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Downie DL, Rao P, David-Ferdon C, Courtney S, Lee JS, Kugley S, MacDonald PDM, Barnes K, Fisher S, Andreadis JL, Chaitram J, Mauldin MR, Salerno RM, Schiffer J, Gundlapalli AV. Literature Review of Pathogen Agnostic Molecular Testing of Clinical Specimens From Difficult-to-Diagnose Patients: Implications for Public Health. Health Secur 2024; 22:93-107. [PMID: 38608237 PMCID: PMC11044852 DOI: 10.1089/hs.2023.0100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/15/2023] [Accepted: 08/15/2023] [Indexed: 04/14/2024] Open
Abstract
To better identify emerging or reemerging pathogens in patients with difficult-to-diagnose infections, it is important to improve access to advanced molecular testing methods. This is particularly relevant for cases where conventional microbiologic testing has been unable to detect the pathogen and the patient's specimens test negative. To assess the availability and utility of such testing for human clinical specimens, a literature review of published biomedical literature was conducted. From a corpus of more than 4,000 articles, a set of 34 reports was reviewed in detail for data on where the testing was being performed, types of clinical specimens tested, pathogen agnostic techniques and methods used, and results in terms of potential pathogens identified. This review assessed the frequency of advanced molecular testing, such as metagenomic next generation sequencing that has been applied to clinical specimens for supporting clinicians in caring for difficult-to-diagnose patients. Specimen types tested were from cerebrospinal fluid, respiratory secretions, and other body tissues and fluids. Publications included case reports and series, and there were several that involved clinical trials, surveillance studies, research programs, or outbreak situations. Testing identified both known human pathogens (sometimes in new sites) and previously unknown human pathogens. During this review, there were no apparent coordinated efforts identified to develop regional or national reports on emerging or reemerging pathogens. Therefore, development of a coordinated sentinel surveillance system that applies advanced molecular methods to clinical specimens which are negative by conventional microbiological diagnostic testing would provide a foundation for systematic characterization of emerging and underdiagnosed pathogens and contribute to national biodefense strategy goals.
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Affiliation(s)
- Diane L. Downie
- Diane L. Downie, PhD, MPH, is Deputy Associate Director for Science, Office of Readiness and Response; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Preetika Rao
- Preetika Rao, MPH, is a Health Scientist; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Corinne David-Ferdon
- Corinne David-Ferdon, PhD, is Associate Director of Science, Office of Public Health Data, Surveillance, and Technology; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Sean Courtney
- Sean Courtney, PhD, is a Health Scientist, at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Justin S. Lee
- Justin Lee, DVM, PhD, is a Health Scientist, Division of Global Health Protection; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Shannon Kugley
- Shannon Kugley, MLIS, is a Research Public Health Analyst; in Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC
| | - Pia D. M. MacDonald
- Pia D. M. MacDonald, PhD, MPH, is a Senior Infectious Disease Epidemiologist; in Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC
| | - Keegan Barnes
- Keegan Barnes is a Public Health Analyst; in Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC
| | - Shelby Fisher
- Shelby Fisher, MPH, is an Epidemiologist; in Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC
| | - Joanne L. Andreadis
- Joanne L. Andreadis, PhD, is Associate Director for Science, at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Jasmine Chaitram
- Jasmine Chaitram, MPH, is Branch Chief, at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Matthew R. Mauldin
- Matthew R. Mauldin, PhD, is Health Scientists, Office of Readiness and Response; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Reynolds M. Salerno
- Reynolds M. Salerno, PhD, is Director, Division of Laboratory Systems; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Jarad Schiffer
- Jarad Schiffer, MS, is Health Scientists, Office of Readiness and Response; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Adi V. Gundlapalli
- Adi V. Gundlapalli, MD, PhD, is a Senior Advisor, Data Readiness and Response, Office of Public Health Data, Surveillance, and Technology; at the US Centers for Disease Control and Prevention, Atlanta, GA
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Li C, Wang W, Zhang X, Xiao P, Li Z, Wang P, Shi N, Zhou H, Lu H, Gao X, Zhang H, Jin N. Metavirome Analysis and Identification of Midge-Borne Viruses from Yunnan Province, China, in 2021. Viruses 2023; 15:1817. [PMID: 37766224 PMCID: PMC10535587 DOI: 10.3390/v15091817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/24/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Midges are widely distributed globally and can transmit various human and animal diseases through blood-sucking. As part of this study, 259,300 midges were collected from four districts in Yunnan province, China, to detect the viral richness and diversity using metavirome analysis techniques. As many as 26 virus families were detected, and the partial sequences of bluetongue virus (BTV), dengue virus (DENV), and Getah virus (GETV) were identified by phylogenetic analysis and PCR amplification. Two BTV gene fragments, 866 bps for the VP2 gene of BTV type 16 and 655 bps for the VP5 gene of BTV type 21, were amplified. The nucleotide sequence identities of the two amplified BTV fragments were 94.46% and 98.81%, respectively, with two classical BTV-16 (GenBank: JN671907) and BTV-21 strains (GenBank: MK250961) isolated in Yunnan province. Furthermore, the BTV-16 DH2021 strain was successfully isolated in C6/36 cells, and the peak value of the copy number reached 3.13 × 107 copies/μL after five consecutive BHK-21 cell passages. Moreover, two 2054 bps fragments including the E gene of DENV genotype Asia II were amplified and shared the highest identity with the DENV strain isolated in New Guinea in 1944. A length of 656 bps GETV gene sequence encoded the partial capsid protein, and it shared the highest identity of 99.68% with the GETV isolated from Shandong province, China, in 2017. Overall, this study emphasizes the importance of implementing prevention and control strategies for viral diseases transmitted by midges in China.
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Affiliation(s)
- Chenghui Li
- College of Agriculture, Yanbian University, Yanji 133002, China; (C.L.); (X.G.)
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (X.Z.); (Z.L.); (P.W.); (H.L.)
| | - Wei Wang
- Institute of Virology, Wenzhou University, Wenzhou 325035, China; (W.W.); (P.X.)
| | - Xuancheng Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (X.Z.); (Z.L.); (P.W.); (H.L.)
- College of Veterinary Medicine, Jilin University, Changchun 130062, China;
| | - Pengpeng Xiao
- Institute of Virology, Wenzhou University, Wenzhou 325035, China; (W.W.); (P.X.)
| | - Zhuoxin Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (X.Z.); (Z.L.); (P.W.); (H.L.)
| | - Peng Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (X.Z.); (Z.L.); (P.W.); (H.L.)
| | - Ning Shi
- College of Veterinary Medicine, Jilin University, Changchun 130062, China;
| | - Hongning Zhou
- Yunnan Institute of Parasitic Diseases, Puer 665000, China;
| | - Huijun Lu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (X.Z.); (Z.L.); (P.W.); (H.L.)
| | - Xu Gao
- College of Agriculture, Yanbian University, Yanji 133002, China; (C.L.); (X.G.)
| | - He Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (X.Z.); (Z.L.); (P.W.); (H.L.)
| | - Ningyi Jin
- College of Agriculture, Yanbian University, Yanji 133002, China; (C.L.); (X.G.)
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (X.Z.); (Z.L.); (P.W.); (H.L.)
- Institute of Virology, Wenzhou University, Wenzhou 325035, China; (W.W.); (P.X.)
- College of Veterinary Medicine, Jilin University, Changchun 130062, China;
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3
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Wang X, Stelzer-Braid S, Scotch M, Rawlinson WD. Detection of respiratory viruses directly from clinical samples using next-generation sequencing: A literature review of recent advances and potential for routine clinical use. Rev Med Virol 2022; 32:e2375. [PMID: 35775736 PMCID: PMC9539958 DOI: 10.1002/rmv.2375] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/01/2022] [Accepted: 06/20/2022] [Indexed: 11/15/2022]
Abstract
Acute respiratory infection is the third most frequent cause of mortality worldwide, causing over 4.25 million deaths annually. Although most diagnosed acute respiratory infections are thought to be of viral origin, the aetiology often remains unclear. The advent of next‐generation sequencing (NGS) has revolutionised the field of virus discovery and identification, particularly in the detection of unknown respiratory viruses. We systematically reviewed the application of NGS technologies for detecting respiratory viruses from clinical samples and outline potential barriers to the routine clinical introduction of NGS. The five databases searched for studies published in English from 01 January 2010 to 01 February 2021, which led to the inclusion of 52 studies. A total of 14 different models of NGS platforms were summarised from included studies. Among these models, second‐generation sequencing platforms (e.g., Illumina sequencers) were used in the majority of studies (41/52, 79%). Moreover, NGS platforms have proven successful in detecting a variety of respiratory viruses, including influenza A/B viruses (9/52, 17%), SARS‐CoV‐2 (21/52, 40%), parainfluenza virus (3/52, 6%), respiratory syncytial virus (1/52, 2%), human metapneumovirus (2/52, 4%), or a viral panel including other respiratory viruses (16/52, 31%). The review of NGS technologies used in previous studies indicates the advantages of NGS technologies in novel virus detection, virus typing, mutation identification, and infection cluster assessment. Although there remain some technical and ethical challenges associated with NGS use in clinical laboratories, NGS is a promising future tool to improve understanding of respiratory viruses and provide a more accurate diagnosis with simultaneous virus characterisation.
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Affiliation(s)
- Xinye Wang
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Sacha Stelzer-Braid
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Matthew Scotch
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.,Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - William D Rawlinson
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
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Suminda GGD, Bhandari S, Won Y, Goutam U, Kanth Pulicherla K, Son YO, Ghosh M. High-throughput sequencing technologies in the detection of livestock pathogens, diagnosis, and zoonotic surveillance. Comput Struct Biotechnol J 2022; 20:5378-5392. [PMID: 36212529 PMCID: PMC9526013 DOI: 10.1016/j.csbj.2022.09.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 12/03/2022] Open
Abstract
Increasing globalization, agricultural intensification, urbanization, and climatic changes have resulted in a significant recent increase in emerging infectious zoonotic diseases. Zoonotic diseases are becoming more common, so innovative, effective, and integrative research is required to better understand their transmission, ecological implications, and dynamics at wildlife-human interfaces. High-throughput sequencing (HTS) methodologies have enormous potential for unraveling these contingencies and improving our understanding, but they are only now beginning to be realized in livestock research. This study investigates the current state of use of sequencing technologies in the detection of livestock pathogens such as bovine, dogs (Canis lupus familiaris), sheep (Ovis aries), pigs (Sus scrofa), horses (Equus caballus), chicken (Gallus gallus domesticus), and ducks (Anatidae) as well as how it can improve the monitoring and detection of zoonotic infections. We also described several high-throughput sequencing approaches for improved detection of known, unknown, and emerging infectious agents, resulting in better infectious disease diagnosis, as well as surveillance of zoonotic infectious diseases. In the coming years, the continued advancement of sequencing technologies will improve livestock research and hasten the development of various new genomic and technological studies on farm animals.
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5
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Zang L, Liu Y, Song X, Cai L, Liu K, Luo T, Zhang R. Unique T4-like phages in high-altitude lakes above 4500 m on the Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 801:149649. [PMID: 34428653 DOI: 10.1016/j.scitotenv.2021.149649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/24/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Viruses are the most abundant biological entities in the biosphere; however, little is known about viral ecology in high altitude lakes. Here, we characterized viruses from 13 lakes, nine of which located ≥4500 m above sea level, on the Tibetan Plateau, the highest plateau on Earth. The abundance of virus-like particle (VLP) in Tibetan lakes ranged from 4.8 ± 0.2 × 105 VLPs mL-1 to 6.0 ± 0.2 × 107 VLPs mL-1 and the virus-to-bacterium ratio was in the lower range of values reported for other lakes. The viral population size was positively correlated with turbidity and negatively correlated with particulate organic carbon concentration. Highly diverse VLP morphologies, including large (~300 nm) morphotypes, were observed. Phylogenetic analysis of T4-like bacteriophages based on major capsid gene (g23) identified a novel viral group, which were detected in abundance in hyposaline and mesosaline Tibetan lakes. Adaptation to lake evolution, water source (glacier-fed or non-glacier-fed) and environmental conditions (e.g., salinity, phosphorus concentration and productivity) are likely responsible for the variation in T4-like myovirus community composition in contrasting Tibetan lakes. This first investigation of viruses in high-altitude alpine lakes above 4500 m could contribute to our understanding of viral ecology in global alpine lakes.
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Affiliation(s)
- Lin Zang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Science, Beijing 100101, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China; University of Chinese Academy of Science, Beijing 100101, China.
| | - Xuanying Song
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Tingwei Luo
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, China.
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Utilizing the VirIdAl Pipeline to Search for Viruses in the Metagenomic Data of Bat Samples. Viruses 2021; 13:v13102006. [PMID: 34696436 PMCID: PMC8541124 DOI: 10.3390/v13102006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/30/2021] [Accepted: 10/02/2021] [Indexed: 12/27/2022] Open
Abstract
According to various estimates, only a small percentage of existing viruses have been discovered, naturally much less being represented in the genomic databases. High-throughput sequencing technologies develop rapidly, empowering large-scale screening of various biological samples for the presence of pathogen-associated nucleotide sequences, but many organisms are yet to be attributed specific loci for identification. This problem particularly impedes viral screening, due to vast heterogeneity in viral genomes. In this paper, we present a new bioinformatic pipeline, VirIdAl, for detecting and identifying viral pathogens in sequencing data. We also demonstrate the utility of the new software by applying it to viral screening of the feces of bats collected in the Moscow region, which revealed a significant variety of viruses associated with bats, insects, plants, and protozoa. The presence of alpha and beta coronavirus reads, including the MERS-like bat virus, deserves a special mention, as it once again indicates that bats are indeed reservoirs for many viral pathogens. In addition, it was shown that alignment-based methods were unable to identify the taxon for a large proportion of reads, and we additionally applied other approaches, showing that they can further reveal the presence of viral agents in sequencing data. However, the incompleteness of viral databases remains a significant problem in the studies of viral diversity, and therefore necessitates the use of combined approaches, including those based on machine learning methods.
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7
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Virome in adult Aedes albopictus captured during different seasons in Guangzhou City, China. Parasit Vectors 2021; 14:415. [PMID: 34407871 PMCID: PMC8371599 DOI: 10.1186/s13071-021-04922-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 08/03/2021] [Indexed: 01/09/2023] Open
Abstract
Background The mosquito Aedes albopictus is an important vector for many pathogens. Understanding the virome in Ae. albopictus is critical for assessing the risk of disease transmission, implementation of vector control measures, and health system strengthening. Methods In this study, viral metagenomic and PCR methods were used to reveal the virome in adult Ae. albopictus captured in different areas and during different seasons in Guangzhou, China. Results The viral composition of adult Ae. albopictus varied mainly between seasons. Over 50 viral families were found, which were specific to vertebrates, invertebrates, plants, fungi, bacteria, and protozoa. In rural areas, Siphoviridae (6.5%) was the most common viral family harbored by mosquitoes captured during winter and spring, while Luteoviridae (1.1%) was the most common viral family harbored by mosquitoes captured during summer and autumn. Myoviridae (7.0% and 1.3%) was the most common viral family in mosquitoes captured in urban areas during all seasons. Hepatitis B virus (HBV) was detected by PCR in a female mosquito pool. The first near full-length HBV genome from Ae. albopictus was amplified, which showed a high level of similarity with human HBV genotype B sequences. Human parechovirus (HPeV) was detected in male and female mosquito pools, and the sequences were clustered with HPeV 1 and 3 sequences. Conclusions Large numbers of viral species were found in adult Ae. albopictus, including viruses from vertebrates, insects, and plants. The viral composition in Ae. albopictus mainly varied between seasons. Herein, we are the first to report the detection of HPeV and HBV in mosquitoes. This study not only provides valuable information for the control and prevention of mosquito-borne diseases, but it also demonstrates the feasibility of xenosurveillance. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-04922-z.
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8
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Advances in monitoring soil microbial community dynamic and function. J Appl Genet 2020; 61:249-263. [PMID: 32062778 DOI: 10.1007/s13353-020-00549-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 01/17/2020] [Accepted: 02/06/2020] [Indexed: 12/22/2022]
Abstract
Microorganisms are vital to the overall ecosystem functioning, stability, and sustainability. Soil fertility and health depend on chemical composition and also on the qualitative and quantitative nature of microorganisms inhabiting it. Historically, denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE), single-strand conformation polymorphism, DNA amplification fingerprinting, amplified ribosomal DNA restriction analysis, terminal restriction fragment length polymorphism, length heterogeneity PCR, and ribosomal intergenic spacer analysis were used to assess soil microbial community structure (SMCS), abundance, and diversity. However, these methods had significant shortcomings and limitations for application in land reclamation monitoring. SMCS has been primarily determined by phospholipid fatty acid (PLFA) analysis. This method provides a direct measure of viable biomass in addition to a biochemical profile of the microbial community. PLFA has limitations such as overlap in the composition of microorganisms and the specificity of PLFAs signature. In recent years, high-throughput next-generation sequencing has dramatically increased the resolution and detectable spectrum of diverse microbial phylotypes from environmental samples and it plays a significant role in microbial ecology studies. Next-generation sequencings using 454, Illumina, SOLiD, and Ion Torrent platforms are rapid and flexible. The two methods, PLFA and next-generation sequencing, are useful in detecting changes in microbial community diversity and structure in different ecosystems. Single-molecule real-time (SMRT) and nanopore sequencing technologies represent third-generation sequencing (TGS) platforms that have been developed to address the shortcomings of second-generation sequencing (SGS). Enzymatic and soil respiration analyses are performed to further determine soil quality and microbial activities. Other valuable methods that are being recently applied to microbial function and structures include NanoSIM, GeoChip, and DNA stable staple isotope probing (DNA-SIP) technologies. They are powerful metagenomics tool for analyzing microbial communities, including their structure, metabolic potential, diversity, and their impact on ecosystem functions. This review is a critical analysis of current methods used in monitoring soil microbial community dynamic and functions.
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Kiselev D, Matsvay A, Abramov I, Dedkov V, Shipulin G, Khafizov K. Current Trends in Diagnostics of Viral Infections of Unknown Etiology. Viruses 2020; 12:E211. [PMID: 32074965 PMCID: PMC7077230 DOI: 10.3390/v12020211] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 12/27/2022] Open
Abstract
Viruses are evolving at an alarming rate, spreading and inconspicuously adapting to cutting-edge therapies. Therefore, the search for rapid, informative and reliable diagnostic methods is becoming urgent as ever. Conventional clinical tests (PCR, serology, etc.) are being continually optimized, yet provide very limited data. Could high throughput sequencing (HTS) become the future gold standard in molecular diagnostics of viral infections? Compared to conventional clinical tests, HTS is universal and more precise at profiling pathogens. Nevertheless, it has not yet been widely accepted as a diagnostic tool, owing primarily to its high cost and the complexity of sample preparation and data analysis. Those obstacles must be tackled to integrate HTS into daily clinical practice. For this, three objectives are to be achieved: (1) designing and assessing universal protocols for library preparation, (2) assembling purpose-specific pipelines, and (3) building computational infrastructure to suit the needs and financial abilities of modern healthcare centers. Data harvested with HTS could not only augment diagnostics and help to choose the correct therapy, but also facilitate research in epidemiology, genetics and virology. This information, in turn, could significantly aid clinicians in battling viral infections.
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Affiliation(s)
- Daniel Kiselev
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- I.M. Sechenov First Moscow State Medical University, 119146 Moscow, Russia
| | - Alina Matsvay
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- Moscow Institute of Physics and Technology, National Research University, 117303 Moscow, Russia
| | - Ivan Abramov
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
| | - Vladimir Dedkov
- Pasteur Institute, Federal Service on Consumers’ Rights Protection and Human Well-Being Surveillance, 197101 Saint-Petersburg, Russia;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119146 Moscow, Russia
| | - German Shipulin
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
| | - Kamil Khafizov
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- Moscow Institute of Physics and Technology, National Research University, 117303 Moscow, Russia
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10
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Han D, Li Z, Li R, Tan P, Zhang R, Li J. mNGS in clinical microbiology laboratories: on the road to maturity. Crit Rev Microbiol 2019; 45:668-685. [PMID: 31691607 DOI: 10.1080/1040841x.2019.1681933] [Citation(s) in RCA: 160] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metagenomic next-generation sequencing (mNGS) is increasingly being applied in clinical laboratories for unbiased culture-independent diagnosis. Whether it can be a next routine pathogen identification tool has become a topic of concern. We review the current implementation of this new technology for infectious disease diagnostics and discuss the feasibility of transforming mNGS into a routine diagnostic test. Since 2008, numerous studies from over 20 countries have revealed the practicality of mNGS in the work-up of undiagnosed infectious diseases. mNGS performs well in identifying rare, novel, difficult-to-detect and coinfected pathogens directly from clinical samples and presents great potential in resistance prediction by sequencing the antibiotic resistance genes, providing new diagnostic evidence that can be used to guide treatment options and improve antibiotic stewardship. Many physicians recognized mNGS as a last resort method to address clinical infection problems. Although several hurdles, such as workflow validation, quality control, method standardisation, and data interpretation, remain before mNGS can be implemented routinely in clinical laboratories, they are temporary and can be overcome by rapidly evolving technologies. With more validated workflows, lower cost and turnaround time, and simplified interpretation criteria, mNGS will be widely accepted in clinical practice. Overall, mNGS is transforming the landscape of clinical microbiology laboratories, and to ensure that it is properly utilised in clinical diagnosis, both physicians and microbiologists should have a thorough understanding of the power and limitations of this method.
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Affiliation(s)
- Dongsheng Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Ziyang Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Rui Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Ping Tan
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
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11
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Zhang D, Lou X, Yan H, Pan J, Mao H, Tang H, Shu Y, Zhao Y, Liu L, Li J, Chen J, Zhang Y, Ma X. Metagenomic analysis of viral nucleic acid extraction methods in respiratory clinical samples. BMC Genomics 2018; 19:773. [PMID: 30359242 PMCID: PMC6202819 DOI: 10.1186/s12864-018-5152-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/09/2018] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Numerous protocols for viral enrichment and genome amplification have been created. However, the direct identification of viral genomes from clinical specimens using next-generation sequencing (NGS) still has its challenges. As a selected viral nucleic acid extraction method may determine the sensitivity and reliability of NGS, it is still valuable to evaluate the extraction efficiency of different extraction kits using clinical specimens directly. RESULTS In this study, we performed qRT-PCR and viral metagenomic analysis of the extraction efficiency of four commonly used Qiagen extraction kits: QIAamp Viral RNA Mini Kit (VRMK), QIAamp MinElute Virus Spin Kit (MVSK), RNeasy Mini Kit (RMK), and RNeasy Plus Micro Kit (RPMK), using a mixed respiratory clinical sample without any pre-treatment. This sample contained an adenovirus (ADV), influenza virus A (Flu A), human parainfluenza virus 3 (PIV3), human coronavirus OC43 (OC43), and human metapneumovirus (HMPV). The quantity and quality of the viral extracts were significantly different among these kits. The highest threshold cycle(Ct)values for ADV and OC43 were obtained by using the RPMK. The MVSK had the lowest Ct values for ADV and PIV3. The RMK revealed the lowest detectability for HMPV and PIV3. The most effective rate of NGS data at 67.47% was observed with the RPMK. The other three kits ranged between 12.1-26.79% effectiveness rates for the NGS data. Most importantly, compared to the other three kits the highest proportion of non-host reads was obtained by the RPMK. The MVSK performed best with the lowest Ct value of 20.5 in the extraction of ADV, while the RMK revealed the best extraction efficiency by NGS analysis. CONCLUSIONS The evaluation of viral nucleic acid extraction efficiency is different between NGS and qRT-PCR analysis. The RPMK was most applicable for the metagenomic analysis of viral RNA and enabled more sensitive identification of the RNA virus genome in respiratory clinical samples. In addition, viral RNA extraction kits were also applicable for metagenomic analysis of the DNA virus. Our results highlighted the importance of nucleic acid extraction kit selection, which has a major impact on the yield and number of viral reads by NGS analysis. Therefore, the choice of extraction method for a given viral pathogen needs to be carefully considered.
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Affiliation(s)
- Dan Zhang
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, 102206, China.,Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Xiuyu Lou
- Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Hao Yan
- Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Junhang Pan
- Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Haiyan Mao
- Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Hongfeng Tang
- Department of Pathology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310013, China
| | - Yan Shu
- Department of Pathology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310013, China
| | - Yun Zhao
- Department of Pathology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310013, China
| | - Lei Liu
- Department of Pathology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310013, China
| | - Junping Li
- Department of Pathology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310013, China
| | - Jiang Chen
- College Of Medical Technology, Zhejiang Chinese Medical University, Hangzhou, 310013, China
| | - Yanjun Zhang
- Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China.
| | - Xuejun Ma
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, 102206, China.
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12
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Xiao P, Han J, Zhang Y, Li C, Guo X, Wen S, Tian M, Li Y, Wang M, Liu H, Ren J, Zhou H, Lu H, Jin N. Metagenomic Analysis of Flaviviridae in Mosquito Viromes Isolated From Yunnan Province in China Reveals Genes From Dengue and Zika Viruses. Front Cell Infect Microbiol 2018; 8:359. [PMID: 30406038 PMCID: PMC6207848 DOI: 10.3389/fcimb.2018.00359] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 09/24/2018] [Indexed: 12/21/2022] Open
Abstract
More than 6,000 mosquitoes of six species from six sites were collected and tested for their virome using metagenomics sequencing and bioinformatic analysis. The identified viral sequences belonged to more than 50 viral families. The results were verified by PCR of selected viruses in all mosquitoes, followed by phylogenetic analysis. In the present study, we identified the partial dengue virus (DENV), Zika virus (ZIKV), and Japanese encephalitis virus (JEV) sequences in mosquitoes. Metagenomic analysis and the PCR amplification revealed three DENV sequences, one of which encodes a partial envelope protein. Two ZIKV sequences both encoding partial nonstructural protein 3 and one JEV sequence encoding the complete envelope protein were identified. There was variability in the viral titers of the newly isolated virus JEV-China/YN2016-1 of different passage viruses. The newly identified Zika virus gene from ZIKV-China/YN2016-1 was an Asian genotype and shared the highest nucleotide sequence identity (97.1%) with a ZIKV sequence from Thailand isolated in 2004. Phylogenetic analysis of ZIKV-China/YN2016-1 and ZIKV-China/YN2016-2 with known Flavivirus genes indicated that ZIKV has propagated in Yunnan province, China.
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Affiliation(s)
- Pengpeng Xiao
- Yanbian University Medical College, Yanji, China.,Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Jicheng Han
- Yanbian University Medical College, Yanji, China.,Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Ying Zhang
- College of Veterinary Medicine, College of Animal Science, Jilin University, Changchun, China
| | - Chenghui Li
- Yanbian University Medical College, Yanji, China.,Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Xiaofang Guo
- Yunnan Institute of Parasitic Diseases, Simao, China
| | - Shubo Wen
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Mingyao Tian
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Yiquan Li
- Yanbian University Medical College, Yanji, China.,Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Maopeng Wang
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Institute of Virology, Wenzhou University, Wenzhou, China
| | - Hao Liu
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Jingqiang Ren
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Division of Economic Animal Epidemic, Institute of Special Economic Animal and Plant Sciences, Changchun, China
| | - Hongning Zhou
- Yunnan Institute of Parasitic Diseases, Simao, China
| | - Huijun Lu
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Ningyi Jin
- Yanbian University Medical College, Yanji, China.,Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
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13
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Xiao P, Li C, Zhang Y, Han J, Guo X, Xie L, Tian M, Li Y, Wang M, Liu H, Ren J, Zhou H, Lu H, Jin N. Metagenomic Sequencing From Mosquitoes in China Reveals a Variety of Insect and Human Viruses. Front Cell Infect Microbiol 2018; 8:364. [PMID: 30406041 PMCID: PMC6202873 DOI: 10.3389/fcimb.2018.00364] [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: 04/13/2018] [Accepted: 10/01/2018] [Indexed: 12/18/2022] Open
Abstract
We collected 8,700 mosquitoes in three sites in China, which belonged to seven species. Their viromes were tested using metagenomic sequencing and bioinformatic analysis. The abundant viral sequences were detected and annotated belonging to more than 50 viral taxonomic families. The results were verified by PCR, followed by phylogenetic analysis. In the present study, we identified partial viral genes of dengue virus (DENV), a novel circovirus (CCV), densovirus (DNV), Japanese encephalitis virus (JEV), and Wuhan mosquito virus (WMV) in mosquitoes. Metagenomic analysis and PCR amplification revealed three DENV sequences, which were as homologous to the NS3 gene of DENV from Singapore isolated in 2005, with at least 91% nucleotide (nt) identity. Seven fragments of JEV encoding structural proteins were identified belonging to genotype I. They all shared high homology with structural protein genes of JEV isolated from Laos in 2009. The production of infectious virus particles of the newly isolated virus YunnanJEV2017-4 increased after passage from the BHK-21 cell line to the Vero cell line. Novel circovirus-related genes were identified and as being related to an unnamed gene of a mosquito circovirus (MCCV) sequence from the USA isolated in 2011, with at least 41% nt identity: this distant relationship suggests that the parent virus might belong to a novel circovirus genus. Additionally, numerous known viruses and some unknown viruses were also detected in mosquitoes from Yunnan province, China, which will be tested for propagation.
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Affiliation(s)
- Pengpeng Xiao
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Yanbian University Medical College, Yanji, China.,Institute of Virology, Wenzhou University, Wenzhou, China
| | - Chenghui Li
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Yanbian University Medical College, Yanji, China
| | - Ying Zhang
- College of Veterinary Medicine, College of Animal Science, Jilin University, Changchun, China
| | - Jicheng Han
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Yanbian University Medical College, Yanji, China
| | - Xiaofang Guo
- Yunnan Institute of Parasitic Diseases, Simao, China
| | - Lv Xie
- Yunnan Institute of Parasitic Diseases, Simao, China
| | - Mingyao Tian
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Yiquan Li
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Yanbian University Medical College, Yanji, China
| | - Maopeng Wang
- Institute of Virology, Wenzhou University, Wenzhou, China
| | - Hao Liu
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Jingqiang Ren
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Division of Economic Animal Epidemic, Institute of Special Economic Animal and Plant Sciences, Changchun, China
| | - Hongning Zhou
- Yunnan Institute of Parasitic Diseases, Simao, China
| | - Huijun Lu
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Ningyi Jin
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Yanbian University Medical College, Yanji, China
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14
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Viral Metagenomics Approaches for High-Resolution Screening of Multiplexed Arthropod and Plant Viral Communities. Methods Mol Biol 2018; 1746:77-95. [PMID: 29492888 DOI: 10.1007/978-1-4939-7683-6_7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Viral metagenomic approaches have become essential for culture-independent and sequence-independent viral detection and characterization. This chapter describes an accurate and efficient approach to (1) concentrate viral particles from arthropods and plants, (2) remove contaminating non-encapsidated nucleic acids, (3) extract and amplify both viral DNA and RNA, and (4) analyze high-throughput sequencing (HTS) data by bioinformatics. Using this approach, up to 96 arthropod or plant samples can be multiplexed in a single HTS library.
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15
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Schlaberg R, Chiu CY, Miller S, Procop GW, Weinstock G. Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection. Arch Pathol Lab Med 2017; 141:776-786. [PMID: 28169558 DOI: 10.5858/arpa.2016-0539-ra] [Citation(s) in RCA: 319] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - Metagenomic sequencing can be used for detection of any pathogens using unbiased, shotgun next-generation sequencing (NGS), without the need for sequence-specific amplification. Proof-of-concept has been demonstrated in infectious disease outbreaks of unknown causes and in patients with suspected infections but negative results for conventional tests. Metagenomic NGS tests hold great promise to improve infectious disease diagnostics, especially in immunocompromised and critically ill patients. OBJECTIVE - To discuss challenges and provide example solutions for validating metagenomic pathogen detection tests in clinical laboratories. A summary of current regulatory requirements, largely based on prior guidance for NGS testing in constitutional genetics and oncology, is provided. DATA SOURCES - Examples from 2 separate validation studies are provided for steps from assay design, and validation of wet bench and bioinformatics protocols, to quality control and assurance. CONCLUSIONS - Although laboratory and data analysis workflows are still complex, metagenomic NGS tests for infectious diseases are increasingly being validated in clinical laboratories. Many parallels exist to NGS tests in other fields. Nevertheless, specimen preparation, rapidly evolving data analysis algorithms, and incomplete reference sequence databases are idiosyncratic to the field of microbiology and often overlooked.
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Affiliation(s)
- Robert Schlaberg
- From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock)
| | - Charles Y Chiu
- From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock)
| | - Steve Miller
- From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock)
| | - Gary W Procop
- From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock)
| | - George Weinstock
- From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock)
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- From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock)
| | -
- From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock)
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16
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Ali R, Blackburn RM, Kozlakidis Z. Next-Generation Sequencing and Influenza Virus: A Short Review of the Published Implementation Attempts. HAYATI JOURNAL OF BIOSCIENCES 2016. [DOI: 10.1016/j.hjb.2016.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
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17
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Hiraoka S, Yang CC, Iwasaki W. Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond. Microbes Environ 2016; 31:204-12. [PMID: 27383682 PMCID: PMC5017796 DOI: 10.1264/jsme2.me16024] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Metagenomic approaches are now commonly used in microbial ecology to study microbial communities in more detail, including many strains that cannot be cultivated in the laboratory. Bioinformatic analyses make it possible to mine huge metagenomic datasets and discover general patterns that govern microbial ecosystems. However, the findings of typical metagenomic and bioinformatic analyses still do not completely describe the ecology and evolution of microbes in their environments. Most analyses still depend on straightforward sequence similarity searches against reference databases. We herein review the current state of metagenomics and bioinformatics in microbial ecology and discuss future directions for the field. New techniques will allow us to go beyond routine analyses and broaden our knowledge of microbial ecosystems. We need to enrich reference databases, promote platforms that enable meta- or comprehensive analyses of diverse metagenomic datasets, devise methods that utilize long-read sequence information, and develop more powerful bioinformatic methods to analyze data from diverse perspectives.
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Affiliation(s)
- Satoshi Hiraoka
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo
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18
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Propionibacterium acnes: Disease-Causing Agent or Common Contaminant? Detection in Diverse Patient Samples by Next-Generation Sequencing. J Clin Microbiol 2016; 54:980-7. [PMID: 26818667 PMCID: PMC4809928 DOI: 10.1128/jcm.02723-15] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/16/2016] [Indexed: 01/01/2023] Open
Abstract
Propionibacterium acnes is the most abundant bacterium on human skin, particularly in sebaceous areas. P. acnes is suggested to be an opportunistic pathogen involved in the development of diverse medical conditions but is also a proven contaminant of human clinical samples and surgical wounds. Its significance as a pathogen is consequently a matter of debate. In the present study, we investigated the presence of P. acnes DNA in 250 next-generation sequencing data sets generated from 180 samples of 20 different sample types, mostly of cancerous origin. The samples were subjected to either microbial enrichment, involving nuclease treatment to reduce the amount of host nucleic acids, or shotgun sequencing. We detected high proportions of P. acnes DNA in enriched samples, particularly skin tissue-derived and other tissue samples, with the levels being higher in enriched samples than in shotgun-sequenced samples. P. acnes reads were detected in most samples analyzed, though the proportions in most shotgun-sequenced samples were low. Our results show that P. acnes can be detected in practically all sample types when molecular methods, such as next-generation sequencing, are employed. The possibility of contamination from the patient or other sources, including laboratory reagents or environment, should therefore always be considered carefully when P. acnes is detected in clinical samples. We advocate that detection of P. acnes always be accompanied by experiments validating the association between this bacterium and any clinical condition.
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19
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Abstract
The characterization of the human blood-associated viral community (also called blood virome) is essential for epidemiological surveillance and to anticipate new potential threats for blood transfusion safety. Currently, the risk of blood-borne agent transmission of well-known viruses (HBV, HCV, HIV and HTLV) can be considered as under control in high-resource countries. However, other viruses unknown or unsuspected may be transmitted to recipients by blood-derived products. This is particularly relevant considering that a significant proportion of transfused patients are immunocompromised and more frequently subjected to fatal outcomes. Several measures to prevent transfusion transmission of unknown viruses have been implemented including the exclusion of at-risk donors, leukocyte reduction of donor blood, and physicochemical treatment of the different blood components. However, up to now there is no universal method for pathogen inactivation, which would be applicable for all types of blood components and, equally effective for all viral families. In addition, among available inactivation procedures of viral genomes, some of them are recognized to be less effective on non-enveloped viruses, and inadequate to inactivate higher viral titers in plasma pools or derivatives. Given this, there is the need to implement new methodologies for the discovery of unknown viruses that may affect blood transfusion. Viral metagenomics combined with High Throughput Sequencing appears as a promising approach for the identification and global surveillance of new and/or unexpected viruses that could impair blood transfusion safety.
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Affiliation(s)
- V Sauvage
- Département d'études des agents transmissibles par le sang, Institut national de la transfusion sanguine (INTS), Centre national de référence des hépatites virales B et C et du VIH en transfusion, 75015 Paris, France.
| | - M Eloit
- PathoQuest, bâtiment François-Jacob, 25, rue du Dr-Roux, 75015 Paris, France; Inserm U1117, Biology of Infection Unit, Laboratory of Pathogen Discovery, Institut Pasteur, 28, rue du Docteur-Roux, 75724 Paris, France
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20
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Mourier T, Mollerup S, Vinner L, Hansen TA, Kjartansdóttir KR, Guldberg Frøslev T, Snogdal Boutrup T, Nielsen LP, Willerslev E, Hansen AJ. Characterizing novel endogenous retroviruses from genetic variation inferred from short sequence reads. Sci Rep 2015; 5:15644. [PMID: 26493184 PMCID: PMC4616055 DOI: 10.1038/srep15644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 09/21/2015] [Indexed: 02/06/2023] Open
Abstract
From Illumina sequencing of DNA from brain and liver tissue from the lion, Panthera leo, and tumor samples from the pike-perch, Sander lucioperca, we obtained two assembled sequence contigs with similarity to known retroviruses. Phylogenetic analyses suggest that the pike-perch retrovirus belongs to the epsilonretroviruses, and the lion retrovirus to the gammaretroviruses. To determine if these novel retroviral sequences originate from an endogenous retrovirus or from a recently integrated exogenous retrovirus, we assessed the genetic diversity of the parental sequences from which the short Illumina reads are derived. First, we showed by simulations that we can robustly infer the level of genetic diversity from short sequence reads. Second, we find that the measures of nucleotide diversity inferred from our retroviral sequences significantly exceed the level observed from Human Immunodeficiency Virus infections, prompting us to conclude that the novel retroviruses are both of endogenous origin. Through further simulations, we rule out the possibility that the observed elevated levels of nucleotide diversity are the result of co-infection with two closely related exogenous retroviruses.
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Affiliation(s)
- Tobias Mourier
- Centre for GeoGenetics, Museum of Natural History of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Sarah Mollerup
- Centre for GeoGenetics, Museum of Natural History of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Museum of Natural History of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Arn Hansen
- Centre for GeoGenetics, Museum of Natural History of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Kristín Rós Kjartansdóttir
- Centre for GeoGenetics, Museum of Natural History of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Tobias Guldberg Frøslev
- Centre for GeoGenetics, Museum of Natural History of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Torsten Snogdal Boutrup
- Section for Virology, National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
| | - Lars Peter Nielsen
- Department for Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Museum of Natural History of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Anders J Hansen
- Centre for GeoGenetics, Museum of Natural History of Denmark, University of Copenhagen, Copenhagen, Denmark
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21
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Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing. Sci Rep 2015; 5:13201. [PMID: 26285800 PMCID: PMC4541070 DOI: 10.1038/srep13201] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 07/14/2015] [Indexed: 01/05/2023] Open
Abstract
Although nearly one fifth of all human cancers have an infectious aetiology, the causes for the majority of cancers remain unexplained. Despite the enormous data output from high-throughput shotgun sequencing, viral DNA in a clinical sample typically constitutes a proportion of host DNA that is too small to be detected. Sequence variation among virus genomes complicates application of sequence-specific, and highly sensitive, PCR methods. Therefore, we aimed to develop and characterize a method that permits sensitive detection of sequences despite considerable variation. We demonstrate that our low-stringency in-solution hybridization method enables detection of <100 viral copies. Furthermore, distantly related proviral sequences may be enriched by orders of magnitude, enabling discovery of hitherto unknown viral sequences by high-throughput sequencing. The sensitivity was sufficient to detect retroviral sequences in clinical samples. We used this method to conduct an investigation for novel retrovirus in samples from three cancer types. In accordance with recent studies our investigation revealed no retroviral infections in human B-cell lymphoma cells, cutaneous T-cell lymphoma or colorectal cancer biopsies. Nonetheless, our generally applicable method makes sensitive detection possible and permits sequencing of distantly related sequences from complex material.
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22
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Abstract
Respiratory tract infection increases the risk of secondary bacterial infection and causes mortality. Despite advances in the field of targeted molecular diagnostics, there are still failed attempts in identifying a valid causative etiological agent in a large proportion of respiratory tract infections. To date, a comprehensive list of human respiratory infection-associated eukaryotic viruses has been identified. However, there has been little progress towards the characterisation of the viruses that infect bacteria (phages), which are capable of mediating the transfer of virulence genes into non-pathogenic bacterial species to cause respiratory tract infections. With the advent of next-generation-sequencing, the application of an unbiased comparative metagenomic survey on the viral communities within the human respiratory tract may reveal to us how the phage virome changes between healthy individuals and respiratory tract infection patients. With this useful information, it will be feasible to develop an alternative phage-based diagnostic panel for respiratory tract infections. The review herein presents the current status of human airway microbiome research and highlights potential gaps which can be translated into research possibilities for future work on respiratory tract infection diagnosis.
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Affiliation(s)
- Chun Kiat Lee
- 1School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA, Australia2Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, Singapore
| | - Stephen James Bent
- 3The Robinson Research Institute, School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide 5005, Australia
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Wang Y, Wang H, Xu K, Ni P, Zhang H, Ma J, Yang H, Xu F. A survey of overlooked viral infections in biological experiment systems. PLoS One 2014; 9:e105348. [PMID: 25144530 PMCID: PMC4140767 DOI: 10.1371/journal.pone.0105348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 07/23/2014] [Indexed: 12/04/2022] Open
Abstract
It is commonly accepted that there are many unknown viruses on the planet. For the known viruses, do we know their prevalence, even in our experimental systems? Here we report a virus survey using recently published small (s)RNA sequencing datasets. The sRNA reads were assembled and contigs were screened for virus homologues against the NCBI nucleotide (nt) database using the BLASTn program. To our surprise, approximately 30% (28 out of 94) of publications had highly scored viral sequences in their datasets. Among them, only two publications reported virus infections. Though viral vectors were used in some of the publications, virus sequences without any identifiable source appeared in more than 20 publications. By determining the distributions of viral reads and the antiviral RNA interference (RNAi) pathways using the sRNA profiles, we showed evidence that many of the viruses identified were indeed infecting and generated host RNAi responses. As virus infections affect many aspects of host molecular biology and metabolism, the presence and impact of viruses needs to be actively investigated in experimental systems.
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Affiliation(s)
- Yajing Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
| | - Hui Wang
- NERC/Centre for Ecology and Hydrology, Wallingford, Oxfordshire, United Kingdom
- Beijing Genome Institute (BGI), Yantian District, Shenzhen, China
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Kunhan Xu
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China
| | - Peixiang Ni
- BGI-Tianjin, Airport Economic Area, Tianjin, China
| | - Huan Zhang
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China
| | - Jinmin Ma
- Beijing Genome Institute (BGI), Yantian District, Shenzhen, China
| | - Huanming Yang
- Beijing Genome Institute (BGI), Yantian District, Shenzhen, China
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Prince Aljawhra Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
- James D. Watson Institute of Genome Science, Hangzhou, China
| | - Feng Xu
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China
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Quiñones-Mateu ME, Avila S, Reyes-Teran G, Martinez MA. Deep sequencing: becoming a critical tool in clinical virology. J Clin Virol 2014; 61:9-19. [PMID: 24998424 DOI: 10.1016/j.jcv.2014.06.013] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/12/2014] [Accepted: 06/14/2014] [Indexed: 02/07/2023]
Abstract
Population (Sanger) sequencing has been the standard method in basic and clinical DNA sequencing for almost 40 years; however, next-generation (deep) sequencing methodologies are now revolutionizing the field of genomics, and clinical virology is no exception. Deep sequencing is highly efficient, producing an enormous amount of information at low cost in a relatively short period of time. High-throughput sequencing techniques have enabled significant contributions to multiples areas in virology, including virus discovery and metagenomics (viromes), molecular epidemiology, pathogenesis, and studies of how viruses to escape the host immune system and antiviral pressures. In addition, new and more affordable deep sequencing-based assays are now being implemented in clinical laboratories. Here, we review the use of the current deep sequencing platforms in virology, focusing on three of the most studied viruses: human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus.
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Affiliation(s)
- Miguel E Quiñones-Mateu
- University Hospital Translational Laboratory, University Hospitals Case Medical Center, Cleveland, OH, USA; Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Santiago Avila
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Gustavo Reyes-Teran
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Miguel A Martinez
- Fundació irsicaixa, Universitat Autònoma de Barcelona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
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Bialasiewicz S, McVernon J, Nolan T, Lambert SB, Zhao G, Wang D, Nissen MD, Sloots TP. Detection of a divergent Parainfluenza 4 virus in an adult patient with influenza like illness using next-generation sequencing. BMC Infect Dis 2014; 14:275. [PMID: 24885416 PMCID: PMC4038074 DOI: 10.1186/1471-2334-14-275] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 04/11/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Human Parainfluenza viruses are a common cause of both upper and lower respiratory tract infections, particularly in children. Of the four Parainfluenza virus serotypes, Parainfluenza 4 is least well characterised from both the clinical, epidemiological and genetic perspectives. METHODS Flocked nose or throat swabs from a previous study investigating viral prevalence in community-based adults suffering from influenza like illness were used as the basis for this study. Samples in which no virus was detected using a 16 viral respiratory pathogen real-time PCR panel were barcoded and pyrosequenced using the Roche 454 GS FLX Titanium chemistry. The sequences were analysed using the VirusHunter bioinformatic pipeline. Sanger sequencing was used to complete the detected Parainfluenza 4 coding region. RESULTS A variant Parainfluenza 4 subtype b strain (QLD-01) was discovered in an otherwise healthy adult who presented with influenza like illness. Strain QLD-01 shared genomic similarities with both a and b subtypes. The extent of divergence of this genome from the 5 available whole Parainfluenza 4 genomes impacted the predicted binding efficiencies of the majority of published Parainfluenza 4 PCR assays. CONCLUSIONS These findings further support a possible role for Parainfluenza 4 in the aetiology of adult respiratory disease within the community setting, and highlight the caution needed to be used in designing PCR assays from limited sequence information or in using proprietary commercial PCR assays.
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Affiliation(s)
- Seweryn Bialasiewicz
- Queensland Children’s Medical Research Institute, The University of Queensland, Brisbane, Qld, Australia
- Queensland Paediatric Infectious Diseases Laboratory, The Royal Children’s Hospital, Brisbane, Qld, Australia
- Sir Albert Sakzewski Virus Research Centre, Building C28, Back Rd, Herston, QLD 4029, Australia
| | - Jodie McVernon
- Murdoch Children’s Research Institute & Melbourne School of Population Health, The University of Melbourne, Parkville, Vic, Australia
| | - Terry Nolan
- Murdoch Children’s Research Institute & Melbourne School of Population Health, The University of Melbourne, Parkville, Vic, Australia
| | - Stephen B Lambert
- Queensland Children’s Medical Research Institute, The University of Queensland, Brisbane, Qld, Australia
| | - Guoyan Zhao
- Departments of Molecular Microbiology and Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - David Wang
- Departments of Molecular Microbiology and Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael D Nissen
- Queensland Children’s Medical Research Institute, The University of Queensland, Brisbane, Qld, Australia
- Queensland Paediatric Infectious Diseases Laboratory, The Royal Children’s Hospital, Brisbane, Qld, Australia
| | - Theo P Sloots
- Queensland Children’s Medical Research Institute, The University of Queensland, Brisbane, Qld, Australia
- Queensland Paediatric Infectious Diseases Laboratory, The Royal Children’s Hospital, Brisbane, Qld, Australia
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