viral agents of disease in humans display an RNA genome, and frequently evolve very fast, due to the fact that most of their polymerases are devoid of proofreading activity. Therefore, their detection, genetic characterization, and epidemiological surveillance are rather challenging. This review (part of the Curated Collection on Advances in Molecular Epidemiology of Infectious Diseases) describes many of the methods that, throughout the last few decades, have been used for viral detection and analysis. Despite the challenge of having to deal with high genetic diversity, the majority of these methods still depend on the amplification of viral genomic sequences, using sequence-specific or sequence-independent approaches, exploring thermal profiles or a single nucleic acid amplification temperature. Furthermore, viral populations, and especially those with RNA genomes, are not usually genetically uniform but encompass swarms of genetically related, though distinct, viral genomes known as viral quasispecies. Therefore, sequence analysis of viral amplicons needs to take this fact into consideration, as it constitutes a potential analytic problem. Possible technical approaches to deal with it are also described here. *This article is part of a curated collection.
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Dias M, Pattabiraman C, Siddappa S, Gowda M, Shet A, Smith D, Muehlemann B, Tamma K, Solomon T, Jones T, Krishna S. Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum. Wellcome Open Res 2019; 3:44. [PMID: 30167467 PMCID: PMC6085601 DOI: 10.12688/wellcomeopenres.14438.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2019] [Indexed: 12/02/2022] Open
Abstract
Background: Mosquito-borne flaviviruses, such as dengue and Japanese encephalitis virus (JEV), cause life-threatening diseases, particularly in the tropics. Methods: Here we performed unbiased metagenomic sequencing of RNA extracted from the serum of four patients and the plasma of one patient, all hospitalized at a tertiary care centre in South India with severe or prolonged febrile illness, together with the serum from one healthy control, in 2014. Results: We identified and assembled a complete dengue virus type 3 sequence from a case of severe dengue fever. We also identified a small number of JEV sequences in the serum of two adults with febrile illness, including one with severe dengue. Phylogenetic analysis revealed that the dengue sequence belonged to genotype III. It has an estimated divergence time of 13.86 years from the most highly related Indian strains. In total, 11 amino acid substitutions were predicted for this strain in the antigenic envelope protein, when compared to the parent strain used for development of the first commercial dengue vaccine. Conclusions: We demonstrate that both genome assembly and detection of a low number of viral sequences are possible through the unbiased sequencing of clinical material. These methods may help ascertain causal agents for febrile illnesses with no known cause.
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Affiliation(s)
- Mary Dias
- St. John's Medical College and Hospital, Bangalore, 560034, India
| | - Chitra Pattabiraman
- National Institute of Mental Health and Neurosciences, India, Bangalore, 560029, India
| | - Shilpa Siddappa
- Centre for Cellular and Molecular Platforms, Bangalore, 560065, India
| | - Malali Gowda
- Trans-Disciplinary University, Foundation for Revitalization of Local Health Traditions, Bangalore, 560064, India
| | - Anita Shet
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, 21205, USA
| | - Derek Smith
- Center for Pathogen Evolution, Department of
Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
- World Health Organization
Collaborating Center for Modeling, Evolution, and Control of Emerging Infectious Diseases, Cambridge, CB2 3EJ, UK
| | - Barbara Muehlemann
- Center for Pathogen Evolution, Department of
Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
- World Health Organization
Collaborating Center for Modeling, Evolution, and Control of Emerging Infectious Diseases, Cambridge, CB2 3EJ, UK
| | | | - Tom Solomon
- Institute of Infection and Global Health, and National Institute for Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, L69 7BE, UK
| | - Terry Jones
- Center for Pathogen Evolution, Department of
Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
- World Health Organization
Collaborating Center for Modeling, Evolution, and Control of Emerging Infectious Diseases, Cambridge, CB2 3EJ, UK
| | - Sudhir Krishna
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560065, India
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15
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Abstract
RNA viruses are diverse, abundant, and rapidly evolving. Genetic data have been generated from virus populations since the late 1970s and used to understand their evolution, emergence, and spread, culminating in the generation and analysis of many thousands of viral genome sequences. Despite this wealth of data, evolutionary genetics has played a surprisingly small role in our understanding of virus evolution. Instead, studies of RNA virus evolution have been dominated by two very different perspectives, the experimental and the comparative, that have largely been conducted independently and sometimes antagonistically. Here, we review the insights that these two approaches have provided over the last 40 years. We show that experimental approaches using in vitro and in vivo laboratory models are largely focused on short-term intrahost evolutionary mechanisms, and may not always be relevant to natural systems. In contrast, the comparative approach relies on the phylogenetic analysis of natural virus populations, usually considering data collected over multiple cycles of virus-host transmission, but is divorced from the causative evolutionary processes. To truly understand RNA virus evolution it is necessary to meld experimental and comparative approaches within a single evolutionary genetic framework, and to link viral evolution at the intrahost scale with that which occurs over both epidemiological and geological timescales. We suggest that the impetus for this new synthesis may come from methodological advances in next-generation sequencing and metagenomics.
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Affiliation(s)
- Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, New South Wales 2006, Australia
- Charles Perkins Centre, The University of Sydney, New South Wales 2006, Australia
- School of Life and Environmental Sciences, The University of Sydney, New South Wales 2006, Australia
- Sydney Medical School, The University of Sydney, New South Wales 2006, Australia
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Abstract
How virulence evolves after a virus jumps to a new host species is central to disease emergence. Our current understanding of virulence evolution is based on insights drawn from two perspectives that have developed largely independently: long-standing evolutionary theory based on limited real data examples that often lack a genomic basis, and experimental studies of virulence-determining mutations using cell culture or animal models. A more comprehensive understanding of virulence mutations and their evolution can be achieved by bridging the gap between these two research pathways through the phylogenomic analysis of virus genome sequence data as a guide to experimental study.
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Affiliation(s)
- Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia.
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17
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Ellwanger JH, Zambra FMB, Guimarães RL, Chies JAB. MicroRNA-Related Polymorphisms in Infectious Diseases-Tiny Changes With a Huge Impact on Viral Infections and Potential Clinical Applications. Front Immunol 2018; 9:1316. [PMID: 29963045 PMCID: PMC6010531 DOI: 10.3389/fimmu.2018.01316] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/28/2018] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are single-stranded sequences of non-coding RNA with approximately 22 nucleotides that act posttranscriptionally on gene expression. miRNAs are important gene regulators in physiological contexts, but they also impact the pathogenesis of various diseases. The role of miRNAs in viral infections has been explored by different authors in both population-based as well as in functional studies. However, the effect of miRNA polymorphisms on the susceptibility to viral infections and on the clinical course of these diseases is still an emerging topic. Thus, this review will compile and organize the findings described in studies that evaluated the effects of genetic variations on miRNA genes and on their binding sites, in the context of human viral diseases. In addition to discussing the basic aspects of miRNAs biology, we will cover the studies that investigated miRNA polymorphisms in infections caused by hepatitis B virus, hepatitis C virus, human immunodeficiency virus, Epstein–Barr virus, and human papillomavirus. Finally, emerging topics concerning the importance of miRNA genetic variants will be presented, focusing on the context of viral infectious diseases.
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Affiliation(s)
- Joel Henrique Ellwanger
- Laboratório de Imunobiologia e Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Francis Maria Báo Zambra
- Laboratório de Imunobiologia e Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Rafael Lima Guimarães
- Departamento de Genética, Universidade Federal do Pernambuco (UFPE), Recife, Brazil.,Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco (UFPE), Recife, Brazil
| | - José Artur Bogo Chies
- Laboratório de Imunobiologia e Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
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18
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Dias M, Pattabiraman C, Siddappa S, Gowda M, Shet A, Smith D, Muehlemann B, Tamma K, Solomon T, Jones T, Krishna S. Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum. Wellcome Open Res 2018; 3:44. [PMID: 30167467 PMCID: PMC6085601 DOI: 10.12688/wellcomeopenres.14438.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2018] [Indexed: 08/17/2023] Open
Abstract
Background: Mosquito-borne flaviviruses, such as dengue and Japanese encephalitis virus (JEV), cause life-threatening diseases, particularly in the tropics. Methods: Here we performed unbiased metagenomic sequencing of RNA extracted from the serum of four patients and the plasma of one patient, all hospitalized at a tertiary care centre in South India with severe or prolonged febrile illness, together with the serum from one healthy control, in 2014. Results: We identified and assembled a complete dengue virus type 3 sequence from a case of severe dengue fever. We also identified a small number of JEV sequences in the serum of two adults with febrile illness, including one with severe dengue. Phylogenetic analysis revealed that the dengue sequence belonged to genotype III. It has an estimated divergence time of 13.86 years from the most highly related Indian strains. In total, 11 amino acid substitutions were predicted for this strain in the antigenic envelope protein, when compared to the parent strain used for development of the first commercial dengue vaccine. Conclusions: We demonstrate that both genome assembly and detection of a low number of viral sequences are possible through the unbiased sequencing of clinical material. These methods may help ascertain causal agents for febrile illnesses with no known cause.
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Affiliation(s)
- Mary Dias
- St. John's Medical College and Hospital, Bangalore, 560034, India
| | - Chitra Pattabiraman
- National Institute of Mental Health and Neurosciences, India, Bangalore, 560029, India
| | - Shilpa Siddappa
- Centre for Cellular and Molecular Platforms, Bangalore, 560065, India
| | - Malali Gowda
- Trans-Disciplinary University, Foundation for Revitalization of Local Health Traditions, Bangalore, 560064, India
| | - Anita Shet
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, 21205, USA
| | - Derek Smith
- Center for Pathogen Evolution, Department of
Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
- World Health Organization
Collaborating Center for Modeling, Evolution, and Control of Emerging Infectious Diseases, Cambridge, CB2 3EJ, UK
| | - Barbara Muehlemann
- Center for Pathogen Evolution, Department of
Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
- World Health Organization
Collaborating Center for Modeling, Evolution, and Control of Emerging Infectious Diseases, Cambridge, CB2 3EJ, UK
| | | | - Tom Solomon
- Institute of Infection and Global Health, and National Institute for Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, L69 7BE, UK
| | - Terry Jones
- Center for Pathogen Evolution, Department of
Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
- World Health Organization
Collaborating Center for Modeling, Evolution, and Control of Emerging Infectious Diseases, Cambridge, CB2 3EJ, UK
| | - Sudhir Krishna
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560065, India
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19
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Feau N, Beauseigle S, Bergeron MJ, Bilodeau GJ, Birol I, Cervantes-Arango S, Dhillon B, Dale AL, Herath P, Jones SJ, Lamarche J, Ojeda DI, Sakalidis ML, Taylor G, Tsui CK, Uzunovic A, Yueh H, Tanguay P, Hamelin RC. Genome-Enhanced Detection and Identification (GEDI) of plant pathogens. PeerJ 2018; 6:e4392. [PMID: 29492338 PMCID: PMC5825881 DOI: 10.7717/peerj.4392] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/29/2018] [Indexed: 12/17/2022] Open
Abstract
Plant diseases caused by fungi and Oomycetes represent worldwide threats to crops and forest ecosystems. Effective prevention and appropriate management of emerging diseases rely on rapid detection and identification of the causal pathogens. The increase in genomic resources makes it possible to generate novel genome-enhanced DNA detection assays that can exploit whole genomes to discover candidate genes for pathogen detection. A pipeline was developed to identify genome regions that discriminate taxa or groups of taxa and can be converted into PCR assays. The modular pipeline is comprised of four components: (1) selection and genome sequencing of phylogenetically related taxa, (2) identification of clusters of orthologous genes, (3) elimination of false positives by filtering, and (4) assay design. This pipeline was applied to some of the most important plant pathogens across three broad taxonomic groups: Phytophthoras (Stramenopiles, Oomycota), Dothideomycetes (Fungi, Ascomycota) and Pucciniales (Fungi, Basidiomycota). Comparison of 73 fungal and Oomycete genomes led the discovery of 5,939 gene clusters that were unique to the targeted taxa and an additional 535 that were common at higher taxonomic levels. Approximately 28% of the 299 tested were converted into qPCR assays that met our set of specificity criteria. This work demonstrates that a genome-wide approach can efficiently identify multiple taxon-specific genome regions that can be converted into highly specific PCR assays. The possibility to easily obtain multiple alternative regions to design highly specific qPCR assays should be of great help in tackling challenging cases for which higher taxon-resolution is needed.
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Affiliation(s)
- Nicolas Feau
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | | | | | | | - Inanc Birol
- BC Cancer agency, Genome Sciences Centre, Vancouver, BC, Canada
| | - Sandra Cervantes-Arango
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - Braham Dhillon
- Department of Plant Pathology, University of Arkansas at Fayetteville, Fayetteville, AR, United States of America
| | - Angela L. Dale
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
- FPInnovations, Vancouver, BC, Canada
| | - Padmini Herath
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - Steven J.M. Jones
- BC Cancer agency, Genome Sciences Centre, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Josyanne Lamarche
- Canadian Forest Service, Natural Resources Canada, Quebec city, Quebec, Canada
| | - Dario I. Ojeda
- Department of Biology Unit of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Monique L. Sakalidis
- Department of Plant, Soil & Microbial Sciences and Department of Forestry, Michigan State University, East Lansing, MI, United States of America
| | - Greg Taylor
- BC Cancer agency, Genome Sciences Centre, Vancouver, BC, Canada
| | - Clement K.M. Tsui
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - Hesther Yueh
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - Philippe Tanguay
- Canadian Forest Service, Natural Resources Canada, Quebec city, Quebec, Canada
| | - Richard C. Hamelin
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
- Foresterie et géomatique, Institut de Biologie Intégrative des Systèmes, Laval University, Quebec city, Quebec, Canada
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20
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Shi M, Zhang YZ, Holmes EC. Meta-transcriptomics and the evolutionary biology of RNA viruses. Virus Res 2017; 243:83-90. [PMID: 29111455 PMCID: PMC7127328 DOI: 10.1016/j.virusres.2017.10.016] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/19/2017] [Accepted: 10/20/2017] [Indexed: 12/20/2022]
Abstract
Meta-transcriptomics (bulk RNA-Seq) is a powerful new way to characterise viromes. Meta-transcriptomic data are changing our understanding of virus evolution. Invertebrates harbor an enormous phylogenetic and genomic diversity of RNA viruses. Present sampling schemes have only revealed a miniscule fraction of the virosphere. The new wealth of virus genomic data presents a major challenge to classification.
Metagenomics is transforming the study of virus evolution, allowing the full assemblage of virus genomes within a host sample to be determined rapidly and cheaply. The genomic analysis of complete transcriptomes, so-called meta-transcriptomics, is providing a particularly rich source of data on the global diversity of RNA viruses and their evolutionary history. Herein we review some of the insights that meta-transcriptomics has provided on the fundamental patterns and processes of virus evolution, with a focus on the recent discovery of a multitude of novel invertebrate viruses. In particular, meta-transcriptomics shows that the RNA virus world is more fluid than previously realized, with relatively frequent changes in genome length and structure. As well as having a transformative impact on studies of virus evolution, meta-transcriptomics presents major new challenges for virus classification, with the greater sampling of host taxa now filling many of the gaps on virus phylogenies that were previously used to define taxonomic groups. Given that most viruses in the future will likely be characterized using metagenomics approaches, and that we have evidently only sampled a tiny fraction of the total virosphere, we suggest that proposals for virus classification pay careful attention to the wonders unearthed in this new age of virus discovery.
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Affiliation(s)
- Mang Shi
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia; State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Yong-Zhen Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia; State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China.
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21
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Doggett NA, Mukundan H, Lefkowitz EJ, Slezak TR, Chain PS, Morse S, Anderson K, Hodge DR, Pillai S. Culture-Independent Diagnostics for Health Security. Health Secur 2017; 14:122-42. [PMID: 27314653 DOI: 10.1089/hs.2015.0074] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The past decade has seen considerable development in the diagnostic application of nonculture methods, including nucleic acid amplification-based methods and mass spectrometry, for the diagnosis of infectious diseases. The implications of these new culture-independent diagnostic tests (CIDTs) include bypassing the need to culture organisms, thus potentially affecting public health surveillance systems, which continue to use isolates as the basis of their surveillance programs and to assess phenotypic resistance to antimicrobial agents. CIDTs may also affect the way public health practitioners detect and respond to a bioterrorism event. In response to a request from the Department of Homeland Security, Los Alamos National Laboratory and the Centers for Disease Control and Prevention cosponsored a workshop to review the impact of CIDTs on the rapid detection and identification of biothreat agents. Four panel discussions were held that covered nucleic acid amplification-based diagnostics, mass spectrometry, antibody-based diagnostics, and next-generation sequencing. Exploiting the extensive expertise available at this workshop, we identified the key features, benefits, and limitations of the various CIDT methods for providing rapid pathogen identification that are critical to the response and mitigation of a bioterrorism event. After the workshop we conducted a thorough review of the literature, investigating the current state of these 4 culture-independent diagnostic methods. This article combines information from the literature review and the insights obtained at the workshop.
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22
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Sarig O, Sprecher E. The Molecular Revolution in Cutaneous Biology: Era of Next-Generation Sequencing. J Invest Dermatol 2017; 137:e79-e82. [PMID: 28411851 DOI: 10.1016/j.jid.2016.02.818] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/22/2015] [Accepted: 02/01/2016] [Indexed: 11/20/2022]
Abstract
Like any true conceptual revolution, next-generation sequencing (NGS) has not only radically changed research and clinical practice, it has also modified scientific culture. With the possibility to investigate DNA contents of any organism and in any context, including in somatic disorders or in tissues carrying complex microbial populations, it initially seemed as if the genetic underpinning of any biological phenomenon could now be deciphered in an almost streamlined fashion. However, over the past recent years, we have once again come to understand that there is no such a thing as great opportunities without great challenges. The steadily expanding use of NGS and related applications is now facing biologists and physicians with novel technological obstacles, analytical hurdles and increasingly pressing ethical questions.
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Affiliation(s)
- Ofer Sarig
- Department of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Eli Sprecher
- Department of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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23
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Pereira A, Figueira L, Nunes M, Esteves A, Cotão AJ, Vieira ML, Maia C, Campino L, Parreira R. Multiple Phlebovirus (Bunyaviridae) genetic groups detected in Rhipicephalus , Hyalomma and Dermacentor ticks from southern Portugal. Ticks Tick Borne Dis 2017; 8:45-52. [DOI: 10.1016/j.ttbdis.2016.09.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 09/23/2016] [Accepted: 09/23/2016] [Indexed: 01/22/2023]
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Bueno-Sancho V, Bunting DCE, Yanes LJ, Yoshida K, Saunders DGO. Field Pathogenomics: An Advanced Tool for Wheat Rust Surveillance. Methods Mol Biol 2017; 1659:13-28. [PMID: 28856637 DOI: 10.1007/978-1-4939-7249-4_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Traditionally, diagnostic tools for plant pathogens were limited to the analysis of purified pathogen isolates subjected to phenotypic characterization and/or PCR-based genotypic analysis. However, these approaches detect only already known pathogenic agents, may not always recognize novel races, and can introduce bias in the results. Recent advances in next-generation sequencing technologies have provided new opportunities to integrate high-resolution genotype data into pathogen surveillance programs. Here, we describe some of the key bioinformatics analysis used in the newly developed "Field Pathogenomics" pathogen surveillance technique. This technique is based on RNA-seq data generated directly form pathogen-infected plant leaf samples collected in the field, providing a unique opportunity to characterize the pathogen population and its host directly in their natural environment. We describe two main analyses: (1) a phylogenetic analysis of the pathogen isolates that have been collected to understand how they are related to each other, and (2) a population structure analysis to provide insight into the genetic substructure within the pathogen population. This provides a high-resolution representation of pathogen population dynamics directly in the field, providing new insights into pathogen biology, population structure, and pathogenesis.
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Affiliation(s)
- Vanessa Bueno-Sancho
- Earlham Institute, Norwich Research Park, Norwich, UK
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Daniel C E Bunting
- Earlham Institute, Norwich Research Park, Norwich, UK
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Luis J Yanes
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Kentaro Yoshida
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Diane G O Saunders
- Earlham Institute, Norwich Research Park, Norwich, UK.
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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25
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17 th Century Variola Virus Reveals the Recent History of Smallpox. Curr Biol 2016; 26:3407-3412. [PMID: 27939314 PMCID: PMC5196022 DOI: 10.1016/j.cub.2016.10.061] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 10/20/2016] [Accepted: 10/31/2016] [Indexed: 11/23/2022]
Abstract
Smallpox holds a unique position in the history of medicine. It was the first disease for which a vaccine was developed and remains the only human disease eradicated by vaccination. Although there have been claims of smallpox in Egypt, India, and China dating back millennia [1-4], the timescale of emergence of the causative agent, variola virus (VARV), and how it evolved in the context of increasingly widespread immunization, have proven controversial [4-9]. In particular, some molecular-clock-based studies have suggested that key events in VARV evolution only occurred during the last two centuries [4-6] and hence in apparent conflict with anecdotal historical reports, although it is difficult to distinguish smallpox from other pustular rashes by description alone. To address these issues, we captured, sequenced, and reconstructed a draft genome of an ancient strain of VARV, sampled from a Lithuanian child mummy dating between 1643 and 1665 and close to the time of several documented European epidemics [1, 2, 10]. When compared to vaccinia virus, this archival strain contained the same pattern of gene degradation as 20th century VARVs, indicating that such loss of gene function had occurred before ca. 1650. Strikingly, the mummy sequence fell basal to all currently sequenced strains of VARV on phylogenetic trees. Molecular-clock analyses revealed a strong clock-like structure and that the timescale of smallpox evolution is more recent than often supposed, with the diversification of major viral lineages only occurring within the 18th and 19th centuries, concomitant with the development of modern vaccination.
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26
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Goodman LB, Anderson RR, Slater M, Ortenberg E, Renshaw RW, Chilson BD, Laverack MA, Beeby JS, Dubovi EJ, Glaser AL. High-throughput Detection of Respiratory Pathogens in Animal Specimens by Nanoscale PCR. J Vis Exp 2016. [PMID: 27929456 PMCID: PMC5226323 DOI: 10.3791/54781] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Nanoliter scale real-time PCR uses spatial multiplexing to allow multiple assays to be run in parallel on a single plate without the typical drawbacks of combining reactions together. We designed and evaluated a panel based on this principle to rapidly identify the presence of common disease agents in dogs and horses with acute respiratory illness. This manuscript describes a nanoscale diagnostic PCR workflow for sample preparation, amplification, and analysis of target pathogen sequences, focusing on procedures that are different from microliter scale reactions. In the respiratory panel presented, 18 assays were each set up in triplicate, accommodating up to 48 samples per plate. A universal extraction and pre-amplification workflow was optimized for high-throughput sample preparation to accommodate multiple matrices and DNA and RNA based pathogens. Representative data are presented for one RNA target (influenza A matrix) and one DNA target (equine herpesvirus 1). The ability to quickly and accurately test for a comprehensive, syndrome-based group of pathogens is a valuable tool for improving efficiency and ergonomics of diagnostic testing and for acute respiratory disease diagnosis and management.
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Affiliation(s)
- Laura B Goodman
- Population Medicine and Diagnostic Sciences, Cornell University Animal Health Diagnostic Center;
| | - Renee R Anderson
- Population Medicine and Diagnostic Sciences, Cornell University Animal Health Diagnostic Center
| | | | | | - Randall W Renshaw
- Population Medicine and Diagnostic Sciences, Cornell University Animal Health Diagnostic Center
| | - Brittany D Chilson
- Population Medicine and Diagnostic Sciences, Cornell University Animal Health Diagnostic Center
| | - Melissa A Laverack
- Population Medicine and Diagnostic Sciences, Cornell University Animal Health Diagnostic Center
| | - John S Beeby
- Population Medicine and Diagnostic Sciences, Cornell University Animal Health Diagnostic Center
| | - Edward J Dubovi
- Population Medicine and Diagnostic Sciences, Cornell University Animal Health Diagnostic Center
| | - Amy L Glaser
- Population Medicine and Diagnostic Sciences, Cornell University Animal Health Diagnostic Center
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Lam TTY, Zhu H, Guan Y, Holmes EC. Genomic Analysis of the Emergence, Evolution, and Spread of Human Respiratory RNA Viruses. Annu Rev Genomics Hum Genet 2016; 17:193-218. [PMID: 27216777 DOI: 10.1146/annurev-genom-083115-022628] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The emergence and reemergence of rapidly evolving RNA viruses-particularly those responsible for respiratory diseases, such as influenza viruses and coronaviruses-pose a significant threat to global health, including the potential of major pandemics. Importantly, recent advances in high-throughput genome sequencing enable researchers to reveal the genomic diversity of these viral pathogens at much lower cost and with much greater precision than they could before. In particular, the genome sequence data generated allow inferences to be made on the molecular basis of viral emergence, evolution, and spread in human populations in real time. In this review, we introduce recent computational methods that analyze viral genomic data, particularly in combination with metadata such as sampling time, geographic location, and virulence. We then outline the insights these analyses have provided into the fundamental patterns and processes of evolution and emergence in human respiratory RNA viruses, as well as the major challenges in such genomic analyses.
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Affiliation(s)
- Tommy T-Y Lam
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China; , ,
- Joint Influenza Research Center and Joint Institute of Virology, Shantou University Medical College, Shantou 515041, China
- State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China
| | - Huachen Zhu
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China; , ,
- Joint Influenza Research Center and Joint Institute of Virology, Shantou University Medical College, Shantou 515041, China
- State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China
| | - Yi Guan
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China; , ,
- Joint Influenza Research Center and Joint Institute of Virology, Shantou University Medical College, Shantou 515041, China
- State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China
- Department of Microbiology, Guangxi Medical University, Nanning 530021, China
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia;
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Fraser TA, Charleston M, Martin A, Polkinghorne A, Carver S. The emergence of sarcoptic mange in Australian wildlife: an unresolved debate. Parasit Vectors 2016; 9:316. [PMID: 27255333 PMCID: PMC4890250 DOI: 10.1186/s13071-016-1578-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/09/2016] [Indexed: 11/23/2022] Open
Abstract
Due to its suspected increase in host range and subsequent global diversification, Sarcoptes scabiei has important implications at a global scale for wildlife conservation and animal and human health. The introduction of this pathogen into new locations and hosts has been shown to produce high morbidity and mortality, a situation observed recently in Australian and North American wildlife. Of the seven native animal species in Australia known to be infested by S. scabiei, the bare-nosed wombat (Vombatus ursinus) suffers the greatest with significant population declines having been observed in New South Wales and Tasmania. The origins of sarcoptic mange in Australian native animals are poorly understood, with the most consistent conclusion being that mange was introduced by settlers and their dogs and subsequently becoming a major burden to native wildlife. Four studies exist addressing the origins of mange in Australia, but all Australian S. scabiei samples derive from only two of these studies. This review highlights this paucity of phylogenetic knowledge of S. scabiei within Australia, and suggests further research is needed to confidently determine the origin, or multiple origins, of this parasite. At the global scale, numerous genetic studies have attempted to reveal how the host species and host geographic location influence S. scabiei phylogenetics. This review includes an analysis of the global literature, revealing that inconsistent use of gene loci across studies significantly influences phylogenetic inference. Furthermore, by performing a contemporary analytical approach on existing data, it is apparent that (i) new S. scabiei samples, (ii) appropriate gene loci targets, and (iii) advanced phylogenetic approaches are necessary to more confidently comprehend the origins of mange in Australia. Advancing this field of research will aid in understanding the mechanisms of spillover for mange and other parasites globally.
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Affiliation(s)
- Tamieka A Fraser
- School of Biological Sciences, University of Tasmania, Sandy Bay, 7001, TAS, Australia. .,Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, 91 Sippy Downs Drive, Sippy Downs, 4556, QLD, Australia.
| | - Michael Charleston
- School of Biological Sciences, University of Tasmania, Sandy Bay, 7001, TAS, Australia.,School of Information Technologies, University of Sydney, Camperdown, 2006, Sydney, Australia
| | - Alynn Martin
- School of Biological Sciences, University of Tasmania, Sandy Bay, 7001, TAS, Australia
| | - Adam Polkinghorne
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, 91 Sippy Downs Drive, Sippy Downs, 4556, QLD, Australia
| | - Scott Carver
- School of Biological Sciences, University of Tasmania, Sandy Bay, 7001, TAS, Australia
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29
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Luk KC, Berg MG, Naccache SN, Kabre B, Federman S, Mbanya D, Kaptué L, Chiu CY, Brennan CA, Hackett J. Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity. PLoS One 2015; 10:e0141723. [PMID: 26599538 PMCID: PMC4658132 DOI: 10.1371/journal.pone.0141723] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 10/12/2015] [Indexed: 02/06/2023] Open
Abstract
Given the dynamic changes in HIV-1 complexity and diversity, next-generation sequencing (NGS) has the potential to revolutionize strategies for effective HIV global surveillance. In this study, we explore the utility of metagenomic NGS to characterize divergent strains of HIV-1 and to simultaneously screen for other co-infecting viruses. Thirty-five HIV-1-infected Cameroonian blood donor specimens with viral loads of >4.4 log10 copies/ml were selected to include a diverse representation of group M strains. Random-primed NGS libraries, prepared from plasma specimens, resulted in greater than 90% genome coverage for 88% of specimens. Correct subtype designations based on NGS were concordant with sub-region PCR data in 31 of 35 (89%) cases. Complete genomes were assembled for 25 strains, including circulating recombinant forms with relatively limited data available (7 CRF11_cpx, 2 CRF13_cpx, 1 CRF18_cpx, and 1 CRF37_cpx), as well as 9 unique recombinant forms. HPgV (formerly designated GBV-C) co-infection was detected in 9 of 35 (25%) specimens, of which eight specimens yielded complete genomes. The recovered HPgV genomes formed a diverse cluster with genotype 1 sequences previously reported from Ghana, Uganda, and Japan. The extensive genome coverage obtained by NGS improved accuracy and confidence in phylogenetic classification of the HIV-1 strains present in the study population relative to conventional sub-region PCR. In addition, these data demonstrate the potential for metagenomic analysis to be used for routine characterization of HIV-1 and identification of other viral co-infections.
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Affiliation(s)
- Ka-Cheung Luk
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America
| | - Michael G Berg
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America
| | - Samia N Naccache
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
| | - Beniwende Kabre
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
| | - Scot Federman
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
| | | | | | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America.,Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, California, United States of America
| | - Catherine A Brennan
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America
| | - John Hackett
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America
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Yang Y, Garver LS, Bingham KM, Hang J, Jochim RC, Davidson SA, Richardson JH, Jarman RG. Feasibility of Using the Mosquito Blood Meal for Rapid and Efficient Human and Animal Virus Surveillance and Discovery. Am J Trop Med Hyg 2015; 93:1377-82. [PMID: 26416112 DOI: 10.4269/ajtmh.15-0440] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/03/2015] [Indexed: 11/07/2022] Open
Abstract
Mosquito blood meals taken from humans and animals potentially represent a useful source of blood for the detection of blood-borne pathogens. In this feasibility study, Anopheles stephensi mosquitoes were fed with blood meals spiked with dengue virus type 2 (DENV-2) and harvested at serial time points. These mosquitoes are not competent vectors, and the virus is not expected to replicate. Ingested blood was spotted on Whatman FTA cards and stored at room temperature. Mosquito abdomens were removed and stored at -80°C. Control blood meal aliquots were stored in vials or applied onto FTA cards. After 4 weeks of storage, the samples were extracted using beadbeating and QIAamp Viral RNA kit (Qiagen Sciences, Germantown, MD). Recovered viral RNA was analyzed by DENV-2 TaqMan RT-PCR assay and next-generation sequencing (NGS). Overall viral RNA recovery efficiency was 15% from the directly applied dried blood spots and approximately 20% or higher for dried blood spots made by blotting mosquito midgut on FTA cards. Viral RNA in mosquito-ingested blood decreases over time, but remains detectable 24 hours after blood feeding. The viral sequences in FTA-stored specimens can be maintained at room temperature. The strategy has the potential utility in expedited zoonotic virus discovery and blood-borne pathogen surveillance.
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Affiliation(s)
- Yu Yang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland; Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Lindsey S Garver
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland; Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Karen M Bingham
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland; Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland; Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Ryan C Jochim
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland; Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Silas A Davidson
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland; Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Jason H Richardson
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland; Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland; Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
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Dugat T, Lagrée AC, Maillard R, Boulouis HJ, Haddad N. Opening the black box of Anaplasma phagocytophilum diversity: current situation and future perspectives. Front Cell Infect Microbiol 2015; 5:61. [PMID: 26322277 PMCID: PMC4536383 DOI: 10.3389/fcimb.2015.00061] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/31/2015] [Indexed: 01/28/2023] Open
Abstract
Anaplasma phagocytophilum is a zoonotic obligate intracellular bacterium known to be transmitted by ticks belonging to the Ixodes persulcatus complex. This bacterium can infect several mammalian species, and is known to cause diseases with variable symptoms in many domestic animals. Specifically, it is the causative agent of tick-borne fever (TBF), a disease of important economic impact in European domestic ruminants, and human granulocytic anaplasmosis (HGA), an emerging zoonotic disease in Asia, USA and Europe. A. phagocytophilum epidemiological cycles are complex and involve different ecotypes, vectors, and mammalian host species. Moreover, the epidemiology of A. phagocytophilum infection differs greatly between Europe and the USA. These different epidemiological contexts are associated with considerable variations in bacterial strains. Until recently, few A. phagocytophilum molecular typing tools were available, generating difficulties in completely elucidating the epidemiological cycles of this bacterium. Over the last few years, many A. phagocytophilum typing techniques have been developed, permitting in-depth epidemiological exploration. Here, we review the current knowledge and future perspectives regarding A. phagocytophilum epidemiology and phylogeny, and then focus on the molecular typing tools available for studying A. phagocytophilum genetic diversity.
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Affiliation(s)
- Thibaud Dugat
- Laboratoire de Santé Animale, UMR Biologie Moléculaire et Immunologie Parasitaires, Agence Nationale de Sécurité Sanitaire de L'alimentation, de L'environnement et du Travail, Université Paris-Est Paris, France
| | - Anne-Claire Lagrée
- UMR Biologie Moléculaire et Immunologie Parasitaires, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est Paris, France
| | - Renaud Maillard
- UMR Biologie Moléculaire et Immunologie Parasitaires, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est Paris, France ; Unité Pathologie des Ruminants, Ecole Nationale Vétérinaire de Toulouse Toulouse, France
| | - Henri-Jean Boulouis
- UMR Biologie Moléculaire et Immunologie Parasitaires, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est Paris, France
| | - Nadia Haddad
- UMR Biologie Moléculaire et Immunologie Parasitaires, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est Paris, France
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Bellehumeur C, Boyle B, Charette SJ, Harel J, L'Homme Y, Masson L, Gagnon CA. Propidium monoazide (PMA) and ethidium bromide monoazide (EMA) improve DNA array and high-throughput sequencing of porcine reproductive and respiratory syndrome virus identification. J Virol Methods 2015; 222:182-91. [PMID: 26129867 PMCID: PMC7119533 DOI: 10.1016/j.jviromet.2015.06.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 06/11/2015] [Accepted: 06/25/2015] [Indexed: 11/29/2022]
Abstract
Pan-viral DNA array (PVDA) and high-throughput sequencing (HTS) are useful tools to identify novel viruses of emerging diseases. However, both techniques have difficulties to identify viruses in clinical samples because of the host genomic nucleic acid content (hg/cont). Both propidium monoazide (PMA) and ethidium bromide monoazide (EMA) have the capacity to bind free DNA/RNA, but are cell membrane-impermeable. Thus, both are unable to bind protected nucleic acid such as viral genomes within intact virions. However, EMA/PMA modified genetic material cannot be amplified by enzymes. In order to assess the potential of EMA/PMA to lower the presence of amplifiable hg/cont in samples and improve virus detection, serum and lung tissue homogenates were spiked with porcine reproductive and respiratory virus (PRRSV) and were processed with EMA/PMA. In addition, PRRSV RT-qPCR positive clinical samples were also tested. EMA/PMA treatments significantly decreased amplifiable hg/cont and significantly increased the number of PVDA positive probes and their signal intensity compared to untreated spiked lung samples. EMA/PMA treatments also increased the sensitivity of HTS by increasing the number of specific PRRSV reads and the PRRSV percentage of coverage. Interestingly, EMA/PMA treatments significantly increased the sensitivity of PVDA and HTS in two out of three clinical tissue samples. Thus, EMA/PMA treatments offer a new approach to lower the amplifiable hg/cont in clinical samples and increase the success of PVDA and HTS to identify viruses.
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Affiliation(s)
- Christian Bellehumeur
- Groupe de recherche sur les maladies infectieuses du porc (GREMIP), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada; Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Brian Boyle
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Steve J Charette
- Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada; Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
| | - Josée Harel
- Groupe de recherche sur les maladies infectieuses du porc (GREMIP), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada; Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Yvan L'Homme
- Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada; Canadian Food Inspection Agency, Saint-Hyacinthe, QC, Canada
| | - Luke Masson
- Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada; National Research Council Canada, Montréal, QC, Canada
| | - Carl A Gagnon
- Groupe de recherche sur les maladies infectieuses du porc (GREMIP), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada; Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada.
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Ge F, Parker J, Chul Choi S, Layer M, Ross K, Jilly B, Chen J. Preferential Amplification of Pathogenic Sequences. Sci Rep 2015; 5:11047. [PMID: 26067233 PMCID: PMC4464073 DOI: 10.1038/srep11047] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 05/14/2015] [Indexed: 02/07/2023] Open
Abstract
The application of next generation sequencing (NGS) technology in the diagnosis of human pathogens is hindered by the fact that pathogenic sequences, especially viral, are often scarce in human clinical specimens. This known disproportion leads to the requirement of subsequent deep sequencing and extensive bioinformatics analysis. Here we report a method we called “Preferential Amplification of Pathogenic Sequences (PATHseq)” that can be used to greatly enrich pathogenic sequences. Using a computer program, we developed 8-, 9-, and 10-mer oligonucleotides called “non-human primers” that do not match the most abundant human transcripts, but instead selectively match transcripts of human pathogens. Instead of using random primers in the construction of cDNA libraries, the PATHseq method recruits these short non-human primers, which in turn, preferentially amplifies non-human, presumably pathogenic sequences. Using this method, we were able to enrich pathogenic sequences up to 200-fold in the final sequencing library. This method does not require prior knowledge of the pathogen or assumption of the infection; therefore, it provides a fast and sequence-independent approach for detection and identification of human viruses and other pathogens. The PATHseq method, coupled with NGS technology, can be broadly used in identification of known human pathogens and discovery of new pathogens.
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Affiliation(s)
- Fang Ge
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| | - Jayme Parker
- 1] Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA [2] Alaska State Public Health Virology Laboratory, Fairbanks, Alaska, USA
| | - Sang Chul Choi
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| | - Mark Layer
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| | - Katherine Ross
- Alaska State Public Health Laboratories, Anchorage, Alaska, USA
| | - Bernard Jilly
- Alaska State Public Health Laboratories, Anchorage, Alaska, USA
| | - Jack Chen
- 1] Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA [2] Alaska State Public Health Virology Laboratory, Fairbanks, Alaska, USA
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Negeviruses found in multiple species of mosquitoes from southern Portugal: Isolation, genetic diversity, and replication in insect cell culture. Virology 2015; 483:318-28. [PMID: 26057025 DOI: 10.1016/j.virol.2015.04.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 04/10/2015] [Accepted: 04/17/2015] [Indexed: 11/21/2022]
Abstract
In this report, an RT-PCR approach based on the use of degenerate primers allowed the identification of negeviruses in four different species of mosquitoes (Ochlerotatus caspius, Culex pipiens, Cx. theileri and Cx. univittatus) collected in southern Portugal. The genomes of two of these viruses, sequenced to full completion, were shown to encode all the proteins encoded by previously described negeviruses. One of these viruses induces exuberant cytopathic effect in insect cell culture, with no obvious signs of apoptosis induction, replicating very rapidly and allowing for the detection of viral genomes in the infected culture supernatant as soon as 4h post-infection. This virus was also shown to use a dsRNA intermediate, which was found to be fully formed and active 3h after infection. Phylogenetic analysis of two products encoded by the viral ORF1 placed both viruses among Negev virus cluster, in the recently proposed Nelorpivirus taxon.
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The use of -omic tools in the study of disease processes in marine bivalve mollusks. J Invertebr Pathol 2015; 131:137-54. [PMID: 26021714 DOI: 10.1016/j.jip.2015.05.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 04/09/2015] [Accepted: 05/05/2015] [Indexed: 01/01/2023]
Abstract
Our understanding of disease processes and host-pathogen interactions in model species has benefited greatly from the application of medium and high-throughput genomic, metagenomic, epigenomic, transcriptomic, and proteomic analyses. The rate at which new, low-cost, high-throughput -omic technologies are being developed has also led to an expansion in the number of studies aimed at gaining a better understanding of disease processes in bivalves. This review provides a catalogue of the genetic and -omic tools available for bivalve species and examples of how -omics has contributed to the advancement of marine bivalve disease research, with a special focus in the areas of immunity, bivalve-pathogen interactions, mechanisms of disease resistance and pathogen virulence, and disease diagnosis. The analysis of bivalve genomes and transcriptomes has revealed that many immune and stress-related gene families are expanded in the bivalve taxa examined thus far. In addition, the analysis of proteomes confirms that responses to infection are influenced by epigenetic, post-transcriptional, and post-translational modifications. The few studies performed in bivalves show that epigenetic modifications are non-random, suggesting a role for epigenetics in regulating the interactions between bivalves and their environments. Despite the progress -omic tools have enabled in the field of marine bivalve disease processes, there is much more work to be done. To date, only three bivalve genomes have been sequenced completely, with assembly status at different levels of completion. Transcriptome datasets are relatively easy and inexpensive to generate, but their interpretation will benefit greatly from high quality genome assemblies and improved data analysis pipelines. Finally, metagenomic, epigenomic, proteomic, and metabolomic studies focused on bivalve disease processes are currently limited but their expansion should be facilitated as more transcriptome datasets and complete genome sequences become available for marine bivalve species.
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Xiao Y, Sheng ZM, Taubenberger JK. Isolating Viral and Host RNA Sequences from Archival Material and Production of cDNA Libraries for High-Throughput DNA Sequencing. ACTA ACUST UNITED AC 2015; 37:1E.8.1-16. [PMID: 26344216 DOI: 10.1002/9780471729259.mc01e08s37] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The vast majority of surgical biopsy and post-mortem tissue samples are formalin-fixed and paraffin-embedded (FFPE), but this process leads to RNA degradation that limits gene expression analysis. As an example, the viral RNA genome of the 1918 pandemic influenza A virus was previously determined in a 9-year effort by overlapping RT-PCR from post-mortem samples. Using the protocols described here, the full genome of the 1918 virus was determined at high coverage in one high-throughput sequencing run of a cDNA library derived from total RNA of a 1918 FFPE sample after duplex-specific nuclease treatments. This basic methodological approach should assist in the analysis of FFPE tissue samples isolated over the past century from a variety of infectious diseases.
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Affiliation(s)
- Yongli Xiao
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Zong-Mei Sheng
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jeffery K Taubenberger
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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Hubbard A, Lewis CM, Yoshida K, Ramirez-Gonzalez RH, de Vallavieille-Pope C, Thomas J, Kamoun S, Bayles R, Uauy C, Saunders DGO. Field pathogenomics reveals the emergence of a diverse wheat yellow rust population. Genome Biol 2015. [PMID: 25723868 DOI: 10.1186/s13059-015-0590-598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
BACKGROUND Emerging and re-emerging pathogens imperil public health and global food security. Responding to these threats requires improved surveillance and diagnostic systems. Despite their potential, genomic tools have not been readily applied to emerging or re-emerging plant pathogens such as the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici (PST). This is due largely to the obligate parasitic nature of PST, as culturing PST isolates for DNA extraction remains slow and tedious. RESULTS To counteract the limitations associated with culturing PST, we developed and applied a field pathogenomics approach by transcriptome sequencing infected wheat leaves collected from the field in 2013. This enabled us to rapidly gain insights into this emerging pathogen population. We found that the PST population across the United Kingdom (UK) underwent a major shift in recent years. Population genetic structure analyses revealed four distinct lineages that correlated to the phenotypic groups determined through traditional pathology-based virulence assays. Furthermore, the genetic diversity between members of a single population cluster for all 2013 PST field samples was much higher than that displayed by historical UK isolates, revealing a more diverse population of PST. CONCLUSIONS Our field pathogenomics approach uncovered a dramatic shift in the PST population in the UK, likely due to a recent introduction of a diverse set of exotic PST lineages. The methodology described herein accelerates genetic analysis of pathogen populations and circumvents the difficulties associated with obligate plant pathogens. In principle, this strategy can be widely applied to a variety of plant pathogens.
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Hubbard A, Lewis CM, Yoshida K, Ramirez-Gonzalez RH, de Vallavieille-Pope C, Thomas J, Kamoun S, Bayles R, Uauy C, Saunders DGO. Field pathogenomics reveals the emergence of a diverse wheat yellow rust population. Genome Biol 2015; 16:23. [PMID: 25723868 PMCID: PMC4342793 DOI: 10.1186/s13059-015-0590-8] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 01/20/2015] [Indexed: 11/28/2022] Open
Abstract
Background Emerging and re-emerging pathogens imperil public health and global food security. Responding to these threats requires improved surveillance and diagnostic systems. Despite their potential, genomic tools have not been readily applied to emerging or re-emerging plant pathogens such as the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici (PST). This is due largely to the obligate parasitic nature of PST, as culturing PST isolates for DNA extraction remains slow and tedious. Results To counteract the limitations associated with culturing PST, we developed and applied a field pathogenomics approach by transcriptome sequencing infected wheat leaves collected from the field in 2013. This enabled us to rapidly gain insights into this emerging pathogen population. We found that the PST population across the United Kingdom (UK) underwent a major shift in recent years. Population genetic structure analyses revealed four distinct lineages that correlated to the phenotypic groups determined through traditional pathology-based virulence assays. Furthermore, the genetic diversity between members of a single population cluster for all 2013 PST field samples was much higher than that displayed by historical UK isolates, revealing a more diverse population of PST. Conclusions Our field pathogenomics approach uncovered a dramatic shift in the PST population in the UK, likely due to a recent introduction of a diverse set of exotic PST lineages. The methodology described herein accelerates genetic analysis of pathogen populations and circumvents the difficulties associated with obligate plant pathogens. In principle, this strategy can be widely applied to a variety of plant pathogens. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0590-8) contains supplementary material, which is available to authorized users.
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Wang Q, Jia P, Zhao Z. VERSE: a novel approach to detect virus integration in host genomes through reference genome customization. Genome Med 2015; 7:2. [PMID: 25699093 PMCID: PMC4333248 DOI: 10.1186/s13073-015-0126-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 01/05/2015] [Indexed: 12/28/2022] Open
Abstract
Fueled by widespread applications of high-throughput next generation sequencing (NGS) technologies and urgent need to counter threats of pathogenic viruses, large-scale studies were conducted recently to investigate virus integration in host genomes (for example, human tumor genomes) that may cause carcinogenesis or other diseases. A limiting factor in these studies, however, is rapid virus evolution and resulting polymorphisms, which prevent reads from aligning readily to commonly used virus reference genomes, and, accordingly, make virus integration sites difficult to detect. Another confounding factor is host genomic instability as a result of virus insertions. To tackle these challenges and improve our capability to identify cryptic virus-host fusions, we present a new approach that detects Virus intEgration sites through iterative Reference SEquence customization (VERSE). To the best of our knowledge, VERSE is the first approach to improve detection through customizing reference genomes. Using 19 human tumors and cancer cell lines as test data, we demonstrated that VERSE substantially enhanced the sensitivity of virus integration site detection. VERSE is implemented in the open source package VirusFinder 2 that is available at http://bioinfo.mc.vanderbilt.edu/VirusFinder/.
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Affiliation(s)
- Qingguo Wang
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203 USA
| | - Peilin Jia
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203 USA ; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232 USA
| | - Zhongming Zhao
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203 USA ; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232 USA ; Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37232 USA ; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232 USA
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Holmes EC, Zhang YZ. The evolution and emergence of hantaviruses. Curr Opin Virol 2015; 10:27-33. [PMID: 25562117 DOI: 10.1016/j.coviro.2014.12.007] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 11/25/2014] [Accepted: 12/17/2014] [Indexed: 12/20/2022]
Abstract
Hantaviruses are a major class of zoonotic pathogens and cause a variety of severe diseases in humans. For most of the last 50 years rodents have been considered to be the primary hosts of hantaviruses, with hantavirus evolution thought to reflect a process of virus-rodent co-divergence over a time-scale of millions of years, with occasional spill-over into humans. However, recent discoveries have revealed that hantaviruses infect a more diverse range of mammalian hosts, particularly Chiroptera (bats) and Soricomorpha (moles and shrews), and that cross-species transmission at multiple scales has played an important role in hantavirus evolution. As a consequence, the evolution and emergence of hantaviruses is more complex than previously anticipated, and may serve as a realistic model for other viral groups.
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Affiliation(s)
- Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia; State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China.
| | - Yong-Zhen Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
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Pyne S, Vullikanti AKS, Marathe MV. Big Data Applications in Health Sciences and Epidemiology. HANDBOOK OF STATISTICS 2015. [PMCID: PMC7152243 DOI: 10.1016/b978-0-444-63492-4.00008-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Saumyadipta Pyne
- Bioinformatics, CR Rao Advanced Institute of Mathematics, Statistics and Computer Science, University of Hyderabad Campus, Hyderabad, India
- Public Health Foundation of India, New Delhi, India
- Corresponding author:
| | | | - Madhav V. Marathe
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia, USA
- Network Dynamics and Simulation Science Laboratory, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
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Dugat T, Loux V, Marthey S, Moroldo M, Lagrée AC, Boulouis HJ, Haddad N, Maillard R. Comparative genomics of first available bovine Anaplasma phagocytophilum genome obtained with targeted sequence capture. BMC Genomics 2014; 15:973. [PMID: 25400116 PMCID: PMC4239370 DOI: 10.1186/1471-2164-15-973] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 10/30/2014] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Anaplasma phagocytophilum is a zoonotic and obligate intracellular bacterium transmitted by ticks. In domestic ruminants, it is the causative agent of tick-borne fever, which causes significant economic losses in Europe. As A. phagocytophilum is difficult to isolate and cultivate, only nine genome sequences have been published to date, none of which originate from a bovine strain.Our goals were to; 1/ develop a sequencing methodology which efficiently circumvents the difficulties associated with A. phagocytophilum isolation and culture; 2/ describe the first genome of a bovine strain; and 3/ compare it with available genomes, in order to both explore key genomic features at the species level, and to identify candidate genes that could be specific to bovine strains. RESULTS DNA was extracted from a bovine blood sample infected by A. phagocytophilum. Following a whole genome capture approach, A. phagocytophilum DNA was enriched 197-fold in the sample and then sequenced using Illumina technology. In total, 58.9% of obtained reads corresponded to the A. phagocytophilum genome, covering 85.3% of the HZ genome. Then by performing comparisons with nine previously-sequenced A. phagocytophilum genomes, we determined the core genome of these ten strains. Following analysis, 1281 coding DNA sequences, including 1001 complete sequences, were detected in the A. phagocytophilum bovine genome, of which four appeared to be unique to the bovine isolate. These four coding DNA sequences coded for "hypothetical proteins of unknown function" and require further analysis. We also identified nine proteins common to both European domestic ruminants tested. CONCLUSION Using a whole genome capture approach, we have sequenced the first A. phagocytophilum genome isolated from a cow. To the best of our knowledge, this is the first time that this method has been used to selectively enrich pathogenic bacterial DNA from samples also containing host DNA. The four proteins unique to the A. phagocytophilum bovine genome could be involved in host tropism, therefore their functions need to be explored.
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Affiliation(s)
| | | | | | | | | | | | - Nadia Haddad
- Université Paris-Est, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR ENVA Anses UPEC USC INRA, Maisons-Alfort, France.
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Sasaki M, Orba Y, Ueno K, Ishii A, Moonga L, Hang'ombe BM, Mweene AS, Ito K, Sawa H. Metagenomic analysis of the shrew enteric virome reveals novel viruses related to human stool-associated viruses. J Gen Virol 2014; 96:440-452. [PMID: 25381053 DOI: 10.1099/vir.0.071209-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Shrews are small insectivorous mammals that are distributed worldwide. Similar to rodents, shrews live on the ground and are commonly found near human residences. In this study, we investigated the enteric virome of wild shrews in the genus Crocidura using a sequence-independent viral metagenomics approach. A large portion of the shrew enteric virome was composed of insect viruses, whilst novel viruses including cyclovirus, picornavirus and picorna-like virus were also identified. Several cycloviruses, including variants of human cycloviruses detected in cerebrospinal fluid and stools, were detected in wild shrews at a high prevalence rate. The identified picornavirus was distantly related to human parechovirus, inferring the presence of a new genus in this family. The identified picorna-like viruses were characterized as different species of calhevirus 1, which was discovered previously in human stools. Complete or nearly complete genome sequences of these novel viruses were determined in this study and then were subjected to further genetic characterization. Our study provides an initial view of the diversity and distinctiveness of the shrew enteric virome and highlights unique novel viruses related to human stool-associated viruses.
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Affiliation(s)
- Michihito Sasaki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Keisuke Ueno
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Akihiro Ishii
- Hokudai Center for Zoonosis Control in Zambia, PO Box 32379, Lusaka, Zambia
| | - Ladslav Moonga
- Department of Paraclinical Studies, School of Veterinary and Medicine, University of Zambia, PO Box 32379, Lusaka, Zambia
| | - Bernard M Hang'ombe
- Department of Paraclinical Studies, School of Veterinary and Medicine, University of Zambia, PO Box 32379, Lusaka, Zambia
| | - Aaron S Mweene
- Department of Disease Control, School of Veterinary and Medicine, University of Zambia, PO Box 32379, Lusaka, Zambia
| | - Kimihito Ito
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Hirofumi Sawa
- Global Institution for Collaborative Research and Education, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan.,Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
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Malham SK, Rajko-Nenow P, Howlett E, Tuson KE, Perkins TL, Pallett DW, Wang H, Jago CF, Jones DL, McDonald JE. The interaction of human microbial pathogens, particulate material and nutrients in estuarine environments and their impacts on recreational and shellfish waters. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2014; 16:2145-2155. [PMID: 25043898 DOI: 10.1039/c4em00031e] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Anthropogenic activities have increased the load of faecal bacteria, pathogenic viruses and nutrients in rivers, estuaries and coastal areas through point and diffuse sources such as sewage discharges and agricultural runoff. These areas are used by humans for both commercial and recreational activities and are therefore protected by a range of European Directives. If water quality declines in these zones, significant economic losses can occur. Identifying the sources of pollution, however, is notoriously difficult due to the ephemeral nature of discharges, their diffuse source, and uncertainties associated with transport and transformation of the pollutants through the freshwater-marine interface. Further, significant interaction between nutrients, microorganisms and particulates can occur in the water column making prediction of the fate and potential infectivity of human pathogenic organisms difficult to ascertain. This interaction is most prevalent in estuarine environments due to the formation of flocs (suspended sediment) at the marine-freshwater interface. A range of physical, chemical and biological processes can induce the co-flocculation of microorganisms, organic matter and mineral particles resulting in pathogenic organisms becoming potentially protected from a range of biotic (e.g. predation) and abiotic stresses (e.g. UV, salinity). These flocs contain and retain macro- and micro- nutrients allowing the potential survival, growth and transfer of pathogenic organisms to commercially sensitive areas (e.g. beaches, shellfish harvesting waters). The flocs can either be transported directly to the coastal environment or can become deposited in the estuary forming cohesive sediments where pathogens can survive for long periods. Especially in response to storms, these sediments can be subsequently remobilised releasing pulses of potential pathogenic organisms back into the water column leading to contamination of marine waters long after the initial contamination event occurred. Further work, however, is still required to understand and predict the potential human infectivity of pathogenic organisms alongside the better design of early warning systems and surveillance measures for risk assessment purposes.
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Affiliation(s)
- Shelagh K Malham
- Centre for Applied Marine Science, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK
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Naccache SN, Federman S, Veeraraghavan N, Zaharia M, Lee D, Samayoa E, Bouquet J, Greninger AL, Luk KC, Enge B, Wadford DA, Messenger SL, Genrich GL, Pellegrino K, Grard G, Leroy E, Schneider BS, Fair JN, Martínez MA, Isa P, Crump JA, DeRisi JL, Sittler T, Hackett J, Miller S, Chiu CY. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res 2014; 24:1180-92. [PMID: 24899342 PMCID: PMC4079973 DOI: 10.1101/gr.171934.113] [Citation(s) in RCA: 311] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Unbiased next-generation sequencing (NGS) approaches enable comprehensive pathogen detection in the clinical microbiology laboratory and have numerous applications for public health surveillance, outbreak investigation, and the diagnosis of infectious diseases. However, practical deployment of the technology is hindered by the bioinformatics challenge of analyzing results accurately and in a clinically relevant timeframe. Here we describe SURPI (“sequence-based ultrarapid pathogen identification”), a computational pipeline for pathogen identification from complex metagenomic NGS data generated from clinical samples, and demonstrate use of the pipeline in the analysis of 237 clinical samples comprising more than 1.1 billion sequences. Deployable on both cloud-based and standalone servers, SURPI leverages two state-of-the-art aligners for accelerated analyses, SNAP and RAPSearch, which are as accurate as existing bioinformatics tools but orders of magnitude faster in performance. In fast mode, SURPI detects viruses and bacteria by scanning data sets of 7–500 million reads in 11 min to 5 h, while in comprehensive mode, all known microorganisms are identified, followed by de novo assembly and protein homology searches for divergent viruses in 50 min to 16 h. SURPI has also directly contributed to real-time microbial diagnosis in acutely ill patients, underscoring its potential key role in the development of unbiased NGS-based clinical assays in infectious diseases that demand rapid turnaround times.
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Affiliation(s)
- Samia N Naccache
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA
| | - Scot Federman
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA
| | - Narayanan Veeraraghavan
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA
| | - Matei Zaharia
- Department of Computer Science, University of California, Berkeley, California 94720, USA
| | - Deanna Lee
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA
| | - Erik Samayoa
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA
| | - Jerome Bouquet
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA
| | | | - Ka-Cheung Luk
- Abbott Diagnostics, Abbott Park, Illinois 60064, USA
| | - Barryett Enge
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California 94804, USA
| | - Debra A Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California 94804, USA
| | - Sharon L Messenger
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California 94804, USA
| | - Gillian L Genrich
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA
| | - Kristen Pellegrino
- Department of Family and Community Medicine, UCSF, San Francisco, California 94143, USA
| | - Gilda Grard
- Viral Emergent Diseases Unit, Centre International de Recherches Médicales de Franceville, Franceville, BP 769, Gabon
| | - Eric Leroy
- Viral Emergent Diseases Unit, Centre International de Recherches Médicales de Franceville, Franceville, BP 769, Gabon
| | | | - Joseph N Fair
- Metabiota, Inc., San Francisco, California 94104, USA
| | - Miguel A Martínez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62260, Mexico
| | - Pavel Isa
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62260, Mexico
| | - John A Crump
- Division of Infectious Diseases and International Health and the Duke Global Health Institute, Duke University Medical Center, Durham, North Carolina 27708, USA; Kilimanjaro Christian Medical Centre, Moshi, Kilimanjaro, 7393, Tanzania; Centre for International Health, University of Otago, Dunedin, 9054, New Zealand
| | - Joseph L DeRisi
- Department of Biochemistry, UCSF, San Francisco, California 94107, USA
| | - Taylor Sittler
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA
| | - John Hackett
- Abbott Diagnostics, Abbott Park, Illinois 60064, USA
| | - Steve Miller
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA; Department of Medicine, Division of Infectious Diseases, UCSF, San Francisco, California 94143, USA
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Selvaraj C, Sivakamavalli J, Baskaralingam V, Singh SK. Virtual screening of LPXTG competitive SrtA inhibitors targeting signal transduction mechanism in Bacillus anthracis: a combined experimental and theoretical study. J Recept Signal Transduct Res 2014; 34:221-32. [PMID: 24490975 DOI: 10.3109/10799893.2013.876044] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Members of the sortase enzyme super family decorate the surfaces of Bacillus anthracis cell wall with proteins that play key roles in microbial pathogenesis and its biofilm formation. Bacillus anthracis Sortase-A (Ba-SrtA) is a potential target for new therapeutics as it is required for B. anthracis survival and replication within macrophages. An understanding of the binding site pocket and substrate recognition mechanism by SrtA enzymes may serve to be beneficial in the rational development of sortase inhibitors. Here, the LPXTG signal peptide-based competitive inhibitors are screened against the Ba-SrtA and compounds with reasonable inhibition, specificity, and mechanisms of inactivation of SrtA have been covered. The screened compounds are experimentally validated against the phylogenetically similar Gram-positive pathogen B. cereus. In situ microscopic visualizations suggest that these screened compounds showed the microbial and biofilm inhibitory activity against B. cereus. It facilitates the further development of these molecules into useful anti-infective agents to treat infections caused by B. anthracis and other Gram-positive pathogens. These results provide insight into basic design principles for generating new clinically relevant lead molecules. It also provides an alternative strategy where a screened ligand molecule can be used in combination to battle increasingly against the Gram-positive pathogens.
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Affiliation(s)
- Chandrabose Selvaraj
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University , Karaikudi, Tamil Nadu , India and
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