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Li Z, Tang C, Li Y, Zhang Y, Wang G, Peng R, Huang Y, Hu X, Xin H, Cao X, Shen L, Guo T, He Y, Fen B, Huang J, Liang JG, Cui X, Niu L, Yang J, Yang F, Lu G, Gao L, Jin Q, Zhao M, Yin F, Du J. Virome survey of the bat, Rhinolophus affinis, in Hainan Province, China. Microbes Infect 2024; 26:105331. [PMID: 38537769 DOI: 10.1016/j.micinf.2024.105331] [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: 12/08/2023] [Revised: 03/13/2024] [Accepted: 03/21/2024] [Indexed: 04/01/2024]
Abstract
Bats are important mammal reservoirs of zoonotic pathogens. However, due to research limitations involving species, locations, pathogens, or sample types, the full diversity of viruses in bats remains to be discovered. We used next-generation sequencing technology to characterize the mammalian virome and analyze the phylogenetic evolution and diversity of mammalian viruses carried by bats from Haikou City and Tunchang County in Hainan Province, China. We collected 200 pharyngeal swab and anal swab samples from Rhinolophus affinis, combining them into nine pools based on the sample type and collection location. We subjected the samples to next-generation sequencing and conducted bioinformatics analysis. All samples were screened via specific PCR and phylogenetic analysis. The diverse viral reads, closely related to mammals, were assigned into 17 viral families. We discovered many novel bat viruses and identified some closely related to known human/animal pathogens. In the current study, 6 complete genomes and 2 partial genomic sequences of 6 viral families and 8 viral genera have been amplified, among which 5 strains are suggested to be new virus species. These included coronavirus, pestivirus, bastrovirus, bocavirus, papillomavirus, parvovirus, and paramyxovirus. The primary finding is that a SADS-related CoV and a HoBi-like pestivirus identified in R. affinis in Hainan Province could be pathogenic to livestock. This study expands our understanding of bats as a virus reservoir, providing a basis for further research on the transmission of viruses from bats to humans.
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Affiliation(s)
- Zihan Li
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Department of Pathogen Biology, Hainan Medical University, Haikou, 571199, China
| | - Chuanning Tang
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; Department of Pathogen Biology, Hainan Medical University, Haikou, 571199, China
| | - Youyou Li
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; Department of Pathogen Biology, Hainan Medical University, Haikou, 571199, China; The Affiliated Cancer Hospital of Guizhou Medical University, China
| | - Yun Zhang
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; Department of Pathogen Biology, Hainan Medical University, Haikou, 571199, China
| | - Gaoyu Wang
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; Department of Pathogen Biology, Hainan Medical University, Haikou, 571199, China
| | - Ruoyan Peng
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; Department of Pathogen Biology, Hainan Medical University, Haikou, 571199, China
| | - Yi Huang
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; Department of Pathogen Biology, Hainan Medical University, Haikou, 571199, China
| | - Xiaoyuan Hu
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; Department of Pathogen Biology, Hainan Medical University, Haikou, 571199, China
| | - Henan Xin
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Xuefang Cao
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Lingyu Shen
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Tonglei Guo
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Yijun He
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Boxuan Fen
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Juanjuan Huang
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Jian Guo Liang
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Xiuji Cui
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; Department of Pathogen Biology, Hainan Medical University, Haikou, 571199, China
| | - Lina Niu
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; Department of Pathogen Biology, Hainan Medical University, Haikou, 571199, China
| | - Jian Yang
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Fan Yang
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Gang Lu
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; Department of Pathogen Biology, Hainan Medical University, Haikou, 571199, China
| | - Lei Gao
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Mingming Zhao
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; TCM School of Hainan Medical University, Haikou, 571199, China.
| | - Feifei Yin
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; Department of Pathogen Biology, Hainan Medical University, Haikou, 571199, China.
| | - Jiang Du
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
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2
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Cancela F, Marandino A, Panzera Y, Betancour G, Mirazo S, Arbiza J, Ramos N. A combined approach of rolling-circle amplification-single site restriction endonuclease digestion followed by next generation sequencing to characterize the whole genome and intra-host variants of human Torque teno virus. Virus Res 2023; 323:198974. [PMID: 36272542 PMCID: PMC10194382 DOI: 10.1016/j.virusres.2022.198974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022]
Abstract
Torque Teno Virus (TTV) was initially associated with post-transfusion hepatitis, but growing evidence of its ubiquity in humans is compatible to no apparent clinical significance. TTV is a small non-enveloped virus with a circular single-negative-stranded DNA genome, belonging to the Anelloviridae family. Currently, TTVs are divided in seven phylogenetic groups and are further classified into 21 species. Studies about diversity of TTV in different conditions are receiving increasing interest and in this sense, sequencing of whole genomes for better genetic characterization becomes even more important. Since its discovery in 1997, few TTV complete genomes have been reported worldwide. This is probably due, among other reasons, to the great genetic heterogeneity among TTV strains that prevents its amplification and sequencing by conventional PCR and cloning methods. In addition, although metagenomics approach is useful in these cases, it remains a challenging tool for viromic analysis. With the aim of contributing to the expansion of the TTV whole genomes dataset and to study intra-host variants, we employed a methodology that combined a rolling-circle amplification approach followed by EcoRI digestion, generating a DNA fragment of ∼4Kb consistent with TTV genome length which was sequenced by Illumina next generation sequencing. A genogroup 3 full-length consensus TTV genome was obtained and co-infection with other species (at least those with a single EcoRI cleavage site) was not identified. Additionally, bioinformatics analysis allowed to identify the spectrum of TTV intra-host variants which provides evidence of a complex evolution dynamics of these DNA circular viruses, similarly to what occurs with RNA viruses.
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Affiliation(s)
- Florencia Cancela
- Sección Virología, Instituto de Biología e Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ana Marandino
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la Republica, Montevideo, Uruguay
| | - Yanina Panzera
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la Republica, Montevideo, Uruguay
| | - Gabriela Betancour
- Sección Virología, Instituto de Biología e Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Santiago Mirazo
- Sección Virología, Instituto de Biología e Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay; Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la Republica, Montevideo, Uruguay
| | - Juan Arbiza
- Sección Virología, Instituto de Biología e Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Natalia Ramos
- Sección Virología, Instituto de Biología e Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.
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3
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Kumar S, Kumar GS, Maitra SS, Malý P, Bharadwaj S, Sharma P, Dwivedi VD. Viral informatics: bioinformatics-based solution for managing viral infections. Brief Bioinform 2022; 23:6659740. [PMID: 35947964 DOI: 10.1093/bib/bbac326] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 06/26/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Several new viral infections have emerged in the human population and establishing as global pandemics. With advancements in translation research, the scientific community has developed potential therapeutics to eradicate or control certain viral infections, such as smallpox and polio, responsible for billions of disabilities and deaths in the past. Unfortunately, some viral infections, such as dengue virus (DENV) and human immunodeficiency virus-1 (HIV-1), are still prevailing due to a lack of specific therapeutics, while new pathogenic viral strains or variants are emerging because of high genetic recombination or cross-species transmission. Consequently, to combat the emerging viral infections, bioinformatics-based potential strategies have been developed for viral characterization and developing new effective therapeutics for their eradication or management. This review attempts to provide a single platform for the available wide range of bioinformatics-based approaches, including bioinformatics methods for the identification and management of emerging or evolved viral strains, genome analysis concerning the pathogenicity and epidemiological analysis, computational methods for designing the viral therapeutics, and consolidated information in the form of databases against the known pathogenic viruses. This enriched review of the generally applicable viral informatics approaches aims to provide an overview of available resources capable of carrying out the desired task and may be utilized to expand additional strategies to improve the quality of translation viral informatics research.
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Affiliation(s)
- Sanjay Kumar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | - Geethu S Kumar
- Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, Uttar Pradesh, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | | | - Petr Malý
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Shiv Bharadwaj
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Vivek Dhar Dwivedi
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India.,Institute of Advanced Materials, IAAM, 59053 Ulrika, Sweden
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4
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Barber RM, Li Q, Levine JM, Ruone SJ, Levine GJ, Kenny P, Tong S, Schatzberg SJ. Screening for Viral Nucleic Acids in the Cerebrospinal Fluid of Dogs With Central Nervous System Inflammation. Front Vet Sci 2022; 9:850510. [PMID: 35400093 PMCID: PMC8987525 DOI: 10.3389/fvets.2022.850510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/16/2022] [Indexed: 01/17/2023] Open
Abstract
Central nervous system (CNS) inflammation is a common cause of neurological dysfunction in dogs. Most dogs with CNS inflammation are diagnosed with presumptive autoimmune disease. A smaller number are diagnosed with an infectious etiology. Additionally, at necropsy, a subset of dogs with CNS inflammation do not fit previously described patterns of autoimmune disease and an infectious cause is not readily identifiable. Because viral infection is a common cause of meningoencephalitis in people, we hypothesize that a subset of dogs presented with CNS inflammation have an occult viral infection either as a direct cause of CNS inflammation or a trigger for autoimmunity. The goal of this research was to screen cerebrospinal fluid from a large number dogs with CNS inflammation for occult viral infection. One hundred seventy-two dogs with neurological dysfunction and cerebrospinal fluid (CSF) pleocytosis were identified. Of these, 42 had meningoencephalitis of unknown origin, six had steroid-responsive meningitis-arteritis, one had eosinophilic meningoencephalitis, five had documented infection, 21 had and undetermined diagnosis, and 97 had a diagnosis not consistent with primary inflammatory disease of the CNS (e.g., neoplasia). CSF samples were subsequently screened with broadly reactive PCR for eight viral groups: adenovirus, bunyavirus, coronavirus, enterovirus, flavivirus, herpesvirus, paramyxovirus, and parechovirus. No viral nucleic acids were detected from 168 cases screened for eight viral groups, which does not support occult viral infection as a cause of CNS inflammation in dogs. La Crosse virus (LACV) nucleic acids were detected from four cases in Georgia. Subclinical infection was supported in two of these cases but LACV could not be ruled-out as a cause of infection in the other two cases, suggesting further research is warranted to determine if LACV is an occult cause of CNS inflammation in dogs.
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Affiliation(s)
- Renee M. Barber
- Department of Small Animal Medicine and Surgery, University of Georgia College of Veterinary Medicine, Athens, GA, United States
- *Correspondence: Renee M. Barber
| | - Qiang Li
- Becker Animal Hospital, Veterinary Centers of America, San Antonio, TX, United States
| | - Jonathan M. Levine
- Department of Small Animal Clinical Sciences, Texas A&M University College of Veterinary Medicine and Biomedical Sciences, College Station, TX, United States
| | - Susan J. Ruone
- Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Gwendolyn J. Levine
- Department of Veterinary Pathobiology, Texas A&M University College of Veterinary Medicine and Biomedical Sciences, College Station, TX, United States
| | - Patrick Kenny
- Department of Veterinary Clinical Sciences, The Royal Veterinary College, University of London, Hertfordshire, United Kingdom
| | - Suxiang Tong
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Scott J. Schatzberg
- Department of Small Animal Medicine and Surgery, University of Georgia College of Veterinary Medicine, Athens, GA, United States
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5
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Zheng Y, Qiu X, Wang T, Zhang J. The Diagnostic Value of Metagenomic Next-Generation Sequencing in Lower Respiratory Tract Infection. Front Cell Infect Microbiol 2021; 11:694756. [PMID: 34568089 PMCID: PMC8458627 DOI: 10.3389/fcimb.2021.694756] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/24/2021] [Indexed: 01/04/2023] Open
Abstract
Lower respiratory tract infections are associated with high morbidity and mortality and significant clinical harm. Due to the limited ability of traditional pathogen detection methods, anti-infective therapy is mostly empirical. Therefore, it is difficult to adopt targeted drug therapy. In recent years, metagenomic next-generation sequencing (mNGS) technology has provided a promising means for pathogen-specific diagnosis and updated the diagnostic strategy for lower respiratory tract infections. This article reviews the diagnostic value of mNGS for lower respiratory tract infections, the impact of different sampling methods on the detection efficiency of mNGS, and current technical difficulties in the clinical application of mNGS.
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Affiliation(s)
- Yan Zheng
- Department of Respiratory and Critical Care, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China
| | - Xiaojian Qiu
- Department of Respiratory and Critical Care, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China
| | - Ting Wang
- Department of Respiratory and Critical Care, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China
| | - Jie Zhang
- Department of Respiratory and Critical Care, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China
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6
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Folgueiras-González A, van den Braak R, Deijs M, van der Hoek L, de Groof A. A Versatile Processing Workflow to Enable Pathogen Detection in Clinical Samples from Organs Using VIDISCA. Diagnostics (Basel) 2021; 11:diagnostics11050791. [PMID: 33925752 PMCID: PMC8145099 DOI: 10.3390/diagnostics11050791] [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: 02/11/2021] [Revised: 04/16/2021] [Accepted: 04/26/2021] [Indexed: 12/15/2022] Open
Abstract
In recent years, refined molecular methods coupled with powerful high throughput sequencing technologies have increased the potential of virus discovery in clinical samples. However, host genetic material remains a complicating factor that interferes with discovery of novel viruses in solid tissue samples as the relative abundance of the virus material is low. Physical enrichment processing methods, although usually complicated, labor-intensive, and costly, have proven to be successful for improving sensitivity of virus detection in complex samples. In order to further increase detectability, we studied the application of fast and simple high-throughput virus enrichment methods on tissue homogenates. Probe sonication in high EDTA concentrations, organic extraction with Vertrel™ XF, or a combination of both, were applied prior to chromatography-like enrichment using Capto™ Core 700 resin, after which effects on virus detection sensitivity by the VIDISCA method were determined. Sonication in the presence of high concentrations of EDTA showed the best performance with an increased proportion of viral reads, up to 9.4 times, yet minimal effect on the host background signal. When this sonication procedure in high EDTA concentrations was followed by organic extraction with Vertrel™ XF and two rounds of core bead chromatography enrichment, an increase up to 10.5 times in the proportion of viral reads in the processed samples was achieved, with reduction of host background sequencing. We present a simple and semi-high-throughput method that can be used to enrich homogenized tissue samples for viral reads.
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Affiliation(s)
- Alba Folgueiras-González
- Department Discovery & Technology, MSD Animal Health, Wim de Körverstraat 35, P.O. Box 31, 5830 AA Boxmeer, The Netherlands; (A.F.-G.); (R.v.d.B.)
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.D.); (L.v.d.H.)
| | - Robin van den Braak
- Department Discovery & Technology, MSD Animal Health, Wim de Körverstraat 35, P.O. Box 31, 5830 AA Boxmeer, The Netherlands; (A.F.-G.); (R.v.d.B.)
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.D.); (L.v.d.H.)
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.D.); (L.v.d.H.)
| | - Ad de Groof
- Department Discovery & Technology, MSD Animal Health, Wim de Körverstraat 35, P.O. Box 31, 5830 AA Boxmeer, The Netherlands; (A.F.-G.); (R.v.d.B.)
- Correspondence:
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7
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Gil P, Dupuy V, Koual R, Exbrayat A, Loire E, Fall AG, Gimonneau G, Biteye B, Talla Seck M, Rakotoarivony I, Marie A, Frances B, Lambert G, Reveillaud J, Balenghien T, Garros C, Albina E, Eloit M, Gutierrez S. A library preparation optimized for metagenomics of RNA viruses. Mol Ecol Resour 2021; 21:1788-1807. [PMID: 33713395 DOI: 10.1111/1755-0998.13378] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/23/2021] [Accepted: 02/25/2021] [Indexed: 11/28/2022]
Abstract
Our understanding of the viral communities associated to animals has not yet reached the level attained on the bacteriome. This situation is due to, among others, technical challenges in adapting metagenomics using high-throughput sequencing to the study of RNA viromes in animals. Although important developments have been achieved in most steps of viral metagenomics, there is yet a key step that has received little attention: the library preparation. This situation differs from bacteriome studies in which developments in library preparation have largely contributed to the democratisation of metagenomics. Here, we present a library preparation optimized for metagenomics of RNA viruses from insect vectors of viral diseases. The library design allows a simple PCR-based preparation, such as those routinely used in bacterial metabarcoding, that is adapted to shotgun sequencing as required in viral metagenomics. We first optimized our library preparation using mock viral communities and then validated a full metagenomic approach incorporating our preparation in two pilot studies with field-caught insect vectors; one including a comparison with a published metagenomic protocol. Our approach provided a fold increase in virus-like sequences compared to other studies, and nearly-full genomes from new virus species. Moreover, our results suggested conserved trends in virome composition within a population of a mosquito species. Finally, the sensitivity of our approach was compared to a commercial diagnostic PCR for the detection of an arbovirus in field-caught insect vectors. Our approach could facilitate studies on viral communities from animals and the democratization of metagenomics in community ecology of viruses.
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Affiliation(s)
- Patricia Gil
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | - Virginie Dupuy
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | - Rachid Koual
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | - Antoni Exbrayat
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | - Etienne Loire
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | - Assane G Fall
- Laboratoire National de l'Elevage et de Recherches Vétérinaires, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar-Hann, Senegal
| | - Geoffrey Gimonneau
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France.,Laboratoire National de l'Elevage et de Recherches Vétérinaires, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar-Hann, Senegal
| | - Biram Biteye
- Laboratoire National de l'Elevage et de Recherches Vétérinaires, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar-Hann, Senegal
| | - Momar Talla Seck
- Laboratoire National de l'Elevage et de Recherches Vétérinaires, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar-Hann, Senegal
| | - Ignace Rakotoarivony
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | | | | | | | - Julie Reveillaud
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France
| | - Thomas Balenghien
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | - Claire Garros
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | - Emmanuel Albina
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | - Marc Eloit
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France.,The OIE Collaborating Centre for Detection and Identification in Humans of Emerging Animal Pathogens, Institut Pasteur, Paris, France.,École nationale vétérinaire d'Alfort, Maisons-Alfort, France
| | - Serafin Gutierrez
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
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8
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Kubacki J, Fraefel C, Bachofen C. Implementation of next-generation sequencing for virus identification in veterinary diagnostic laboratories. J Vet Diagn Invest 2020; 33:235-247. [PMID: 33357110 DOI: 10.1177/1040638720982630] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The value of next-generation sequencing (NGS)-based applications for testing purposes in human medicine is widely recognized. Although NGS-based metagenomic screening may be of interest in veterinary medicine, in particular for intensively farmed livestock species such as pigs, there is a lack of protocols tailored to veterinary requirements, likely because of the high diversity of species and samples. Therefore, we developed an NGS-based protocol for use in veterinary virology and present here different applications in porcine medicine. To develop the protocol, each step of sample preparation was optimized using porcine samples spiked with various RNA and DNA viruses. The resulting protocol was tested with clinical samples previously confirmed to be positive for specific viruses by a diagnostic laboratory. Additionally, we validated the protocol in an NGS viral metagenomics ring trial and tested the protocol on viral multiplex reference material (NIBSC, U.K.). We applied our ViroScreen protocol successfully for 1) virus identification, 2) virus characterization, and 3) herd screening. We identified torque teno sus virus and atypical porcine pestivirus in a neurologic case, determined the full-length genome sequence of swine influenza A virus in field samples, and screened pigs using pen floor fecal samples and chewing rope liquid.
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Affiliation(s)
- Jakub Kubacki
- Institute of Virology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Cornel Fraefel
- Institute of Virology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Claudia Bachofen
- Institute of Virology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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9
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Jansen SA, Nijhuis W, Leavis HL, Riezebos-Brilman A, Lindemans CA, Schuurman R. Broad Virus Detection and Variant Discovery in Fecal Samples of Hematopoietic Transplant Recipients Using Targeted Sequence Capture Metagenomics. Front Microbiol 2020; 11:560179. [PMID: 33281758 PMCID: PMC7705093 DOI: 10.3389/fmicb.2020.560179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022] Open
Abstract
Pediatric allogeneic hematopoietic stem cell transplantation (HSCT) patients often suffer from gastro-intestinal (GI) disease caused by viruses, Graft-versus-Host Disease (GVHD) or a combination of the two. Currently, the GI eukaryotic virome of HSCT recipients remains relatively understudied, which complicates the understanding of its role in GVHD pathogenicity. As decisions regarding immunosuppressive therapy in the treatment of virus infection or GVHD, respectively, can be completely contradicting, it is crucial to better understand the prevalence and relevance of viruses in the GI tract in the HSCT setting. A real time PCR panel for a set of specific viruses widely used to diagnose the most common causes of GI viral gastroenteritis is possibly insufficient to grasp the full extent of viruses present. Therefore, we applied the targeted sequence capture method ViroCap to residual fecal samples of 11 pediatric allogeneic HSCT recipients with GI symptoms and a suspicion of GVHD, to enrich for nucleic acids of viruses that are known to infect vertebrate hosts. After enrichment, NGS was applied to broadly detect viral sequences. Using ViroCap, we were able to detect viruses such as norovirus and adenovirus (ADV), that had been previously detected using clinical diagnostic PCR on the same sample. In addition, multiple, some of which clinically relevant viruses were detected, including ADV, human rhinovirus (HRV) and BK polyomavirus (BKV). Interestingly, in samples in which specific PCR testing for regular viral GI pathogens did not result in a diagnosis, the ViroCap pipeline led to the detection of viral sequences of human herpesvirus (HHV)-7, BKV, HRV, KI polyomavirus and astrovirus. The latter was an only recently described variant and showed extensive sequence mismatches with the applied real time PCR primers and would therefore not have been detected if tested. Our results indicate that target enrichment of viral nucleic acids through ViroCap leads to sensitive and broad possibly clinically relevant virus detection, including the detection of newer variants in clinical HSCT recipient samples. As such, ViroCap could be a useful detection tool clinically, but also in studying the associations between viral presence and GVHD.
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Affiliation(s)
- Suze A Jansen
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, Netherlands.,Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Wouter Nijhuis
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Helen L Leavis
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | | | - Caroline A Lindemans
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, Netherlands.,Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Rob Schuurman
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
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10
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Ponsero AJ, Hurwitz BL. The Promises and Pitfalls of Machine Learning for Detecting Viruses in Aquatic Metagenomes. Front Microbiol 2019; 10:806. [PMID: 31057513 PMCID: PMC6477088 DOI: 10.3389/fmicb.2019.00806] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/29/2019] [Indexed: 01/21/2023] Open
Abstract
Tools allowing for the identification of viral sequences in host-associated and environmental metagenomes allows for a better understanding of the genetics and ecology of viruses and their hosts. Recently, new approaches using machine learning methods to distinguish viral from bacterial signal using k-mer sequence signatures were published for identifying viral contigs in metagenomes. The promise of these content-based approaches is the ability to discover new viruses, with no or few known relatives. In this perspective paper, we examine the use of the content-based machine learning tool VirFinder for the identification of viral sequences in aquatic metagenomes and explore the possibility of using ecosystem-focused models targeted to marine metagenomes. We discuss the impact of the training set composition on the tool performance and the current limitation for the retrieval of low abundance viral sequences in metagenomes. We identify potential biases that could arise from machine learning approaches for viral hunting in real-world datasets and suggest possible avenues to overcome them.
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Affiliation(s)
- Alise J Ponsero
- Department of Biosystems Engineering, The University of Arizona, Tucson, AZ, United States
| | - Bonnie L Hurwitz
- Department of Biosystems Engineering, The University of Arizona, Tucson, AZ, United States.,BIO5 Institute, The University of Arizona, Tucson, AZ, United States
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11
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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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12
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Diagnosis and characterization of canine distemper virus through sequencing by MinION nanopore technology. Sci Rep 2019; 9:1714. [PMID: 30737428 PMCID: PMC6368598 DOI: 10.1038/s41598-018-37497-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 12/06/2018] [Indexed: 11/08/2022] Open
Abstract
Prompt identification of the causative pathogen of an infectious disease is essential for the choice of treatment or preventive measures. In this perspective, nucleic acids purified from the brain tissue of a dog succumbed after severe neurological signs were processed with the MinION (Oxford Nanopore Technologies, Oxford UK) sequencing technology. Canine distemper virus (CDV) sequence reads were detected. Subsequently, a specific molecular test and immunohistochemistry were used to confirm the presence of CDV RNA and antigen, respectively, in tissues. This study supports the use of the NGS in veterinary clinical practice with potential advantages in terms of rapidity and broad-range of molecular diagnosis.
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13
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Ponsero AJ, Hurwitz BL. The Promises and Pitfalls of Machine Learning for Detecting Viruses in Aquatic Metagenomes. Front Microbiol 2019. [PMID: 31057513 DOI: 10.3389/fmicb.2019.00806/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Tools allowing for the identification of viral sequences in host-associated and environmental metagenomes allows for a better understanding of the genetics and ecology of viruses and their hosts. Recently, new approaches using machine learning methods to distinguish viral from bacterial signal using k-mer sequence signatures were published for identifying viral contigs in metagenomes. The promise of these content-based approaches is the ability to discover new viruses, with no or few known relatives. In this perspective paper, we examine the use of the content-based machine learning tool VirFinder for the identification of viral sequences in aquatic metagenomes and explore the possibility of using ecosystem-focused models targeted to marine metagenomes. We discuss the impact of the training set composition on the tool performance and the current limitation for the retrieval of low abundance viral sequences in metagenomes. We identify potential biases that could arise from machine learning approaches for viral hunting in real-world datasets and suggest possible avenues to overcome them.
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Affiliation(s)
- Alise J Ponsero
- Department of Biosystems Engineering, The University of Arizona, Tucson, AZ, United States
| | - Bonnie L Hurwitz
- Department of Biosystems Engineering, The University of Arizona, Tucson, AZ, United States
- BIO5 Institute, The University of Arizona, Tucson, AZ, United States
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14
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Prakoso D, Dark MJ, Barbet AF, Salemi M, Barr KL, Liu JJ, Wenzlow N, Waltzek TB, Long MT. Viral Enrichment Methods Affect the Detection but Not Sequence Variation of West Nile Virus in Equine Brain Tissue. Front Vet Sci 2018; 5:318. [PMID: 30619900 PMCID: PMC6305279 DOI: 10.3389/fvets.2018.00318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 11/29/2018] [Indexed: 12/17/2022] Open
Abstract
West Nile virus (WNV), a small, positive sense, single stranded RNA virus continues to encroach into new locales with emergence of new viral variants. Neurological disease in the equine can be moderate to severe in the face of low to undetectable virus loads. Physical methods of virus enrichment may increase sensitivity of virus detection and enhance analysis of viral diversity, especially for deep sequencing studies. However, the use of these techniques is limited mainly to non-neural tissues. We investigated the hypothesis that elimination of equine brain RNA enhances viral detection without limiting viral variation. Eight different WNV viral RNA enrichment and host RNA separation methods were evaluated to determine if elimination of host RNA enhanced detection of WNV and increase the repertoire of virus variants for sequencing. Archived brain tissue from 21 different horses was inoculated with WNV, homogenized, before enrichment and separation. The protocols utilized combinations of low-speed centrifugation, syringe filtration, and nuclease treatment. Viral and host RNA were analyzed using real-time PCR targeting the WNV Envelope (E) protein and equine G3PDH to determine relative sensitivity for WNV and host depletion, respectively. To determine the effect of these methods on viral variation, deep sequencing of the E protein was performed. Our results demonstrate that additional separation and enrichment methods resulted in loss of virus in the face of host RNA depletion. DNA sequencing showed no significant difference in total sequence variation between the RNA enrichment protocols. For equine brain infected with WNV, direct RNA extraction followed by host RNA depletion was most suitable. This study highlights the importance of evaluating viral enrichment and separation methods according to tissue type before embarking on studies where quantification of virus and viral variants is essential to the outcome of the study.
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Affiliation(s)
- Dhani Prakoso
- Department of Comparative, Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Michael J Dark
- Department of Comparative, Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Anthony F Barbet
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Marco Salemi
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Kelli L Barr
- Department of Biology, Baylor University, Waco, TX, United States
| | - Junjie J Liu
- Department of Comparative, Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Nanny Wenzlow
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - Thomas B Waltzek
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Maureen T Long
- Department of Comparative, Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
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15
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Parras-Moltó M, Rodríguez-Galet A, Suárez-Rodríguez P, López-Bueno A. Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses. MICROBIOME 2018; 6:119. [PMID: 29954453 PMCID: PMC6022446 DOI: 10.1186/s40168-018-0507-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/19/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Viruses are key players regulating microbial ecosystems. Exploration of viral assemblages is now possible thanks to the development of metagenomics, the most powerful tool available for studying viral ecology and discovering new viruses. Unfortunately, several sources of bias lead to the misrepresentation of certain viruses within metagenomics workflows, hindering the shift from merely descriptive studies towards quantitative comparisons of communities. Therefore, benchmark studies on virus enrichment and random amplification protocols are required to better understand the sources of bias. RESULTS We assessed the bias introduced by viral enrichment on mock assemblages composed of seven DNA viruses, and the bias from random amplification methods on human saliva DNA viromes, using qPCR and deep sequencing, respectively. While iodixanol cushions and 0.45 μm filtration preserved the original composition of nuclease-protected viral genomes, low-force centrifugation and 0.22 μm filtration removed large viruses. Comparison of unamplified and randomly amplified saliva viromes revealed that multiple displacement amplification (MDA) induced stochastic bias from picograms of DNA template. However, the type of bias shifted to systematic using 1 ng, with only a marginal influence by amplification time. Systematic bias consisted of over-amplification of small circular genomes, and under-amplification of those with extreme GC content, a negative bias that was shared with the PCR-based sequence-independent, single-primer amplification (SISPA) method. MDA based on random priming provided by a DNA primase activity slightly outperformed those based on random hexamers and SISPA, which may reflect differences in ability to handle sequences with extreme GC content. SISPA viromes showed uneven coverage profiles, with high coverage peaks in regions with low linguistic sequence complexity. Despite misrepresentation of certain viruses after random amplification, ordination plots based on dissimilarities among contig profiles showed perfect overlapping of related amplified and unamplified saliva viromes and strong separation from unrelated saliva viromes. This result suggests that random amplification bias has a minor impact on beta diversity studies. CONCLUSIONS Benchmark analyses of mock and natural communities of viruses improve understanding and mitigate bias in metagenomics surveys. Bias induced by random amplification methods has only a minor impact on beta diversity studies of human saliva viromes.
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Affiliation(s)
- Marcos Parras-Moltó
- Centro de Biología Molecular Severo Ochoa (Universidad Autónoma de Madrid/Consejo Superior de Investigaciones Científicas), Madrid, Spain
| | - Ana Rodríguez-Galet
- Centro de Biología Molecular Severo Ochoa (Universidad Autónoma de Madrid/Consejo Superior de Investigaciones Científicas), Madrid, Spain
| | - Patricia Suárez-Rodríguez
- Centro de Biología Molecular Severo Ochoa (Universidad Autónoma de Madrid/Consejo Superior de Investigaciones Científicas), Madrid, Spain
| | - Alberto López-Bueno
- Centro de Biología Molecular Severo Ochoa (Universidad Autónoma de Madrid/Consejo Superior de Investigaciones Científicas), Madrid, Spain.
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16
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Complete Genome Sequence of a Swiss Hepatitis E Virus Isolate from the Liver of a Fattening Pig. GENOME ANNOUNCEMENTS 2018; 6:6/9/e00113-18. [PMID: 29496836 PMCID: PMC5834320 DOI: 10.1128/genomea.00113-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present here the full-length genome sequence of a hepatitis E genotype 3 virus (HEV-3) isolate, CH_VW117, from the liver of a healthy fattening pig collected at the slaughter level. Sequence analysis implies that this strain belongs to the newly proposed HEV subtype 3s.
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17
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Abstract
Prokaryotic viruses, or bacteriophages, are viruses that infect bacteria and archaea. These viruses have been known to associate with host systems for decades, yet only recently have their influence on the regulation of host-associated bacteria been appreciated. These studies have been conducted in many host systems, from the base of animal life in the Cnidarian phylum to mammals. These prokaryotic viruses are useful for regulating the number of bacteria in a host ecosystem and for regulating the strains of bacteria useful for the microbiome. These viruses are likely selected by the host to maintain bacterial populations. Viral metagenomics allows researchers to profile the communities of viruses associating with animal hosts, and importantly helps to determine the functional role these viruses play. Further, viral metagenomics show the sphere of viral involvement in gene flow and gene shuffling in an ever-changing host environment. The influence of prokaryotic viruses could, therefore, have a clear impact on host health.
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Affiliation(s)
- Juris A Grasis
- School of Natural Sciences, University of California, Merced, Merced, CA, USA.
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18
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Viral metagenomics of six bat species in close contact with humans in southern China. Arch Virol 2017; 163:73-88. [PMID: 28983731 PMCID: PMC7086785 DOI: 10.1007/s00705-017-3570-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 09/14/2017] [Indexed: 01/28/2023]
Abstract
Accumulating studies have shown that bats could harbor various important pathogenic viruses that could be transmitted to humans and other animals. Extensive metagenomic studies of different organs/tissues from bats have revealed a large number of novel or divergent viruses. To elucidate viral diversity and epidemiological and phylogenetic characteristics, six pooled fecal samples from bats were generated (based on bat species and geographic regions characteristic for virome analysis). These contained 500 fecal samples from six bat species, collected in four geographic regions. Metagenomic analysis revealed a plethora of divergent viruses originally found in bats. Multiple contigs from influenza A virus and coronaviruses in bats shared high identity with those from humans, suggesting possible cross-species transmission, whereas a number of contigs, whose sequences were taxonomically classifiable within Alphapapillomavirus, Betaretrovirus, Alpharetrovirus, Varicellovirus, Cyprinivirus, Chlorovirus and Cucumovirus had low identity to viruses in existing databases, which indicated possible evolution of novel viral species. None of the established caliciviruses and picornaviruses were found in the 500 fecal specimens. Papillomaviruses with high amino acid identity were found in Scotophilus kuhlii and Rhinolophus blythi, challenging the hypotheses regarding the strict host specificity and co-evolution of papillomaviruses. Phylogenetic analysis showed that four bat rotavirus A strains might be tentative G3 strains, according to the Rotavirus Classification Working Group classification.
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19
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Complete Genome Sequences of Two Swiss Hepatitis E Virus Isolates from Human Stool and Raw Pork Sausage. GENOME ANNOUNCEMENTS 2017; 5:5/35/e00888-17. [PMID: 28860248 PMCID: PMC5578846 DOI: 10.1128/genomea.00888-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We present here the full-length genome sequences of two hepatitis E virus genotype 3 (HEV-3) isolates from a human stool sample from a patient with acute hepatitis and a raw sausage containing pig liver. Sequence analysis implies that Swiss HEV isolates may form a novel subgroup of HEV-3 viruses.
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20
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Cui L, Wu B, Zhu X, Guo X, Ge Y, Zhao K, Qi X, Shi Z, Zhu F, Sun L, Zhou M. Identification and genetic characterization of a novel circular single-stranded DNA virus in a human upper respiratory tract sample. Arch Virol 2017; 162:3305-3312. [PMID: 28707271 DOI: 10.1007/s00705-017-3481-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 06/26/2017] [Indexed: 12/22/2022]
Abstract
Metagenomic analysis through high-throughput sequencing is a tool for detecting both known and novel viruses. Using this technique, a novel circular single-stranded DNA (ssDNA) virus genome was discovered in respiratory secretions from a febrile traveler. The virus, named human respiratory-associated PSCV-5-like virus (HRAPLV), has a genome comprising 3,018 bases, with two major putative ORFs inversely encoding capsid (Cap) and replicase (Rep) protein and separated by two intergenic regions. One stem-loop structure was predicted in the larger intergenic region (LIR). The predicted amino acid sequences of the Cap and Rep proteins of HRAPLV showed highest identity to those of porcine stool-associated circular virus 5 isolate CP3 (PoSCV 5) (53.0% and 48.9%, respectively). The host tropism of the virus is unknown, and further study is warranted to determine whether this novel virus is associated with human disease.
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Affiliation(s)
- Lunbiao Cui
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratories of Enteric Pathogenic Microbiology (Ministry of Health), Nanjing, China
| | - Binyao Wu
- Jiangsu International Travel Healthcare Center, Nanjing, China
| | - Xiaojuan Zhu
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratories of Enteric Pathogenic Microbiology (Ministry of Health), Nanjing, China
| | - Xiling Guo
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratories of Enteric Pathogenic Microbiology (Ministry of Health), Nanjing, China
| | - Yiyue Ge
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratories of Enteric Pathogenic Microbiology (Ministry of Health), Nanjing, China
| | - Kangchen Zhao
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratories of Enteric Pathogenic Microbiology (Ministry of Health), Nanjing, China
| | - Xian Qi
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratories of Enteric Pathogenic Microbiology (Ministry of Health), Nanjing, China
| | - Zhiyang Shi
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratories of Enteric Pathogenic Microbiology (Ministry of Health), Nanjing, China
| | - Fengcai Zhu
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratories of Enteric Pathogenic Microbiology (Ministry of Health), Nanjing, China
| | - Lixin Sun
- Jiangsu International Travel Healthcare Center, Nanjing, China.
| | - Minghao Zhou
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratories of Enteric Pathogenic Microbiology (Ministry of Health), Nanjing, China.
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Nkili-Meyong AA, Bigarré L, Labouba I, Vallaeys T, Avarre JC, Berthet N. Contribution of Next-Generation Sequencing to Aquatic and Fish Virology. Intervirology 2017; 59:285-300. [PMID: 28668959 DOI: 10.1159/000477808] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 05/27/2017] [Indexed: 12/13/2022] Open
Abstract
The recent technological advances in nucleic acid sequencing, called next-generation sequencing (NGS), have revolutionized the field of genomics and have also influenced viral research. Aquatic viruses, and especially those infecting fish, have also greatly benefited from NGS technologies, which provide a huge amount of molecular information at a low cost in a relatively short period of time. Here, we review the use of the current high-throughput sequencing platforms with a special focus on the associated challenges (regarding sample preparation and bioinformatics) in their applications to the field of aquatic virology, especially for: (i) discovering novel viruses that may be associated with fish mortalities, (ii) elucidating the mechanisms of pathogenesis, and finally (iii) studying the molecular epidemiology of these pathogens.
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Affiliation(s)
- Andriniaina Andy Nkili-Meyong
- Département Zoonoses et Maladies Emergentes, Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
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22
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Manso CF, Bibby DF, Mbisa JL. Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples. Sci Rep 2017. [PMID: 28646219 PMCID: PMC5482852 DOI: 10.1038/s41598-017-02239-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
RNA viruses cause significant human pathology and are responsible for the majority of emerging zoonoses. Mainstream diagnostic assays are challenged by their intrinsic diversity, leading to false negatives and incomplete characterisation. New sequencing techniques are expanding our ability to agnostically interrogate nucleic acids within diverse sample types, but in the clinical setting are limited by overwhelming host material and ultra-low target frequency. Through selective host RNA depletion and compensatory protocol adjustments for ultra-low RNA inputs, we are able to detect three major blood-borne RNA viruses – HIV, HCV and HEV. We recovered complete genomes and up to 43% of the genome from samples with viral loads of 104 and 103 IU/ml respectively. Additionally, we demonstrated the utility of this method in detecting and characterising members of diverse RNA virus families within a human plasma background, some present at very low levels. By applying this method to a patient sample series, we have simultaneously determined the full genome of both a novel subtype of HCV genotype 6, and a co-infecting human pegivirus. This method builds upon earlier RNA metagenomic techniques and can play an important role in the surveillance and diagnostics of blood-borne viruses.
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Affiliation(s)
- Carmen F Manso
- Antiviral Unit, Virus Reference Department, National Infection Service, Public Health England, Colindale, London, NW9 5EQ, United Kingdom
| | - David F Bibby
- Antiviral Unit, Virus Reference Department, National Infection Service, Public Health England, Colindale, London, NW9 5EQ, United Kingdom.
| | - Jean L Mbisa
- Antiviral Unit, Virus Reference Department, National Infection Service, Public Health England, Colindale, London, NW9 5EQ, United Kingdom
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23
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Kumar A, Murthy S, Kapoor A. Evolution of selective-sequencing approaches for virus discovery and virome analysis. Virus Res 2017; 239:172-179. [PMID: 28583442 PMCID: PMC5819613 DOI: 10.1016/j.virusres.2017.06.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/28/2016] [Accepted: 06/02/2017] [Indexed: 12/11/2022]
Abstract
Description of virus enrichment techniques for metagenomics based virome analysis. Usefulness of recently developed virome capture sequencing techniques. Perspective on negative and positive selection approaches for virome analysis.
Recent advances in sequencing technologies have transformed the field of virus discovery and virome analysis. Once mostly confined to the traditional Sanger sequencing based individual virus discovery, is now entirely replaced by high throughput sequencing (HTS) based virus metagenomics that can be used to characterize the nature and composition of entire viromes. To better harness the potential of HTS for the study of viromes, sample preparation methodologies use different approaches to exclude amplification of non-viral components that can overshadow low-titer viruses. These virus-sequence enrichment approaches mostly focus on the sample preparation methods, like enzymatic digestion of non-viral nucleic acids and size exclusion of non-viral constituents by column filtration, ultrafiltration or density gradient centrifugation. However, recently a new approach of virus-sequence enrichment called virome-capture sequencing, focused on the amplification or HTS library preparation stage, was developed to increase the ability of virome characterization. This new approach has the potential to further transform the field of virus discovery and virome analysis, but its technical complexity and sequence-dependence warrants further improvements. In this review we discuss the different methods, their applications and evolution, for selective sequencing based virome analysis and also propose refinements needed to harness the full potential of HTS for virome analysis.
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Affiliation(s)
- Arvind Kumar
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Satyapramod Murthy
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Amit Kapoor
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA; Department of Pediatrics, College of Medicine and Public Health, Ohio State University, Columbus, OH 43210, USA.
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Thannesberger J, Hellinger HJ, Klymiuk I, Kastner MT, Rieder FJJ, Schneider M, Fister S, Lion T, Kosulin K, Laengle J, Bergmann M, Rattei T, Steininger C. Viruses comprise an extensive pool of mobile genetic elements in eukaryote cell cultures and human clinical samples. FASEB J 2017; 31:1987-2000. [PMID: 28179422 DOI: 10.1096/fj.201601168r] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/09/2017] [Indexed: 01/09/2023]
Abstract
Viruses shape a diversity of ecosystems by modulating their microbial, eukaryotic, or plant host metabolism. The complexity of virus-host interaction networks is progressively fathomed by novel metagenomic approaches. By using a novel metagenomic method, we explored the virome in mammalian cell cultures and clinical samples to identify an extensive pool of mobile genetic elements in all of these ecosystems. Despite aseptic treatment, cell cultures harbored extensive and diverse phage populations with a high abundance of as yet unknown and uncharacterized viruses (viral dark matter). Unknown phages also predominated in the oropharynx and urine of healthy individuals and patients infected with cytomegalovirus despite demonstration of active cytomegalovirus replication. The novelty of viral sequences correlated primarily with the individual evaluated, whereas relative abundance of encoded protein functions was associated with the ecologic niches probed. Together, these observations demonstrate the extensive presence of viral dark matter in human and artificial ecosystems.-Thannesberger, J., Hellinger, H.-J., Klymiuk, I., Kastner, M.-T., Rieder, F. J. J., Schneider, M., Fister, S., Lion, T., Kosulin, K., Laengle, J., Bergmann, M., Rattei, T., Steininger, C. Viruses comprise an extensive pool of mobile genetic elements in eukaryote cell cultures and human clinical samples.
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Affiliation(s)
- Jakob Thannesberger
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria
| | - Hans-Joerg Hellinger
- CUBE-Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Ingeborg Klymiuk
- Center for Medical Research, Core Facility Molecular Biology, Medical University of Graz, Graz, Austria
| | - Marie-Theres Kastner
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria
| | - Franz J J Rieder
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria
| | - Martina Schneider
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria
| | - Susanne Fister
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, University of Veterinary Medicine, Vienna, Austria
| | - Thomas Lion
- Children's Cancer Research Institute, Vienna, Austria
| | - Karin Kosulin
- Children's Cancer Research Institute, Vienna, Austria
| | - Johannes Laengle
- Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Michael Bergmann
- Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Thomas Rattei
- CUBE-Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Christoph Steininger
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria;
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Hjelmsø MH, Hellmér M, Fernandez-Cassi X, Timoneda N, Lukjancenko O, Seidel M, Elsässer D, Aarestrup FM, Löfström C, Bofill-Mas S, Abril JF, Girones R, Schultz AC. Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing. PLoS One 2017; 12:e0170199. [PMID: 28099518 PMCID: PMC5242460 DOI: 10.1371/journal.pone.0170199] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/02/2017] [Indexed: 01/18/2023] Open
Abstract
Viral sewage metagenomics is a novel field of study used for surveillance, epidemiological studies, and evaluation of waste water treatment efficiency. In raw sewage human waste is mixed with household, industrial and drainage water, and virus particles are, therefore, only found in low concentrations. This necessitates a step of sample concentration to allow for sensitive virus detection. Additionally, viruses harbor a large diversity of both surface and genome structures, which makes universal viral genomic extraction difficult. Current studies have tackled these challenges in many different ways employing a wide range of viral concentration and extraction procedures. However, there is limited knowledge of the efficacy and inherent biases associated with these methods in respect to viral sewage metagenomics, hampering the development of this field. By the use of next generation sequencing this study aimed to evaluate the efficiency of four commonly applied viral concentrations techniques (precipitation with polyethylene glycol, organic flocculation with skim milk, monolithic adsorption filtration and glass wool filtration) and extraction methods (Nucleospin RNA XS, QIAamp Viral RNA Mini Kit, NucliSENS® miniMAG®, or PowerViral® Environmental RNA/DNA Isolation Kit) to determine the viriome in a sewage sample. We found a significant influence of concentration and extraction protocols on the detected viriome. The viral richness was largest in samples extracted with QIAamp Viral RNA Mini Kit or PowerViral® Environmental RNA/DNA Isolation Kit. Highest viral specificity were found in samples concentrated by precipitation with polyethylene glycol or extracted with Nucleospin RNA XS. Detection of viral pathogens depended on the method used. These results contribute to the understanding of method associated biases, within the field of viral sewage metagenomics, making evaluation of the current literature easier and helping with the design of future studies.
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Affiliation(s)
- Mathis Hjort Hjelmsø
- Research Group for Genomic Epidemiology, The National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
- * E-mail:
| | - Maria Hellmér
- Division of Microbiology and Production, The National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Xavier Fernandez-Cassi
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology, and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - Natàlia Timoneda
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology, and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
- Institute of Biomedicine of the University of Barcelona, University of Barcelona, Barcelona, Catalonia, Spain
| | - Oksana Lukjancenko
- Research Group for Genomic Epidemiology, The National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Michael Seidel
- Institute of Hydrochemistry, Chair of Analytical Chemistry, Technical University of Munich, Munich, Germany
| | - Dennis Elsässer
- Institute of Hydrochemistry, Chair of Analytical Chemistry, Technical University of Munich, Munich, Germany
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, The National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Charlotta Löfström
- Division of Microbiology and Production, The National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Sílvia Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology, and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - Josep F. Abril
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology, and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
- Institute of Biomedicine of the University of Barcelona, University of Barcelona, Barcelona, Catalonia, Spain
| | - Rosina Girones
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology, and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - Anna Charlotte Schultz
- Division of Microbiology and Production, The National Food Institute, Technical University of Denmark, Søborg, Denmark
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Yang Z, Leonard SR, Mammel MK, Elkins CA, Kulka M. Towards next-generation sequencing analytics for foodborne RNA viruses: Examining the effect of RNA input quantity and viral RNA purity. J Virol Methods 2016; 236:221-230. [DOI: 10.1016/j.jviromet.2016.07.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 06/28/2016] [Accepted: 07/15/2016] [Indexed: 11/15/2022]
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Yeh YT, Tang Y, Sebastian A, Dasgupta A, Perea-Lopez N, Albert I, Lu H, Terrones M, Zheng SY. Tunable and label-free virus enrichment for ultrasensitive virus detection using carbon nanotube arrays. SCIENCE ADVANCES 2016; 2:e1601026. [PMID: 27730213 PMCID: PMC5055386 DOI: 10.1126/sciadv.1601026] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 08/31/2016] [Indexed: 05/13/2023]
Abstract
Viral infectious diseases can erupt unpredictably, spread rapidly, and ravage mass populations. Although established methods, such as polymerase chain reaction, virus isolation, and next-generation sequencing have been used to detect viruses, field samples with low virus count pose major challenges in virus surveillance and discovery. We report a unique carbon nanotube size-tunable enrichment microdevice (CNT-STEM) that efficiently enriches and concentrates viruses collected from field samples. The channel sidewall in the microdevice was made by growing arrays of vertically aligned nitrogen-doped multiwalled CNTs, where the intertubular distance between CNTs could be engineered in the range of 17 to 325 nm to accurately match the size of different viruses. The CNT-STEM significantly improves detection limits and virus isolation rates by at least 100 times. Using this device, we successfully identified an emerging avian influenza virus strain [A/duck/PA/02099/2012(H11N9)] and a novel virus strain (IBDV/turkey/PA/00924/14). Our unique method demonstrates the early detection of emerging viruses and the discovery of new viruses directly from field samples, thus creating a universal platform for effectively remediating viral infectious diseases.
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Affiliation(s)
- Yin-Ting Yeh
- Micro and Nano Integrated Biosystem Laboratory, Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Penn State Material Research Institute, Pennsylvania State University, University Park, PA 16802, USA
| | - Yi Tang
- Department of Veterinary and Biomedical Science, Pennsylvania State University, University Park, PA 16802, USA
| | - Aswathy Sebastian
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Archi Dasgupta
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Nestor Perea-Lopez
- Department of Physics and Center for 2-Dimensional and Layered Materials, Pennsylvania State University, University Park, PA 16802, USA
| | - Istvan Albert
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Huaguang Lu
- Department of Veterinary and Biomedical Science, Pennsylvania State University, University Park, PA 16802, USA
| | - Mauricio Terrones
- Penn State Material Research Institute, Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
- Department of Physics and Center for 2-Dimensional and Layered Materials, Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Department of Materials Science and Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Corresponding author. (M.T.); (S.-Y.Z.)
| | - Si-Yang Zheng
- Micro and Nano Integrated Biosystem Laboratory, Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Penn State Material Research Institute, Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Corresponding author. (M.T.); (S.-Y.Z.)
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Li Y, Wang H, Nie K, Zhang C, Zhang Y, Wang J, Niu P, Ma X. VIP: an integrated pipeline for metagenomics of virus identification and discovery. Sci Rep 2016; 6:23774. [PMID: 27026381 PMCID: PMC4824449 DOI: 10.1038/srep23774] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 03/15/2016] [Indexed: 12/19/2022] Open
Abstract
Identification and discovery of viruses using next-generation sequencing technology is a fast-developing area with potential wide application in clinical diagnostics, public health monitoring and novel virus discovery. However, tremendous sequence data from NGS study has posed great challenge both in accuracy and velocity for application of NGS study. Here we describe VIP (“Virus Identification Pipeline”), a one-touch computational pipeline for virus identification and discovery from metagenomic NGS data. VIP performs the following steps to achieve its goal: (i) map and filter out background-related reads, (ii) extensive classification of reads on the basis of nucleotide and remote amino acid homology, (iii) multiple k-mer based de novo assembly and phylogenetic analysis to provide evolutionary insight. We validated the feasibility and veracity of this pipeline with sequencing results of various types of clinical samples and public datasets. VIP has also contributed to timely virus diagnosis (~10 min) in acutely ill patients, demonstrating its potential in the performance of unbiased NGS-based clinical studies with demand of short turnaround time. VIP is released under GPLv3 and is available for free download at: https://github.com/keylabivdc/VIP.
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Affiliation(s)
- Yang Li
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China
| | - Hao Wang
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 41345, Sweden
| | - Kai Nie
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Chen Zhang
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yi Zhang
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Ji Wang
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Peihua Niu
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xuejun Ma
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
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Karlsson OE, Larsson J, Hayer J, Berg M, Jacobson M. The Intestinal Eukaryotic Virome in Healthy and Diarrhoeic Neonatal Piglets. PLoS One 2016; 11:e0151481. [PMID: 26982708 PMCID: PMC4794121 DOI: 10.1371/journal.pone.0151481] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/29/2016] [Indexed: 12/29/2022] Open
Abstract
Neonatal porcine diarrhoea of uncertain aetiology has been reported from a number of European countries. The aim of the present study was to use viral metagenomics to examine a potential viral involvement in this diarrhoea and to describe the intestinal virome with focus on eukaryotic viruses. Samples from the distal jejunum of 50 diarrhoeic and 19 healthy piglets from 10 affected herds were analysed. The viral fraction of the samples was isolated and nucleic acids (RNA and DNA fractions) were subjected to sequence independent amplification. Samples from diarrhoeic piglets from the same herds were pooled whereas samples from healthy piglets were analysed individually. In total, 29 clinical samples, plus two negative controls and one positive control consisting of a mock metagenome were sequenced using the Ion Torrent platform. The resulting sequence data was subjected to taxonomic classification using Kraken, Diamond and HMMER. In the healthy specimens, eight different mammalian virus families were detected (Adenoviridae, Anelloviridae, Astroviridae, Caliciviridae, Circoviridae, Parvoviridae, Picornaviridae, and Reoviridae) compared to four in the pooled diarrhoeic samples (Anelloviridae, Circoviridae, Picornaviridae, and Reoviridae). It was not possible to associate a particular virus family with the investigated diarrhoea. In conclusion, this study does not support the hypothesis that the investigated diarrhoea was caused by known mammalian viruses. The results do, however, indicate that known mammalian viruses were present in the intestine as early as 24–48 hours after birth, indicating immediate infection post-partum or possibly transplacental infection.
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Affiliation(s)
- Oskar E. Karlsson
- Department of Biomedical Sciences and Veterinary Public Health (BVF), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics (HGEN), SLU, Uppsala, Sweden
- The OIE Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Uppsala, Sweden
- * E-mail:
| | - Jenny Larsson
- Department of Clinical Sciences (KV), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Juliette Hayer
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics (HGEN), SLU, Uppsala, Sweden
| | - Mikael Berg
- Department of Biomedical Sciences and Veterinary Public Health (BVF), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
- The OIE Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Uppsala, Sweden
| | - Magdalena Jacobson
- Department of Clinical Sciences (KV), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
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Using Small RNA Deep Sequencing Data to Detect Human Viruses. BIOMED RESEARCH INTERNATIONAL 2016; 2016:2596782. [PMID: 27066498 PMCID: PMC4811048 DOI: 10.1155/2016/2596782] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 01/13/2016] [Accepted: 02/03/2016] [Indexed: 01/08/2023]
Abstract
Small RNA sequencing (sRNA-seq) can be used to detect viruses in infected hosts without the necessity to have any prior knowledge or specialized sample preparation. The sRNA-seq method was initially used for viral detection and identification in plants and then in invertebrates and fungi. However, it is still controversial to use sRNA-seq in the detection of mammalian or human viruses. In this study, we used 931 sRNA-seq runs of data from the NCBI SRA database to detect and identify viruses in human cells or tissues, particularly from some clinical samples. Six viruses including HPV-18, HBV, HCV, HIV-1, SMRV, and EBV were detected from 36 runs of data. Four viruses were consistent with the annotations from the previous studies. HIV-1 was found in clinical samples without the HIV-positive reports, and SMRV was found in Diffuse Large B-Cell Lymphoma cells for the first time. In conclusion, these results suggest the sRNA-seq can be used to detect viruses in mammals and humans.
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31
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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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Castro-Mejía JL, Muhammed MK, Kot W, Neve H, Franz CMAP, Hansen LH, Vogensen FK, Nielsen DS. Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut. MICROBIOME 2015; 3:64. [PMID: 26577924 PMCID: PMC4650499 DOI: 10.1186/s40168-015-0131-4] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/02/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND The human gut is densely populated with archaea, eukaryotes, bacteria, and their viruses, such as bacteriophages. Advances in high-throughput sequencing (HTS) as well as bioinformatics have opened new opportunities for characterizing the viral communities harbored in our gut. However, limited attention has been given to the efficiency of protocols dealing with extraction of phages from fecal communities prior to HTS and their impact on the metagenomic dataset. RESULTS We describe two optimized methods for extraction of phages from fecal samples based on tangential-flow filtration (TFF) and polyethylene glycol precipitation (PEG) approaches using an adapted method from a published protocol as control (literature-adapted protocol (LIT)). To quantify phage recovery, samples were spiked with low numbers of c2, ϕ29, and T4 phages (representatives of the Siphoviridae, Podoviridae, and Myoviridae families, respectively) and their concentration (plaque-forming units) followed at every step during the extraction procedure. Compared with LIT, TFF and PEG had higher recovery of all spiked phages, yielding up to 16 times more phage particles (PPs) and up to 68 times more phage DNA per volume, increasing thus the chances of extracting low abundant phages. TFF- and PEG-derived metaviromes showed 10% increase in relative abundance of Caudovirales and unclassified phages infecting gut-associated bacteria (>92% for TFF and PEG, 82.4% for LIT). Our methods obtained lower relative abundance of the Myoviridae family (<16%) as compared to the reference protocol (22%). This decline, however, was not considered a true loss of Myoviridae phages but rather a greater level of extraction of Siphoviridae phages (TFF and PEG >32.5%, LIT 22.6%), which was achieved with the enhanced conditions of our procedures (e.g., reduced filter clogging). A high degree of phage diversity in samples extracted using TFF and PEG was documented by transmission electron microscopy. CONCLUSIONS Two procedures (TFF and PEG) for extraction of bacteriophages from fecal samples were optimized using a set of spiked bacteriophages as process control. These protocols are highly efficient tools for extraction and purification of PPs prior to HTS in phage-metavirome studies. Our methods can be easily modified, being thus applicable and adjustable for in principle any solid environmental material in dissolution.
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Affiliation(s)
- Josué L Castro-Mejía
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 26, Frederiksberg, Denmark.
| | - Musemma K Muhammed
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 26, Frederiksberg, Denmark.
| | - Witold Kot
- Department of Biology, Faculty of Science, University of Copenhagen, Universitetsparken 15, Copenhagen, Denmark.
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde, Denmark.
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany.
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany.
| | - Lars H Hansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde, Denmark.
| | - Finn K Vogensen
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 26, Frederiksberg, Denmark.
| | - Dennis S Nielsen
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 26, Frederiksberg, Denmark.
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Host-Associated Metagenomics: A Guide to Generating Infectious RNA Viromes. PLoS One 2015; 10:e0139810. [PMID: 26431175 PMCID: PMC4592258 DOI: 10.1371/journal.pone.0139810] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 09/17/2015] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Metagenomic analyses have been widely used in the last decade to describe viral communities in various environments or to identify the etiology of human, animal, and plant pathologies. Here, we present a simple and standardized protocol that allows for the purification and sequencing of RNA viromes from complex biological samples with an important reduction of host DNA and RNA contaminants, while preserving the infectivity of viral particles. PRINCIPAL FINDINGS We evaluated different viral purification steps, random reverse transcriptions and sequence-independent amplifications of a pool of representative RNA viruses. Viruses remained infectious after the purification process. We then validated the protocol by sequencing the RNA virome of human body lice engorged in vitro with artificially contaminated human blood. The full genomes of the most abundant viruses absorbed by the lice during the blood meal were successfully sequenced. Interestingly, random amplifications differed in the genome coverage of segmented RNA viruses. Moreover, the majority of reads were taxonomically identified, and only 7-15% of all reads were classified as "unknown", depending on the random amplification method. CONCLUSION The protocol reported here could easily be applied to generate RNA viral metagenomes from complex biological samples of different origins. Our protocol allows further virological characterizations of the described viral communities because it preserves the infectivity of viral particles and allows for the isolation of viruses.
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Kohl C, Brinkmann A, Dabrowski PW, Radonić A, Nitsche A, Kurth A. Protocol for metagenomic virus detection in clinical specimens. Emerg Infect Dis 2015; 21:48-57. [PMID: 25532973 PMCID: PMC4285256 DOI: 10.3201/eid2101.140766] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
This protocol can rapidly and reliably detect viruses during disease outbreaks and for detection studies. Sixty percent of emerging viruses have a zoonotic origin, making transmission from animals a major threat to public health. Prompt identification and analysis of these pathogens are indispensable to taking action toward prevention and protection of the affected population. We quantifiably compared classical and modern approaches of virus purification and enrichment in theory and experiments. Eventually, we established an unbiased protocol for detection of known and novel emerging viruses from organ tissues (tissue-based universal virus detection for viral metagenomics [TUViD-VM]). The final TUViD-VM protocol was extensively validated by using real-time PCR and next-generation sequencing. We could increase the amount of detectable virus nucleic acids and improved the detection of viruses <75,000-fold compared with other tested approaches. This TUViD-VM protocol can be used in metagenomic and virome studies to increase the likelihood of detecting viruses from any biological source.
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Datta S, Budhauliya R, Das B, Chatterjee S, Vanlalhmuaka, Veer V. Next-generation sequencing in clinical virology: Discovery of new viruses. World J Virol 2015; 4:265-276. [PMID: 26279987 PMCID: PMC4534817 DOI: 10.5501/wjv.v4.i3.265] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Revised: 03/23/2015] [Accepted: 05/08/2015] [Indexed: 02/05/2023] Open
Abstract
Viruses are a cause of significant health problem worldwide, especially in the developing nations. Due to different anthropological activities, human populations are exposed to different viral pathogens, many of which emerge as outbreaks. In such situations, discovery of novel viruses is utmost important for deciding prevention and treatment strategies. Since last century, a number of different virus discovery methods, based on cell culture inoculation, sequence-independent PCR have been used for identification of a variety of viruses. However, the recent emergence and commercial availability of next-generation sequencers (NGS) has entirely changed the field of virus discovery. These massively parallel sequencing platforms can sequence a mixture of genetic materials from a very heterogeneous mix, with high sensitivity. Moreover, these platforms work in a sequence-independent manner, making them ideal tools for virus discovery. However, for their application in clinics, sample preparation or enrichment is necessary to detect low abundance virus populations. A number of techniques have also been developed for enrichment or viral nucleic acids. In this manuscript, we review the evolution of sequencing; NGS technologies available today as well as widely used virus enrichment technologies. We also discuss the challenges associated with their applications in the clinical virus discovery.
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Daly GM, Leggett RM, Rowe W, Stubbs S, Wilkinson M, Ramirez-Gonzalez RH, Caccamo M, Bernal W, Heeney JL. Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data. PLoS One 2015; 10:e0129059. [PMID: 26098299 PMCID: PMC4476701 DOI: 10.1371/journal.pone.0129059] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 05/04/2015] [Indexed: 12/18/2022] Open
Abstract
The use of next generation sequencing (NGS) to identify novel viral sequences from eukaryotic tissue samples is challenging. Issues can include the low proportion and copy number of viral reads and the high number of contigs (post-assembly), making subsequent viral analysis difficult. Comparison of assembly algorithms with pre-assembly host-mapping subtraction using a short-read mapping tool, a k-mer frequency based filter and a low complexity filter, has been validated for viral discovery with Illumina data derived from naturally infected liver tissue and simulated data. Assembled contig numbers were significantly reduced (up to 99.97%) by the application of these pre-assembly filtering methods. This approach provides a validated method for maximizing viral contig size as well as reducing the total number of assembled contigs that require down-stream analysis as putative viral nucleic acids.
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Affiliation(s)
- Gordon M. Daly
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB30ES, United Kingdom
| | - Richard M. Leggett
- The Genome Analysis Centre (TGAC), Norwich Research Park, Norwich, NR47UH, United Kingdom
| | - William Rowe
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB30ES, United Kingdom
| | - Samuel Stubbs
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB30ES, United Kingdom
| | - Maxim Wilkinson
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB30ES, United Kingdom
| | | | - Mario Caccamo
- The Genome Analysis Centre (TGAC), Norwich Research Park, Norwich, NR47UH, United Kingdom
| | - William Bernal
- Institute of Liver Studies, King's College Hospital, Denmark Hill, London, SE59RS, United Kingdom
| | - Jonathan L. Heeney
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB30ES, United Kingdom
- * E-mail:
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Complete Genome Sequence of a Bovine Viral Diarrhea Virus Subgenotype 1e Strain Isolated in Switzerland. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00636-15. [PMID: 26067971 PMCID: PMC4463535 DOI: 10.1128/genomea.00636-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
We sequenced the complete genome of the bovine viral diarrhea virus (BVDV) strain Carlito. It belongs to the subgenotype 1e that is described in Europe only and represents the second most prevalent subgenotype in Switzerland. This is the first report of a full-length sequence of BVDV-1e.
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Rosseel T, Ozhelvaci O, Freimanis G, Van Borm S. Evaluation of convenient pretreatment protocols for RNA virus metagenomics in serum and tissue samples. J Virol Methods 2015; 222:72-80. [PMID: 26025457 DOI: 10.1016/j.jviromet.2015.05.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 04/28/2015] [Accepted: 05/22/2015] [Indexed: 12/27/2022]
Abstract
Viral metagenomic approaches are increasingly being used for viral discovery. Various strategies are applied to enrich viral sequences, but there is often a lack of knowledge about their effective influence on the viral discovery sensitivity. We evaluate some convenient and widely used approaches for RNA virus discovery in clinical samples in order to reveal their sensitivity and potential bias introduced by the enrichment or amplifications steps. An RNA virus was artificially spiked at a fixed titer in serum and lung tissue, respectively, low and high nucleic acid content matrices. For serum, a simple DNase treatment on the RNA extract gave the maximum gain in proportion of viral sequences (83×), and a subsequent ribosomal RNA removal nearly doubled once more the proportion of viral sequences. For lung tissue, a ribosomal RNA depletion step on the RNA extract had the biggest gain in proportion of viral sequences (32×). We show also that direct sequencing of cDNA is recommended above an extra random PCR amplification step, and a that the virion enrichment strategy (filtration and nuclease treatment) has a beneficial effect for sequencing-based virus discovery. Our findings provide sample-dependent guidelines for targeted virus discovery strategies.
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Affiliation(s)
- Toon Rosseel
- Veterinary and Agrochemical Research Centre CODA/CERVA, Groeselenberg 99, Brussels Belgium
| | - Orkun Ozhelvaci
- Veterinary and Agrochemical Research Centre CODA/CERVA, Groeselenberg 99, Brussels Belgium
| | - Graham Freimanis
- The Pirbright Institute, Ash Rd, Woking GU24 0NF, United Kingdom
| | - Steven Van Borm
- Veterinary and Agrochemical Research Centre CODA/CERVA, Groeselenberg 99, Brussels Belgium.
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Wang J, Moore NE, Murray ZL, McInnes K, White DJ, Tompkins DM, Hall RJ. Discovery of novel virus sequences in an isolated and threatened bat species, the New Zealand lesser short-tailed bat (Mystacina tuberculata). J Gen Virol 2015; 96:2442-2452. [PMID: 25900137 PMCID: PMC4681071 DOI: 10.1099/vir.0.000158] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Bats harbour a diverse array of viruses, including significant human pathogens. Extensive metagenomic studies of material from bats, in particular guano, have revealed a large number of novel or divergent viral taxa that were previously unknown. New Zealand has only two extant indigenous terrestrial mammals, which are both bats, Mystacina tuberculata (the lesser short-tailed bat) and Chalinolobus tuberculatus (the long-tailed bat). Until the human introduction of exotic mammals, these species had been isolated from all other terrestrial mammals for over 1 million years (potentially over 16 million years for M. tuberculata). Four bat guano samples were collected from M. tuberculata roosts on the isolated offshore island of Whenua hou (Codfish Island) in New Zealand. Metagenomic analysis revealed that this species still hosts a plethora of divergent viruses. Whilst the majority of viruses detected were likely to be of dietary origin, some putative vertebrate virus sequences were identified. Papillomavirus, polyomavirus, calicivirus and hepevirus were found in the metagenomic data and subsequently confirmed using independent PCR assays and sequencing. The new hepevirus and calicivirus sequences may represent new genera within these viral families. Our findings may provide an insight into the origins of viral families, given their detection in an isolated host species.
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Affiliation(s)
- Jing Wang
- Institute of Environmental Science & Research (ESR), at the National Centre for Biosecurity & Infectious Disease, PO Box 40158, Upper Hutt 5140, New Zealand
| | - Nicole E Moore
- Institute of Environmental Science & Research (ESR), at the National Centre for Biosecurity & Infectious Disease, PO Box 40158, Upper Hutt 5140, New Zealand
| | - Zak L Murray
- Institute of Environmental Science & Research (ESR), at the National Centre for Biosecurity & Infectious Disease, PO Box 40158, Upper Hutt 5140, New Zealand
| | - Kate McInnes
- Department of Conservation, , 18-32 Manners Street, PO Box 6011, Wellington, New Zealand
| | - Daniel J White
- Landcare Research, Private Bag 1930, Dunedin, New Zealand
| | | | - Richard J Hall
- Institute of Environmental Science & Research (ESR), at the National Centre for Biosecurity & Infectious Disease, PO Box 40158, Upper Hutt 5140, New Zealand
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Ullmann LS, de Camargo Tozato C, Malossi CD, da Cruz TF, Cavalcante RV, Kurissio JK, Cagnini DQ, Rodrigues MV, Biondo AW, Araujo JP. Comparative clinical sample preparation of DNA and RNA viral nucleic acids for a commercial deep sequencing system (Illumina MiSeq(®)). J Virol Methods 2015; 220:60-3. [PMID: 25901649 DOI: 10.1016/j.jviromet.2015.04.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 03/04/2015] [Accepted: 04/08/2015] [Indexed: 12/13/2022]
Abstract
Sequence-independent methods for viral discovery have been widely used for whole genome sequencing of viruses. Different protocols for viral enrichment, library preparation and sequencing have increasingly been more available and at lower costs. However, no study to date has focused on optimization of viral sample preparation for commercial deep sequencing. Accordingly, the aim of the present study was to evaluate an In-House enzymatic protocol for double-stranded DNA (dsDNA) synthesis and also compare the use of a commercially available kit protocol (Nextera XT, Illumina Inc, San Diego, CA, USA) and its combination with a library quantitation kit (Kapa, Kapa Biosystems, Wilmington, MA, USA) for deep sequencing (Illumina Miseq). Two RNA viruses (canine distemper virus and dengue virus) and one ssDNA virus (porcine circovirus type 2) were tested with the optimized protocols. The tested method for dsDNA synthesis has shown satisfactory results and may be used in laboratory setting, particularly when enzymes are already available. Library preparation combining commercial kits (Nextera XT and Kapa) has yielded more reads and genome coverage, probably due to a lack of small fragment recovering at the normalization step of Nextera XT. In addition, libraries may be diluted or concentrated to provide increase on genome coverage with Kapa quantitation.
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Affiliation(s)
- Leila Sabrina Ullmann
- Laboratory of Animal and Human Virology, Department of Microbiology and Immunology, Biosciences Institute, UNESP - Univ Estadual Paulista, Botucatu, 18618-970 São Paulo, Brazil.
| | - Claudia de Camargo Tozato
- Laboratory of Animal and Human Virology, Department of Microbiology and Immunology, Biosciences Institute, UNESP - Univ Estadual Paulista, Botucatu, 18618-970 São Paulo, Brazil.
| | - Camila Dantas Malossi
- Laboratory of Animal and Human Virology, Department of Microbiology and Immunology, Biosciences Institute, UNESP - Univ Estadual Paulista, Botucatu, 18618-970 São Paulo, Brazil.
| | - Tais Fukuta da Cruz
- Laboratory of Animal and Human Virology, Department of Microbiology and Immunology, Biosciences Institute, UNESP - Univ Estadual Paulista, Botucatu, 18618-970 São Paulo, Brazil.
| | - Raíssa Vasconcelos Cavalcante
- Laboratory of Animal and Human Virology, Department of Microbiology and Immunology, Biosciences Institute, UNESP - Univ Estadual Paulista, Botucatu, 18618-970 São Paulo, Brazil.
| | - Jacqueline Kazue Kurissio
- Laboratory of Animal and Human Virology, Department of Microbiology and Immunology, Biosciences Institute, UNESP - Univ Estadual Paulista, Botucatu, 18618-970 São Paulo, Brazil.
| | - Didier Quevedo Cagnini
- Laboratory of Animal and Human Virology, Department of Microbiology and Immunology, Biosciences Institute, UNESP - Univ Estadual Paulista, Botucatu, 18618-970 São Paulo, Brazil.
| | - Marianna Vaz Rodrigues
- Laboratory of Animal and Human Virology, Department of Microbiology and Immunology, Biosciences Institute, UNESP - Univ Estadual Paulista, Botucatu, 18618-970 São Paulo, Brazil.
| | - Alexander Welker Biondo
- Department of Veterinary Medicine, Paraná Federal University, Curitiba 80035-050, Brazil; Department of Pathobiology, University of Illinois, Urbana-Champaign, IL 61802, USA.
| | - João Pessoa Araujo
- Laboratory of Animal and Human Virology, Department of Microbiology and Immunology, Biosciences Institute, UNESP - Univ Estadual Paulista, Botucatu, 18618-970 São Paulo, Brazil.
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Marquardt JU, Andersen JB. Liver cancer oncogenomics: opportunities and dilemmas for clinical applications. Hepat Oncol 2015; 2:79-93. [PMID: 26257864 DOI: 10.2217/hep.14.24] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Primary liver cancers are among the most rapidly evolving malignant tumors worldwide. An underlying chronic inflammatory liver disease, which precedes liver cancer development for several decades and frequently creates a pro-oncogenic microenvironment, impairs progress in therapeutic approaches. Molecular heterogeneity of liver cancer is potentiated by a crosstalk between epithelial tumor and stromal cells that complicate translational efforts to unravel molecular mechanisms of hepatocarcinogenesis with a drugable intend. Next-generation sequencing has greatly advanced our understanding of cancer development. With regards to liver cancer, the unprecedented coverage of next-generation sequencing has created a detailed map of genetic alterations and identified key somatic changes such as CTNNB1 and TP53 as well as several previously unrecognized recurrent disease-causing alterations that could contribute to new therapeutic approaches. Importantly, these investigations indicate that a classical oncogene addiction cannot be assumed for primary liver cancer. Therefore, hepatocarcinogenesis can be considered a paradigm suitable for individualized medicine.
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Affiliation(s)
- Jens U Marquardt
- Department of Medicine I, Universitätsmedizin Mainz, Langenbeckstraße 1, 55131 Mainz, Germany
| | - Jesper B Andersen
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
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Behzadi P, Ranjbar R, Alavian SM. Nucleic Acid-based approaches for detection of viral hepatitis. Jundishapur J Microbiol 2014; 8:e17449. [PMID: 25789132 PMCID: PMC4350052 DOI: 10.5812/jjm.17449] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 05/14/2014] [Accepted: 06/14/2014] [Indexed: 12/12/2022] Open
Abstract
CONTEXT To determining suitable nucleic acid diagnostics for individual viral hepatitis agent, an extensive search using related keywords was done in major medical library and data were collected, categorized, and summarized in different sections. RESULTS Various types of molecular biology tools can be used to detect and quantify viral genomic elements and analyze the sequences. These molecular assays are proper technologies for rapidly detecting viral agents with high accuracy, high sensitivity, and high specificity. Nonetheless, the application of each diagnostic method is completely dependent on viral agent. CONCLUSIONS Despite rapidity, automation, accuracy, cost-effectiveness, high sensitivity, and high specificity of molecular techniques, each type of molecular technology has its own advantages and disadvantages.
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Affiliation(s)
- Payam Behzadi
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
| | - Reza Ranjbar
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
- Corresponding author: Reza Ranjbar, Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran. Tel: +98-21-88039883, E-mail:
| | - Seyed Moayed Alavian
- Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
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43
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Logan G, Freimanis GL, King DJ, Valdazo-González B, Bachanek-Bankowska K, Sanderson ND, Knowles NJ, King DP, Cottam EM. A universal protocol to generate consensus level genome sequences for foot-and-mouth disease virus and other positive-sense polyadenylated RNA viruses using the Illumina MiSeq. BMC Genomics 2014; 15:828. [PMID: 25269623 PMCID: PMC4247156 DOI: 10.1186/1471-2164-15-828] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 09/22/2014] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Next-Generation Sequencing (NGS) is revolutionizing molecular epidemiology by providing new approaches to undertake whole genome sequencing (WGS) in diagnostic settings for a variety of human and veterinary pathogens. Previous sequencing protocols have been subject to biases such as those encountered during PCR amplification and cell culture, or are restricted by the need for large quantities of starting material. We describe here a simple and robust methodology for the generation of whole genome sequences on the Illumina MiSeq. This protocol is specific for foot-and-mouth disease virus (FMDV) or other polyadenylated RNA viruses and circumvents both the use of PCR and the requirement for large amounts of initial template. RESULTS The protocol was successfully validated using five FMDV positive clinical samples from the 2001 epidemic in the United Kingdom, as well as a panel of representative viruses from all seven serotypes. In addition, this protocol was successfully used to recover 94% of an FMDV genome that had previously been identified as cell culture negative. Genome sequences from three other non-FMDV polyadenylated RNA viruses (EMCV, ERAV, VESV) were also obtained with minor protocol amendments. We calculated that a minimum coverage depth of 22 reads was required to produce an accurate consensus sequence for FMDV O. This was achieved in 5 FMDV/O/UKG isolates and the type O FMDV from the serotype panel with the exception of the 5' genomic termini and area immediately flanking the poly(C) region. CONCLUSIONS We have developed a universal WGS method for FMDV and other polyadenylated RNA viruses. This method works successfully from a limited quantity of starting material and eliminates the requirement for genome-specific PCR amplification. This protocol has the potential to generate consensus-level sequences within a routine high-throughput diagnostic environment.
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Affiliation(s)
- Grace Logan
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF United Kingdom
| | - Graham L Freimanis
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF United Kingdom
| | - David J King
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF United Kingdom
| | | | | | - Nicholas D Sanderson
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF United Kingdom
| | - Nick J Knowles
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF United Kingdom
| | - Donald P King
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF United Kingdom
| | - Eleanor M Cottam
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF United Kingdom
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Cuypers L, Snoeck J, Vrancken B, Kerremans L, Vuagniaux G, Verbeeck J, Nevens F, Camacho RJ, Vandamme AM, Van Dooren S. A near-full length genotypic assay for HCV1b. J Virol Methods 2014; 209:126-35. [PMID: 25245140 DOI: 10.1016/j.jviromet.2014.09.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 08/29/2014] [Accepted: 09/09/2014] [Indexed: 02/05/2023]
Abstract
A near-full genome genotypic assay for HCV1b was developed, which may prove useful to investigate antiviral drug resistance, given new combination therapies for HCV1 infection. The assay consists of three partially overlapping PCRs followed by Sanger population or Illumina next-generation sequencing. Seventy-seven therapy-naïve samples, spanning the entire diversity range of currently known HCV1b, were used for optimization of PCRs, of which ten were sequenced using Sanger and of these ten, four using Illumina. The median detection limits for the three regions, 5'UTR-NS2, E2-NS5A and NS4B-NS5B, were 570, 5670 and 56,670 IU/ml respectively. The number of Illumina reads mapped varied according to the software used, Segminator II being the best performing (81%). Consensus Illumina and Sanger sequencing results accord largely (0.013% major discordances). Differences were due almost exclusively to a larger number of ambiguities (presumably minority variants) scored by Illumina (1.50% minor discordances). The assay is easy to perform in an equipped laboratory; nevertheless, it was difficult to reach high sensitivity and reproducibility, due to the high genetic viral variability. This assay proved to be suitable for detecting drug resistance mutations and can also be used for epidemiological research, even though only a limited set of samples was used for validation.
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Affiliation(s)
- Lize Cuypers
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium.
| | - Joke Snoeck
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Bram Vrancken
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Lien Kerremans
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Grégoire Vuagniaux
- Debiopharm SA, Che. Messidor 5-7, P.O. Box 5911, 1002 Lausanne, Switzerland
| | - Jannick Verbeeck
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Frederik Nevens
- Department of Hepatology, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Ricardo J Camacho
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium; Centro de Malária e Outras Doencas Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira 100, 1349-008 Lisbon, Portugal
| | - Anne-Mieke Vandamme
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium; Centro de Malária e Outras Doencas Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira 100, 1349-008 Lisbon, Portugal
| | - Sonia Van Dooren
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
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Abstract
Hepatocellular Carcinoma (HCC) is the third most deadly malignancy worldwide characterized by phenotypic and molecular heterogeneity. In the past two decades, advances in genomic analyses have formed a comprehensive understanding of different underlying pathobiological layers resulting in hepatocarcinogenesis. More recently, improvements of sophisticated next-generation sequencing (NGS) technologies have enabled complete and cost-efficient analyses of cancer genomes at a single nucleotide resolution and advanced into valuable tools in translational medicine. Although the use of NGS in human liver cancer is still in its infancy, great promise rests in the systematic integration of different molecular analyses obtained by these methodologies, i.e., genomics, transcriptomics and epigenomics. This strategy is likely to be helpful in identifying relevant and recurrent pathophysiological hallmarks thereby elucidating our limited understanding of liver cancer. Beside tumor heterogeneity, progress in translational oncology is challenged by the amount of biological information and considerable “noise” in the data obtained from different NGS platforms. Nevertheless, the following review aims to provide an overview of the current status of next-generation approaches in liver cancer, and outline the prospects of these technologies in diagnosis, patient classification, and prediction of outcome. Further, the potential of NGS to identify novel applications for concept clinical trials and to accelerate the development of new cancer therapies will be summarized.
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46
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Cimino PJ, Zhao G, Wang D, Sehn JK, Lewis JS, Duncavage EJ. Detection of viral pathogens in high grade gliomas from unmapped next-generation sequencing data. Exp Mol Pathol 2014; 96:310-5. [PMID: 24704430 DOI: 10.1016/j.yexmp.2014.03.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 03/25/2014] [Indexed: 12/25/2022]
Abstract
Viral pathogens have been implicated in the development of certain cancers including human papillomavirus (HPV) in squamous cell carcinoma and Epstein-Barr virus (EBV) in Burkitt's lymphoma. The significance of viral pathogens in brain tumors is controversial, and human cytomegalovirus (HCMV) has been associated with glioblastoma (GBM) in some but not all studies, making the role of HCMV unclear. In this study we sought to determine if viral pathogen sequences could be identified in an unbiased manner from previously discarded, unmapped, non-human, next-generation sequencing (NGS) reads obtained from targeted oncology, panel-based sequencing of high grade gliomas (HGGs), including GBMs. Twenty one sequential HGG cases were analyzed by a targeted NGS clinical oncology panel containing 151 genes using DNA obtained from formalin-fixed, paraffin-embedded (FFPE) tissue. Sequencing reads that did not map to the human genome (average of 38,000 non-human reads/case (1.9%)) were filtered and low quality reads removed. Extracted high quality reads were then sequentially aligned to the National Center for Biotechnology Information (NCBI) non-redundant nucleotide (nt and nr) databases. Aligned reads were classified based on NCBI taxonomy database and all eukaryotic viral sequences were further classified into viral families. Two viral sequences (both herpesviruses), EBV and Roseolovirus were detected in 5/21 (24%) cases and in 1/21 (5%) cases, respectively. None of the cases had detectable HCMV. Of the five HGG cases with detectable EBV DNA, four had additional material for EBV in situ hybridization (ISH), all of which were negative for expressed viral sequence. Overall, a similar discovery approach using unmapped non-human NGS reads could be used to discover viral sequences in other cancer types.
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Affiliation(s)
- Patrick J Cimino
- Division of Neuropathology, Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, United States
| | - Guoyan Zhao
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, United States
| | - David Wang
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO, United States; Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, United States
| | - Jennifer K Sehn
- Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, United States
| | - James S Lewis
- Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, United States; Department of Otolaryngology Head and Neck Surgery, Washington University School of Medicine, Saint Louis, MO, United States
| | - Eric J Duncavage
- Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, United States.
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Optimization of virus detection in cells using massively parallel sequencing. Biologicals 2013; 42:34-41. [PMID: 24309095 DOI: 10.1016/j.biologicals.2013.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 10/28/2013] [Accepted: 11/08/2013] [Indexed: 11/22/2022] Open
Abstract
Massively parallel sequencing (MPS)-based virus detection has potential regulatory applications. We studied the ability of one of these approaches, based on degenerate oligonucleotide primer (DOP)-polymerase chain reaction (PCR), to detect viral sequences in cell lines known to express viral genes or particles. DOP-PCR was highly sensitive for the detection of small quantities of isolated viral sequences. Detected viral sequences included nodavirus, bracovirus, and endogenous retroviruses in High Five cells, porcine circovirus type 1 and porcine endogenous retrovirus in PK15 cells, human T-cell leukemia virus 1 in MJ cells, human papillomavirus 18 in HeLa cells, human herpesvirus 8 in BCBL-1 cells, and Epstein-Barr Virus in Raji cells. Illumina sequencing (for which primers were most efficiently added using PCR) provided greater sensitivity for virus detection than Roche 454 sequencing. Analyzing nucleic acids extracted both directly from samples and from capsid-enriched preparations provided useful information. Although there are limitations of these methods, these results indicate significant promise for the combination of nonspecific PCR and MPS in identifying contaminants in clinical and biological samples, including cell lines and reagents used to produce vaccines and therapeutic products.
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Li L, McGraw S, Zhu K, Leutenegger CM, Marks SL, Kubiski S, Gaffney P, Dela Cruz FN, Wang C, Delwart E, Pesavento PA. Circovirus in tissues of dogs with vasculitis and hemorrhage. Emerg Infect Dis 2013; 19:534-41. [PMID: 23628223 PMCID: PMC3647419 DOI: 10.3201/eid1904.121390] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
We characterized the complete genome of a novel dog circovirus (DogCV) from the liver of a dog with severe hemorrhagic gastroenteritis, vasculitis, and granulomatous lymphadenitis. DogCV was detected by PCR in fecal samples from 19/168 (11.3%) dogs with diarrhea and 14/204 (6.9%) healthy dogs and in blood from 19/409 (3.3%) of dogs with thrombocytopenia and neutropenia, fever of unknown origin, or past tick bite. Co-infection with other canine pathogens was detected for 13/19 (68%) DogCV-positive dogs with diarrhea. DogCV capsid proteins from different dogs varied by up to 8%. In situ hybridization and transmission electron microscopy detected DogCV in the lymph nodes and spleens of 4 dogs with vascular compromise and histiocytic inflammation. The detection of a circovirus in tissues of dogs expands the known tropism of these viruses to a second mammalian host. Our results indicate that circovirus, alone or in co-infection with other pathogens, might contribute to illness and death in dogs.
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Affiliation(s)
- Linlin Li
- Blood Systems Research Institute, and Department of Laboratory Medicine, University of California, San Francisco, California, USA
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Genetic analysis of West Nile virus isolates from an outbreak in Idaho, United States, 2006-2007. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2013; 10:4486-506. [PMID: 24065039 PMCID: PMC3799518 DOI: 10.3390/ijerph10094486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 09/12/2013] [Accepted: 09/16/2013] [Indexed: 12/26/2022]
Abstract
West Nile virus (WNV) appeared in the U.S. in 1999 and has since become endemic, with yearly summer epidemics causing tens of thousands of cases of serious disease over the past 14 years. Analysis of WNV strains isolated during the 2006–2007 epidemic seasons demonstrates that a new genetic variant had emerged coincidentally with an intense outbreak in Idaho during 2006. The isolates belonging to the new variant carry a 13 nt deletion, termed ID-Δ13, located at the variable region of the 3′UTR, and are genetically related. The analysis of deletions and insertions in the 3′UTR of two major lineages of WNV revealed the presence of conserved repeats and two indel motifs in the variable region of the 3′UTR. One human and two bird isolates from the Idaho 2006–2007 outbreaks were sequenced using Illumina technology and within-host variability was analyzed. Continued monitoring of new genetic variants is important for public health as WNV continues to evolve.
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50
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Hall RJ, Wang J, Todd AK, Bissielo AB, Yen S, Strydom H, Moore NE, Ren X, Huang QS, Carter PE, Peacey M. Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery. J Virol Methods 2013; 195:194-204. [PMID: 24036074 PMCID: PMC7113663 DOI: 10.1016/j.jviromet.2013.08.035] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 08/26/2013] [Accepted: 08/29/2013] [Indexed: 02/06/2023]
Abstract
The effect of simple virus enrichment methods were tested on a metagenomics dataset. Centrifugation, filtration or nuclease-treatment was evaluated. A multi-step enrichment method increased the proportion of virus sequences. This evaluation guides researchers in their choice of enrichment methodology.
The discovery of new or divergent viruses using metagenomics and high-throughput sequencing has become more commonplace. The preparation of a sample is known to have an effect on the representation of virus sequences within the metagenomic dataset yet comparatively little attention has been given to this. Physical enrichment techniques are often applied to samples to increase the number of viral sequences and therefore enhance the probability of detection. With the exception of virus ecology studies, there is a paucity of information available to researchers on the type of sample preparation required for a viral metagenomic study that seeks to identify an aetiological virus in an animal or human diagnostic sample. A review of published virus discovery studies revealed the most commonly used enrichment methods, that were usually quick and simple to implement, namely low-speed centrifugation, filtration, nuclease-treatment (or combinations of these) which have been routinely used but often without justification. These were applied to a simple and well-characterised artificial sample composed of bacterial and human cells, as well as DNA (adenovirus) and RNA viruses (influenza A and human enterovirus), being either non-enveloped capsid or enveloped viruses. The effect of the enrichment method was assessed by both quantitative real-time PCR and metagenomic analysis that incorporated an amplification step. Reductions in the absolute quantities of bacteria and human cells were observed for each method as determined by qPCR, but the relative abundance of viral sequences in the metagenomic dataset remained largely unchanged. A 3-step method of centrifugation, filtration and nuclease-treatment showed the greatest increase in the proportion of viral sequences. This study provides a starting point for the selection of a purification method in future virus discovery studies, and highlights the need for more data to validate the effect of enrichment methods on different sample types, amplification, bioinformatics approaches and sequencing platforms. This study also highlights the potential risks that may attend selection of a virus enrichment method without any consideration for the sample type being investigated.
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Affiliation(s)
- Richard J Hall
- Institute of Environmental Science and Research, at the National Centre for Biosecurity & Infectious Disease, 66 Ward Street, Wallaceville, Upper Hutt 5018, New Zealand.
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