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Qian L, Zhuang Z, Lu J, Wang H, Wang X, Yang S, Ji L, Shen Q, Zhang W, Shan T. Metagenomic survey of viral diversity obtained from feces of piglets with diarrhea. Heliyon 2024; 10:e25616. [PMID: 38375275 PMCID: PMC10875384 DOI: 10.1016/j.heliyon.2024.e25616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 12/02/2023] [Accepted: 01/30/2024] [Indexed: 02/21/2024] Open
Abstract
Pigs are natural host to various zoonotic pathogens including viruses. In this study, we analyzed the viral communities in the feces of 89 piglets with diarrhea under one month old which were collected from six farms in Jiangsu Province of the Eastern China, using the unbiased virus metagenomic method. A total of 89 libraries were constructed, and 46937894 unique sequence reads were generated by Illumina sequencing. Overall, the family Picornaviridae accounted for the majority of the total reads of putative mammalian viruses. Ten novel virus genomes from different family members were discovered, including Parvoviridae (n = 2), Picobirnaviridae (n = 4) and CRESS DNA viruses (n = 4). A large number of phages were identified, which mainly belonged to the order Caudovirales and the family Microviridae. Moreover, some identified viruses were closely related to viruses found in non-porcine hosts, highlighting the potential for cross-species virus dissemination. This study increased our understanding of the fecal virus communities of diarrhea piglets and provided valuable information for virus monitoring and preventing.
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Affiliation(s)
- Lingling Qian
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Zi Zhuang
- Center of Clinical Laboratory, Dushu Lake Hospital Affiliated to Soochow University, Soochow University, Suzhou, Jiangsu, 215000, China
| | - Juan Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Huiying Wang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 200062, China
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Likai Ji
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Tongling Shan
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
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Jansen D, Matthijnssens J. The Emerging Role of the Gut Virome in Health and Inflammatory Bowel Disease: Challenges, Covariates and a Viral Imbalance. Viruses 2023; 15:173. [PMID: 36680214 PMCID: PMC9861652 DOI: 10.3390/v15010173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Virome research is a rapidly growing area in the microbiome field that is increasingly associated with human diseases, such as inflammatory bowel disease (IBD). Although substantial progress has been made, major methodological challenges limit our understanding of the virota. In this review, we describe challenges that must be considered to accurately report the virome composition and the current knowledge on the virome in health and IBD. First, the description of the virome shows strong methodological biases related to wetlab (e.g., VLP enrichment) and bioinformatics approaches (viral identification and classification). Second, IBD patients show consistent viral imbalances characterized by a high relative abundance of phages belonging to the Caudovirales and a low relative abundance of phages belonging to the Microviridae. Simultaneously, a sporadic contraction of CrAss-like phages and a potential expansion of the lysogenic potential of the intestinal virome are observed. Finally, despite numerous studies that have conducted diversity analysis, it is difficult to draw firm conclusions due to methodological biases. Overall, we present the many methodological and environmental factors that influence the virome, its current consensus in health and IBD, and a contributing hypothesis called the "positive inflammatory feedback loop" that may play a role in the pathophysiology of IBD.
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Affiliation(s)
| | - Jelle Matthijnssens
- Laboratory of Viral Metagenomics, Rega Institute, Department of Microbiology, Immunology and Transplantation, University of Leuven, B-3000 Leuven, Belgium
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3
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Kennedy EA, Holtz LR. Gut virome in early life: origins and implications. Curr Opin Virol 2022; 55:101233. [PMID: 35690009 PMCID: PMC9575407 DOI: 10.1016/j.coviro.2022.101233] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 12/15/2022]
Abstract
The human body is colonized by a multitude of bacteria, fungi, and viruses, which play important roles in health and disease. Microbial colonization during early life is thought to be a particularly important period with lasting consequences for health. Viral populations in the gut are particularly dynamic in early life before they stabilize in adulthood. The composition of the early-life virome is increasingly recognized as a determinant of disease later in life. Here, we review the development of the virome in healthy infants, as well as the role of the early-life virome in the development of disease states including diarrhea, malnutrition, and autoimmune diseases.
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Affiliation(s)
- Elizabeth A Kennedy
- Washington University School of Medicine, Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, St. Louis, MO 63110, USA
| | - Lori R Holtz
- Washington University School of Medicine, Department of Pediatrics, St. Louis, MO 63110, USA.
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4
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Allali I, Abotsi RE, Tow LA, Thabane L, Zar HJ, Mulder NM, Nicol MP. Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research. MICROBIOME 2021; 9:241. [PMID: 34911583 PMCID: PMC8672519 DOI: 10.1186/s40168-021-01195-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/14/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We, therefore, conducted a systematic survey of African human microbiome studies to provide an overview and identify research gaps. Our secondary objectives were: (i) to determine the number of peer-reviewed publications; (ii) to identify the extent to which the researches focused on diseases identified by the World Health Organization [WHO] State of Health in the African Region Report as being the leading causes of morbidity and mortality in 2018; (iii) to describe the extent and pattern of collaborations between researchers in Africa and the rest of the world; and (iv) to identify leadership and funders of the studies. METHODOLOGY We systematically searched Medline via PubMed, Scopus, CINAHL, Academic Search Premier, Africa-Wide Information through EBSCOhost, and Web of Science from inception through to 1st April 2020. We included studies that characterized samples from African populations using next-generation sequencing approaches. Two reviewers independently conducted the literature search, title and abstract, and full-text screening, as well as data extraction. RESULTS We included 168 studies out of 5515 records retrieved. Most studies were published in PLoS One (13%; 22/168), and samples were collected from 33 of the 54 African countries. The country where most studies were conducted was South Africa (27/168), followed by Kenya (23/168) and Uganda (18/168). 26.8% (45/168) focused on diseases of significant public health concern in Africa. Collaboration between scientists from the United States of America and Africa was most common (96/168). The first and/or last authors of 79.8% of studies were not affiliated with institutions in Africa. Major funders were the United States of America National Institutes of Health (45.2%; 76/168), Bill and Melinda Gates Foundation (17.8%; 30/168), and the European Union (11.9%; 20/168). CONCLUSIONS There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. There is a need for local leadership, capacity building, intra-continental collaboration, and national government investment in microbiome research within Africa. Video Abstract.
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Affiliation(s)
- Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Centre of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Regina E Abotsi
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
- Department of Pharmaceutical Microbiology, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana
| | - Lemese Ah Tow
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Lehana Thabane
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
- Biostatistics Unit, Father Sean O'Sullivan Research Centre, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Departments of Paediatrics and Anaesthesia, McMaster University, Hamilton, Ontario, Canada
- Centre for Evaluation of Medicine, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton Health Sciences, Hamilton, Ontario, Canada
- Centre for Evidence-based Health Care, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
- MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Nicola M Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark P Nicol
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- School of Biomedical Sciences, University of Western Australia, M504, Perth, WA, 6009, Australia.
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Van Espen L, Bak EG, Beller L, Close L, Deboutte W, Juel HB, Nielsen T, Sinar D, De Coninck L, Frithioff-Bøjsøe C, Fonvig CE, Jacobsen S, Kjærgaard M, Thiele M, Fullam A, Kuhn M, Holm JC, Bork P, Krag A, Hansen T, Arumugam M, Matthijnssens J. A Previously Undescribed Highly Prevalent Phage Identified in a Danish Enteric Virome Catalog. mSystems 2021; 6:e0038221. [PMID: 34665009 PMCID: PMC8525569 DOI: 10.1128/msystems.00382-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 09/02/2021] [Indexed: 01/06/2023] Open
Abstract
Gut viruses are important, yet often neglected, players in the complex human gut microbial ecosystem. Recently, the number of human gut virome studies has been increasing; however, we are still only scratching the surface of the immense viral diversity. In this study, 254 virus-enriched fecal metagenomes from 204 Danish subjects were used to generate the Danish Enteric Virome Catalog (DEVoC) containing 12,986 nonredundant viral scaffolds, of which the majority was previously undescribed, encoding 190,029 viral genes. The DEVoC was used to compare 91 healthy DEVoC gut viromes from children, adolescents, and adults that were used to create the DEVoC. Gut viromes of healthy Danish subjects were dominated by phages. While most phage genomes (PGs) only occurred in a single subject, indicating large virome individuality, 39 PGs were present in more than 10 healthy subjects. Among these 39 PGs, the prevalences of three PGs were associated with age. To further study the prevalence of these 39 prevalent PGs, 1,880 gut virome data sets of 27 studies from across the world were screened, revealing several age-, geography-, and disease-related prevalence patterns. Two PGs also showed a remarkably high prevalence worldwide-a crAss-like phage (20.6% prevalence), belonging to the tentative AlphacrAssvirinae subfamily, and a previously undescribed circular temperate phage infecting Bacteroides dorei (14.4% prevalence), called LoVEphage because it encodes lots of viral elements. Due to the LoVEphage's high prevalence and novelty, public data sets in which the LoVEphage was detected were de novo assembled, resulting in an additional 18 circular LoVEphage-like genomes (67.9 to 72.4 kb). IMPORTANCE Through generation of the DEVoC, we added numerous previously uncharacterized viral genomes and genes to the ever-increasing worldwide pool of human gut viromes. The DEVoC, the largest human gut virome catalog generated from consistently processed fecal samples, facilitated the analysis of the 91 healthy Danish gut viromes. Characterizing the biggest cohort of healthy gut viromes from children, adolescents, and adults to date confirmed the previously established high interindividual variation in human gut viromes and demonstrated that the effect of age on the gut virome composition was limited to the prevalence of specific phage (groups). The identification of a previously undescribed prevalent phage illustrates the usefulness of developing virome catalogs, and we foresee that the DEVoC will benefit future analysis of the roles of gut viruses in human health and disease.
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Affiliation(s)
- Lore Van Espen
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Emilie Glad Bak
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leen Beller
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Lila Close
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Ward Deboutte
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Helene Bæk Juel
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Trine Nielsen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Deniz Sinar
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Lander De Coninck
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Christine Frithioff-Bøjsøe
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Children’s Obesity Clinic, accredited European Centre for Obesity Management, Department of Paediatrics, Copenhagen University Hospital Holbaek, Holbaek, Denmark
| | - Cilius Esmann Fonvig
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Children’s Obesity Clinic, accredited European Centre for Obesity Management, Department of Paediatrics, Copenhagen University Hospital Holbaek, Holbaek, Denmark
| | - Suganya Jacobsen
- Department of Gastroenterology and Hepatology, Centre for Liver Research, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Maria Kjærgaard
- Department of Gastroenterology and Hepatology, Centre for Liver Research, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Maja Thiele
- Department of Gastroenterology and Hepatology, Centre for Liver Research, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Anthony Fullam
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Michael Kuhn
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jens-Christian Holm
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Children’s Obesity Clinic, accredited European Centre for Obesity Management, Department of Paediatrics, Copenhagen University Hospital Holbaek, Holbaek, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany
- Yonsei Frontier Lab (YFL), Yonsei University, Seoul, South Korea
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Aleksander Krag
- Department of Gastroenterology and Hepatology, Centre for Liver Research, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manimozhiyan Arumugam
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jelle Matthijnssens
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
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Anh NT, Nhu LNT, Hong NTT, Phuc TM, Tam PTT, Huong DT, Anh TT, Deng X, Nghia HDT, Nguyen TT, Van Hung N, Thuan ND, Phuong PTH, Chau NVV, Baker S, Delwart E, Thwaites G, Van Tan L. Viral Metagenomic Analysis of Cerebrospinal Fluid from Patients with Acute Central Nervous System Infections of Unknown Origin, Vietnam. Emerg Infect Dis 2021; 27:205-213. [PMID: 33350920 PMCID: PMC7774551 DOI: 10.3201/eid2701.202723] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Central nervous system (CNS) infection is a serious neurologic condition, although the etiology remains unknown in >50% of patients. We used metagenomic next-generation sequencing to detect viruses in 204 cerebrospinal fluid (CSF) samples from patients with acute CNS infection who were enrolled from Vietnam hospitals during 2012–2016. We detected 8 viral species in 107/204 (52.4%) of CSF samples. After virus-specific PCR confirmation, the detection rate was lowered to 30/204 (14.7%). Enteroviruses were the most common viruses detected (n = 23), followed by hepatitis B virus (3), HIV (2), molluscum contagiosum virus (1), and gemycircularvirus (1). Analysis of enterovirus sequences revealed the predominance of echovirus 30 (9). Phylogenetically, the echovirus 30 strains belonged to genogroup V and VIIb. Our results expanded knowledge about the clinical burden of enterovirus in Vietnam and underscore the challenges of identifying a plausible viral pathogen in CSF of patients with CNS infections.
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7
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Pratama AA, Bolduc B, Zayed AA, Zhong ZP, Guo J, Vik DR, Gazitúa MC, Wainaina JM, Roux S, Sullivan MB. Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation. PeerJ 2021; 9:e11447. [PMID: 34178438 PMCID: PMC8210812 DOI: 10.7717/peerj.11447] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 04/22/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Viruses influence global patterns of microbial diversity and nutrient cycles. Though viral metagenomics (viromics), specifically targeting dsDNA viruses, has been critical for revealing viral roles across diverse ecosystems, its analyses differ in many ways from those used for microbes. To date, viromics benchmarking has covered read pre-processing, assembly, relative abundance, read mapping thresholds and diversity estimation, but other steps would benefit from benchmarking and standardization. Here we use in silico-generated datasets and an extensive literature survey to evaluate and highlight how dataset composition (i.e., viromes vs bulk metagenomes) and assembly fragmentation impact (i) viral contig identification tool, (ii) virus taxonomic classification, and (iii) identification and curation of auxiliary metabolic genes (AMGs). RESULTS The in silico benchmarking of five commonly used virus identification tools show that gene-content-based tools consistently performed well for long (≥3 kbp) contigs, while k-mer- and blast-based tools were uniquely able to detect viruses from short (≤3 kbp) contigs. Notably, however, the performance increase of k-mer- and blast-based tools for short contigs was obtained at the cost of increased false positives (sometimes up to ∼5% for virome and ∼75% bulk samples), particularly when eukaryotic or mobile genetic element sequences were included in the test datasets. For viral classification, variously sized genome fragments were assessed using gene-sharing network analytics to quantify drop-offs in taxonomic assignments, which revealed correct assignations ranging from ∼95% (whole genomes) down to ∼80% (3 kbp sized genome fragments). A similar trend was also observed for other viral classification tools such as VPF-class, ViPTree and VIRIDIC, suggesting that caution is warranted when classifying short genome fragments and not full genomes. Finally, we highlight how fragmented assemblies can lead to erroneous identification of AMGs and outline a best-practices workflow to curate candidate AMGs in viral genomes assembled from metagenomes. CONCLUSION Together, these benchmarking experiments and annotation guidelines should aid researchers seeking to best detect, classify, and characterize the myriad viruses 'hidden' in diverse sequence datasets.
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Affiliation(s)
- Akbar Adjie Pratama
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States of America
| | - Benjamin Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States of America
| | - Ahmed A. Zayed
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States of America
| | - Zhi-Ping Zhong
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States of America
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, United States of America
| | - Jiarong Guo
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States of America
| | - Dean R. Vik
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States of America
| | | | - James M. Wainaina
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States of America
- Infectious Diseases Institute at The Ohio State University, Ohio State University, Columbus, OH, United States of America
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Matthew B. Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States of America
- Environmental and Geodetic Engineering, Ohio State University, Department of Civil, Columbus, OH, United States of America
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8
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Gold-Watts A, Aamodt G, Gandhimathi S, Sudha R, Bastien S. Understanding Adolescents' Perceptions of Diarrhea: A Formative Research Study of a Visual Scale to Measure Self-Reported Diarrhea in Low-Resource Settings. Front Public Health 2021; 9:561367. [PMID: 34113594 PMCID: PMC8185169 DOI: 10.3389/fpubh.2021.561367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 04/19/2021] [Indexed: 12/03/2022] Open
Abstract
Introduction: Although water, sanitation, and hygiene interventions are effective in reducing diarrhea, there are methodological issues regarding the research tools used to evaluate their health impact. Moreover, there is limited research on individuals' subjective interpretations of diarrheal illness which may introduce further limitations in relying on self-reported data. Therefore, we conducted a study that aims to understand adolescents' perceptions of diarrheal illness in rural Tamil Nadu, India. Next, we wish to explore the acceptability of the Bristol Stool Form Scale to assess self-reported diarrhea in water, sanitation, and hygiene interventions involving adolescent participants in low-resource settings. Materials and Methods: The study was conducted as part of the formative research phase in the cultural adaptation of Project SHINE, a school-based educational water, sanitation, and hygiene intervention in Thirumalaikodi, Tamil Nadu, India. A convergent parallel mixed-methods study design with a purposive sampling strategy was used. Qualitative data included 10 in-depth interviews with student participants aged 13–14. Quantitative data were collected through interviewer-administered face-to-face surveys (n = 14) and one-week stool diaries (n = 14). Each data set was analyzed separately and compiled during the interpretation of the findings. Results: Across all data sets, diarrhea was reported to be perceived as unhealthy and an irregular occurrence among participants. Participants also reported diarrheal-taboos, local methods to cure or control diarrhea, and discussed how diarrheal illness can lead to absenteeism or withdrawal from school and social activities. Moreover, participants were able to understand and answer questions about their stool using the Bristol Stool Form Scale, suggesting that is an acceptable tool. Discussion: Visual tools demonstrate promise in improving self-reported diarrheal illness among adolescents in low-resource settings in India. However, until we address diarrhea-related taboos it will be difficult to address methodological issues in the assessment and reporting of diarrheal illness among adolescents.
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Affiliation(s)
- Anise Gold-Watts
- Department of Public Health, Faculty of Landscape and Society, Norwegian University of Life Sciences, Ås, Norway
| | - Geir Aamodt
- Department of Public Health, Faculty of Landscape and Society, Norwegian University of Life Sciences, Ås, Norway
| | | | - Rajamani Sudha
- Department of Obstetrics and Gynecology Nursing, Sri Narayani College and School of Nursing, Vellore, India
| | - Sheri Bastien
- Department of Public Health, Faculty of Landscape and Society, Norwegian University of Life Sciences, Ås, Norway.,Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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9
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Taboada B, Morán P, Serrano-Vázquez A, Iša P, Rojas-Velázquez L, Pérez-Juárez H, López S, Torres J, Ximenez C, Arias CF. The gut virome of healthy children during the first year of life is diverse and dynamic. PLoS One 2021; 16:e0240958. [PMID: 33852569 PMCID: PMC8046192 DOI: 10.1371/journal.pone.0240958] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/30/2021] [Indexed: 01/21/2023] Open
Abstract
In this work, we determined the diversity and dynamics of the gut virome of infants during the first year of life. Fecal samples were collected monthly, from birth to one year of age, from three healthy children living in a semi-rural village in Mexico. Most of the viral reads were classified into six families of bacteriophages including five dsDNA virus families of the order Caudovirales, with Siphoviridae and Podoviridae being the most abundant. Eukaryotic viruses were detected as early as two weeks after birth and remained present all along the first year of life. Thirty-four different eukaryotic virus families were found, where eight of these families accounted for 98% of all eukaryotic viral reads: Anelloviridae, Astroviridae, Caliciviridae, Genomoviridae, Parvoviridae, Picornaviridae, Reoviridae and the plant-infecting viruses of the Virgaviridae family. Some viruses in these families are known human pathogens, and it is surprising that they were found during the first year of life in infants without gastrointestinal symptoms. The eukaryotic virus species richness found in this work was higher than that observed in previous studies; on average between 7 and 24 virus species were identified per sample. The richness and abundance of the eukaryotic virome significantly increased during the second semester of life, probably because of an increased environmental exposure of infants with age. Our findings suggest an early and permanent contact of infants with a diverse array of bacteriophages and eukaryotic viruses, whose composition changes over time. The bacteriophages and eukaryotic viruses found in these children could represent a metastable virome, whose potential influence on the development of the infant's immune system or on the health of the infants later in life, remains to be investigated.
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Affiliation(s)
- Blanca Taboada
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Patricia Morán
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Angélica Serrano-Vázquez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Pavel Iša
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Liliana Rojas-Velázquez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Horacio Pérez-Juárez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Javier Torres
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
- * E-mail: (CFA); (CX); (JT)
| | - Cecilia Ximenez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
- * E-mail: (CFA); (CX); (JT)
| | - Carlos F. Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- * E-mail: (CFA); (CX); (JT)
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10
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Virome of Bat Guano from Nine Northern California Roosts. J Virol 2021; 95:JVI.01713-20. [PMID: 33115864 DOI: 10.1128/jvi.01713-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/17/2020] [Indexed: 12/12/2022] Open
Abstract
Bats are hosts to a large variety of viruses, including many capable of cross-species transmissions to other mammals, including humans. We characterized the virome in guano from five common bat species in 9 Northern California roosts and from a pool of 5 individual bats. Genomes belonging to 14 viral families known to infect mammals and 17 viral families infecting insects or of unknown tropism were detected. Nearly complete or complete genomes of a novel parvovirus, astrovirus, nodavirus, circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses, and densoviruses, and more partial genomes of a novel alphacoronavirus and a bunyavirus were characterized. Lower numbers of reads with >90% amino acid identity to previously described calicivirus, circovirus, adenoviruses, hepatovirus, bocaparvoviruses, and polyomavirus in other bat species were also found, likely reflecting their wide distribution among different bats. Unexpectedly, a few sequence reads of canine parvovirus 2 and the recently described mouse kidney parvovirus were also detected and their presence confirmed by PCR; these possibly originated from guano contamination by carnivores and rodents. The majority of eukaryotic viral reads were highly divergent, indicating that numerous viruses still remain to be characterized, even from such a heavily investigated order as Chiroptera.IMPORTANCE Characterizing the bat virome is important for understanding viral diversity and detecting viral spillover between animal species. Using an unbiased metagenomics method, we characterize the virome in guano collected from multiple roosts of common Northern California bat species. We describe several novel viral genomes and report the detection of viruses with close relatives reported in other bat species, likely reflecting cross-species transmissions. Viral sequences from well-known carnivore and rodent parvoviruses were also detected, whose presence are likely the result of contamination from defecation and urination atop guano and which reflect the close interaction of these mammals in the wild.
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11
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Gregory AC, Zablocki O, Zayed AA, Howell A, Bolduc B, Sullivan MB. The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut. Cell Host Microbe 2020; 28:724-740.e8. [PMID: 32841606 PMCID: PMC7443397 DOI: 10.1016/j.chom.2020.08.003] [Citation(s) in RCA: 303] [Impact Index Per Article: 75.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/14/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022]
Abstract
The gut microbiome profoundly affects human health and disease, and their infecting viruses are likely as important, but often missed because of reference database limitations. Here, we (1) built a human Gut Virome Database (GVD) from 2,697 viral particle or microbial metagenomes from 1,986 individuals representing 16 countries, (2) assess its effectiveness, and (3) report a meta-analysis that reveals age-dependent patterns across healthy Westerners. The GVD contains 33,242 unique viral populations (approximately species-level taxa) and improves average viral detection rates over viral RefSeq and IMG/VR nearly 182-fold and 2.6-fold, respectively. GVD meta-analyses show highly personalized viromes, reveal that inter-study variability from technical artifacts is larger than any "disease" effect at the population level, and document how viral diversity changes from human infancy into senescence. Together, this compact foundational resource, these standardization guidelines, and these meta-analysis findings provide a systematic toolkit to help maximize our understanding of viral roles in health and disease.
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Affiliation(s)
- Ann C Gregory
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Olivier Zablocki
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Ahmed A Zayed
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Allison Howell
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Benjamin Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA.
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12
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Rivadulla E, Romalde JL. A Comprehensive Review on Human Aichi Virus. Virol Sin 2020; 35:501-516. [PMID: 32342286 PMCID: PMC7223127 DOI: 10.1007/s12250-020-00222-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 02/28/2020] [Indexed: 12/16/2022] Open
Abstract
Although norovirus, rotavirus, adenovirus and Astrovirus are considered the most important viral agents transmitted by food and water, in recent years other viruses, such as Aichi virus (AiV), have emerged as responsible for gastroenteritis outbreaks associated with different foods. AiV belongs to the genus Kobuvirus of the family Picornaviridae. It is a virus with icosahedral morphology that presents a single stranded RNA genome with positive sense (8280 nucleotides) and a poly (A) chain. AiV was first detected from clinical samples and in recent years has been involved in acute gastroenteritis outbreaks from different world regions. Furthermore, several studies conducted in Japan, Germany, France, Tunisia and Spain showed a high prevalence of AiV antibodies in adults (between 80% and 99%), which is indicative of a large exposure to this virus. The aim of this review is to bring together all the discovered information about the emerging pathogen human Aichi virus (AiV), discussing the possibles routes of transmission, new detection techniques and future research. Although AiV is responsible for a low percentage of gastroenteritis outbreaks, the high seroprevalence shown by human populations indicates an evident role as an enteric agent. The low percentage of AiV detection could be explained by the fact that the pathogen is more associated to subclinical infections. Further studies will be needed to clarify the real impact of AiV in human health and its importance as a causative gastroenteritis agent worldwide.
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Affiliation(s)
- Enrique Rivadulla
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, 15782, Santiago, Spain
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, 15782, Santiago, Spain.
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13
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Ugboko HU, Nwinyi OC, Oranusi SU, Oyewale JO. Childhood diarrhoeal diseases in developing countries. Heliyon 2020; 6:e03690. [PMID: 32322707 PMCID: PMC7160433 DOI: 10.1016/j.heliyon.2020.e03690] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/03/2019] [Accepted: 03/25/2020] [Indexed: 12/27/2022] Open
Abstract
Diarrhoeal diseases collectively constitute a serious public health challenge globally, especially as the leading cause of death in children (after respiratory diseases). Childhood diarrhoea affecting children under the age of five accounts for approximately 63% of the global burden. Accurate and timely detection of the aetiology of these diseases is very crucial; but conventional methods, apart from being laborious and time-consuming, often fail to identify difficult-to-culture pathogens. The aetiological agent of an average of up to 40% of cases of diarrhoea cannot be identified. This review gives an overview of the recent trends in the epidemiology and treatment of diarrhoea and aims at highlighting the potentials of metagenomics technique as a diagnostic method for enteric infections.
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Affiliation(s)
- Harriet U Ugboko
- Microbiology Research Unit, Department of Biological Sciences, Covenant University, Canaanland, KM 10, Idiroko Road, P.M.B, 1023, Ota, Ogun State, Nigeria
| | - Obinna C Nwinyi
- Microbiology Research Unit, Department of Biological Sciences, Covenant University, Canaanland, KM 10, Idiroko Road, P.M.B, 1023, Ota, Ogun State, Nigeria
| | - Solomon U Oranusi
- Microbiology Research Unit, Department of Biological Sciences, Covenant University, Canaanland, KM 10, Idiroko Road, P.M.B, 1023, Ota, Ogun State, Nigeria
| | - John O Oyewale
- Microbiology Research Unit, Department of Biological Sciences, Covenant University, Canaanland, KM 10, Idiroko Road, P.M.B, 1023, Ota, Ogun State, Nigeria
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14
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Mohammad HA, Madi NM, Al-Nakib W. Analysis of viral diversity in stool samples from infants and children with acute gastroenteritis in Kuwait using Metagenomics approach. Virol J 2020; 17:10. [PMID: 32000795 PMCID: PMC6993487 DOI: 10.1186/s12985-020-1287-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 01/20/2020] [Indexed: 12/27/2022] Open
Abstract
Background Current molecular target-dependent methods are used to detect only known viruses. However, metagenomics based on next-generation sequencing (NGS) technique is a target-independent assay that enables simultaneous detection and genomic characterisation of all microorganisms present in a sample. In this study, we aimed to develop a metagenomics approach using NGS to identify and characterise viruses in stool samples from infants and children with Acute Gastroenteritis (AGE) in Kuwait. Methods We have investigated 84 stool samples from infants and children aged one month to ten years old with signs and symptoms of gastroenteritis who attended Mubarak Al-Kabeer and Al-Amiri hospitals in Kuwait from January to December 2017. A metagenomics approach using NGS to characterise viruses in clinical samples was used. Also, the commercial Real-Time PCR assay was used to detect viruses causing gastroenteritis. Results Metagenomics analysis revealed an average of 280,768 reads in which 5% of the reads were derived from viruses. The analysis of viral sequences verified that single infection of human adenovirus was the leading cause of gastroenteritis among infants and children, which was detected in 23.2% of the patients, followed by a mixed infection of human adenovirus and other viruses, which was detected in 20.9% of patients. Also, the newly discovered viruses known to cause gastroenteritis were detected, such as astrovirus MLB2, primate bocaparvovirus-1, Aichivirus A, cardiovirus, parechovirus A, astrovirus VA4, cosavirus-F, and bufavirus-3. Our results showed 71% agreement (k = 0.445, P = 0.000) between multiplex Real-Time PCR, which is used as a routine diagnostic test and metagenomics approach in the detection of viruses causing gastroenteritis in clinical samples. Conclusion Despite the difficulties in sample preparation and analysis process, we showed that metagenomics approach is a powerful and promising tool for the detection and characterisation of different viruses in clinical samples.
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Affiliation(s)
- Hawraa Adel Mohammad
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, P.O.Box 24923, 13110, Safat, Kuwait
| | - Nada Mohammed Madi
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, P.O.Box 24923, 13110, Safat, Kuwait.
| | - Widad Al-Nakib
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, P.O.Box 24923, 13110, Safat, Kuwait
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15
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Anh NT, Hong NTT, Nhu LNT, Thanh TT, Lau CY, Limmathurotsakul D, Deng X, Rahman M, Chau NVV, van Doorn HR, Thwaites G, Delwart E, Tan LV. Viruses in Vietnamese Patients Presenting with Community-Acquired Sepsis of Unknown Cause. J Clin Microbiol 2019; 57:e00386-19. [PMID: 31217274 PMCID: PMC6711913 DOI: 10.1128/jcm.00386-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/12/2019] [Indexed: 12/28/2022] Open
Abstract
Community-acquired (CA) sepsis is a major public health problem worldwide, yet the etiology remains unknown for >50% of the patients. Here we applied metagenomic next-generation sequencing (mNGS) to characterize the human virome in 492 clinical samples (384 sera, 92 pooled nasal and throat swabs, 10 stools, and 6 cerebrospinal fluid samples) from 386 patients (213 adults and 173 children) presenting with CA sepsis who were recruited from 6 hospitals across Vietnam between 2013 and 2015. Specific monoplex PCRs were used subsequently to confirm the presence of viral sequences detected by mNGS. We found sequences related to 47 viral species belonging to 21 families in 358 of 386 (93%) patients, including viruses known to cause human infections. After PCR confirmation, human viruses were found in 52 of 386 patients (13.4%); picornavirus (enteroviruses [n = 14], rhinovirus [n = 5], and parechovirus [n = 2]), hepatitis B virus (n = 10), cytomegalovirus (n = 9), Epstein-Barr virus (n = 5), and rotavirus A (n = 3) were the most common viruses detected. Recently discovered viruses were also found (gemycircularvirus [n = 5] and WU polyomavirus, Saffold virus, salivirus, cyclovirus-VN, and human pegivirus 2 [HPgV2] [n, 1 each]), adding to the growing literature about the geographic distribution of these novel viruses. Notably, sequences related to numerous viruses not previously reported in human tissues were also detected. To summarize, we identified 21 viral species known to be infectious to humans in 52 of 386 (13.4%) patients presenting with CA sepsis of unknown cause. The study, however, cannot directly impute sepsis causation to the viruses identified. The results highlight the fact that it remains a challenge to establish the causative agents in CA sepsis patients, especially in tropical settings such as Vietnam.
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Affiliation(s)
- Nguyen To Anh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | - Tran Tan Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Chuen-Yen Lau
- Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Direk Limmathurotsakul
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol Oxford Tropical Research Unit, Bangkok, Thailand
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Motiur Rahman
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Le Van Tan
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
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