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Tao X, Wang G, Wei W, Su J, Chen X, Shi M, Liao Y, Qin T, Wu Y, Lu B, Liang H, Ye L, Jiang J. A bibliometric analysis of m6A methylation in viral infection from 2000 to 2022. Virol J 2024; 21:20. [PMID: 38238848 PMCID: PMC10797797 DOI: 10.1186/s12985-024-02294-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 01/11/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) methylation has become an active research area in viral infection, while little bibliometric analysis has been performed. In this study, we aim to visualize hotspots and trends using bibliometric analysis to provide a comprehensive and objective overview of the current research dynamics in this field. METHODS The data related to m6A methylation in viral infection were obtained through the Web of Science Core Collection form 2000 to 2022. To reduce bias, the literature search was conducted on December 1, 2022. Bibliometric and visual analyzes were performed using CiteSpace and Bibliometrix package. After screening, 319 qualified records were retrieved. RESULTS These publications mainly came from 28 countries led by China and the United States (the US), with the US ranking highest in terms of total link strength.The most common keywords were m6A, COVID-19, epitranscriptomics, METTL3, hepatitis B virus, innate immunity and human immunodeficiency virus 1. The thematic map showed that METTL3, plant viruses, cancer progression and type I interferon (IFN-I) reflected a good development trend and might become a research hotspot in the future, while post-transcriptional modification, as an emerging or declining theme, might not develop well. CONCLUSIONS In conclusion, m6A methylation in viral infection is an increasingly important topic in articles. METTL3, plant viruses, cancer progression and IFN-I may still be research hotspots and trends in the future.
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Affiliation(s)
- Xing Tao
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Gang Wang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Wudi Wei
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
- Biosafety Level -3 Laboratory, Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Jinming Su
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
- Biosafety Level -3 Laboratory, Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Xiu Chen
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Minjuan Shi
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Yinlu Liao
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Tongxue Qin
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Yuting Wu
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Beibei Lu
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Hao Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China.
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China.
- Biosafety Level -3 Laboratory, Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China.
| | - Li Ye
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China.
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China.
| | - Junjun Jiang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China.
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China.
- Biosafety Level -3 Laboratory, Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China.
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Mafokwane T, Djikeng A, Nesengani LT, Dewar J, Mapholi O. Gastrointestinal Infection in South African Children under the Age of 5 years: A Mini Review. Gastroenterol Res Pract 2023; 2023:1906782. [PMID: 37663241 PMCID: PMC10469397 DOI: 10.1155/2023/1906782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 07/14/2023] [Accepted: 07/24/2023] [Indexed: 09/05/2023] Open
Abstract
Objective To estimate gastroenteritis disease and its etiological agents in children under the age of 5 years living in South Africa. Methods A mini literature review of pertinent articles published in ScienceDirect, PubMed, GoogleScholar, and Scopus was conducted using search terms: "Gastroenteritis in children," "Gastroenteritis in the world," Gastroenteritis in South Africa," "Prevalence of gastroenteritis," "Epidemiological surveillance of gastroenteritis in the world," and "Causes of gastroenteritis". Results A total of 174 published articles were included in this mini review. In the last 20 years, the mortality rate resulting from diarrhea in children under the age of 5 years has declined and this is influenced by improved hygiene practices, awareness programs, an improved water and sanitation supply, and the availability of vaccines. More modern genomic amplification techniques were used to re-analyze stool specimens collected from children in eight low-resource settings in Asia, South America, and Africa reported improved sensitivity of pathogen detection to about 65%, that viruses were the main etiological agents in patients with diarrhea aged from 0 to 11 months but that Shigella, followed by sapovirus and enterotoxigenic Escherichia coli had a high incidence in children aged 12-24 months. In addition, co-infections were noted in nearly 10% of diarrhea cases, with rotavirus and Shigella being the main co-infecting agents together with adenovirus, enteropathogenic E. coli, Clostridium jejuni, or Clostridium coli. Conclusions This mini review outlines the epidemiology and trends relating to parasitic, viral, and bacterial agents responsible for gastroenteritis in children in South Africa. An increase in sequence-independent diagnostic approaches will improve the identification of pathogens to resolve undiagnosed cases of gastroenteritis. Emerging state and national surveillance systems should focus on improving the identification of gastrointestinal pathogens in children and the development of further vaccines against gastrointestinal pathogens.
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Affiliation(s)
- Tshepo Mafokwane
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Science Campus, Florida, Johannesburg, South Africa
| | - Appolinaire Djikeng
- Department of Agriculture, College of Agriculture and Environmental Sciences, University of South Africa Science Campus, Florida, Johannesburg, South Africa
- Centre for Tropical Livestock Genetics and Health (CTLGH), Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Lucky T. Nesengani
- Department of Agriculture, College of Agriculture and Environmental Sciences, University of South Africa Science Campus, Florida, Johannesburg, South Africa
| | - John Dewar
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Science Campus, Florida, Johannesburg, South Africa
| | - Olivia Mapholi
- Department of Agriculture, College of Agriculture and Environmental Sciences, University of South Africa Science Campus, Florida, Johannesburg, South Africa
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François S, Nazki S, Vickers SH, Fournié G, Perrins CM, Broadbent AJ, Pybus OG, Hill SC. Genetic diversity, recombination and cross-species transmission of a waterbird gammacoronavirus in the wild. J Gen Virol 2023; 104. [PMID: 37589541 DOI: 10.1099/jgv.0.001883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023] Open
Abstract
Viruses emerging from wildlife can cause outbreaks in humans and domesticated animals. Predicting the emergence of future pathogens and mitigating their impacts requires an understanding of what shapes virus diversity and dynamics in wildlife reservoirs. In order to better understand coronavirus ecology in wild species, we sampled birds within a coastal freshwater lagoon habitat across 5 years, focussing on a large population of mute swans (Cygnus olor) and the diverse species that they interact with. We discovered and characterised the full genome of a divergent gammacoronavirus belonging to the Goose coronavirus CB17 species. We investigated the genetic diversity and dynamics of this gammacoronavirus using untargeted metagenomic sequencing of 223 faecal samples from swans of known age and sex, and RT-PCR screening of 1632 additional bird samples. The virus circulated persistently within the bird community; virus prevalence in mute swans exhibited seasonal variations, but did not change with swan age-class or epidemiological year. One whole genome was fully characterised, and revealed that the virus originated from a recombination event involving an undescribed gammacoronavirus species. Multiple lineages of this gammacoronavirus co-circulated within our study population. Viruses from this species have recently been detected in aquatic birds from both the Anatidae and Rallidae families, implying that host species habitat sharing may be important in shaping virus host range. As the host range of the Goose coronavirus CB17 species is not limited to geese, we propose that this species name should be updated to 'Waterbird gammacoronavirus 1'. Non-invasive sampling of bird coronaviruses may provide a tractable model system for understanding the evolutionary and cross-species dynamics of coronaviruses.
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Affiliation(s)
- Sarah François
- Department of Biology, University of Oxford, South Park Road, Oxford, OX1 3SY, UK
| | - Salik Nazki
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7FZ, UK
- The Pirbright Institute, Ash Rd, Pirbright, Woking GU24 0NF, UK
| | - Stephen H Vickers
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
| | - Guillaume Fournié
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, Marcy l'Etoile, France
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint-Gènes-Champanelle, France
| | | | - Andrew J Broadbent
- The Pirbright Institute, Ash Rd, Pirbright, Woking GU24 0NF, UK
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD20742, USA
| | - Oliver G Pybus
- Department of Biology, University of Oxford, South Park Road, Oxford, OX1 3SY, UK
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
| | - Sarah C Hill
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
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Pérez-Cataluña A, Randazzo W, Martínez-Blanch JF, Codoñer FM, Sánchez G. Sample and library preparation approaches for the analysis of the virome of irrigation water. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:4450-4457. [PMID: 36823282 DOI: 10.1002/jsfa.12522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 02/14/2023] [Accepted: 02/23/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND The virome (i.e. community of mainly RNA and DNA eukaryotic viruses and bacteriophages) of waters is yet to be extensively explored. In particular, the virome of waters used for irrigation could therefore potentially carry viral pathogens that can contaminate fresh produce. One problem in obtaining viral sequences from irrigation waters is the relatively low amount of virus particles, as well as the presence of human, bacterial and protozoan cells. The present aimed study was to compare different processing, amplification, and sequencing approaches for virome characterization in irrigation waters. RESULTS Our analyses considered percentages of viral reads, values for diversity indices and number of families found in sequencing results. The results obtained suggest that enrichment protocols using two (bezonase and microccocal nuclease) or four enzymes at once (bezonase, microccocal nuclease, DNAse and RNase), regardless of an Amicon filtration step, are more appropriate than separated enzymatic treatments for virome characterization in irrigation water. The NetoVIR protocol combined with the ScriptSeq v2 RNA-Seq Library (P0-L20 protocol) showed the highest percentages of RNA viruses and identified the higher number of families. CONCLUSION Although virome characterization applied in irrigation waters is an important tool for protecting public health by informing on circulating human and zoonotic infections, optimized and standardized procedures should be followed to reduce the variability of results related to either the sample itself and the downstream bioinformatics analyses. Our results show that virome characterization can be an important tool in the discovery of pathogenic viruses in the environment and can be used to inform and optimize reference-based detection methods provided that appropriate and rigorous controls are included. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Alba Pérez-Cataluña
- Department of Preservation and Food Safety Technologies, IATA-CSIC, Valencia, Spain
| | - Walter Randazzo
- Department of Preservation and Food Safety Technologies, IATA-CSIC, Valencia, Spain
| | | | - Francisco M Codoñer
- ADM-Lifesequencing - Health and Wellness - Adm Nutrition, Valencia, Spain
- Danone Nutricia Research, Singapore, Singapore
| | - Gloria Sánchez
- Department of Preservation and Food Safety Technologies, IATA-CSIC, Valencia, Spain
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Makori TO, Bargul JL, Lambisia AW, Mwanga MJ, Murunga N, de Laurent ZR, Lewa CS, Mutunga M, Kellam P, Cotten M, Nokes DJ, Phan M, Agoti CN. Genomic epidemiology of the rotavirus G2P[4] strains in coastal Kenya pre- and post-rotavirus vaccine introduction, 2012-8. Virus Evol 2023; 9:vead025. [PMID: 37207000 PMCID: PMC10190042 DOI: 10.1093/ve/vead025] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/07/2023] [Accepted: 04/14/2023] [Indexed: 05/21/2023] Open
Abstract
The introduction of rotavirus vaccines into the national immunization programme in many countries has led to a decline in childhood diarrhoea disease burden. Coincidentally, the incidence of some rotavirus group A (RVA) genotypes has increased, which may result from non-vaccine-type replacement. Here, we investigate the evolutionary genomics of rotavirus G2P[4] which has shown an increase in countries that introduced the monovalent Rotarix® vaccine. We examined sixty-three RVA G2P[4] strains sampled from children (aged below 13 years) admitted to Kilifi County Hospital, coastal Kenya, pre- (2012 to June 2014) and post-(July 2014 to 2018) rotavirus vaccine introduction. All the sixty-three genome sequences showed a typical DS-1-like genome constellation (G2-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2). Pre-vaccine G2 sequences predominantly classified as sub-lineage IVa-3 and co-circulated with low numbers of sub-lineage IVa-1 strains, whereas post-vaccine G2 sequences mainly classified into sub-lineage IVa-3. In addition, in the pre-vaccine period, P[4] sub-lineage IVa strains co-circulated with low numbers of P[4] lineage II strains, but P[4] sub-lineage IVa strains predominated in the post-vaccine period. On the global phylogeny, the Kenyan pre- and post-vaccine G2P[4] strains clustered separately, suggesting that different virus populations circulated in the two periods. However, the strains from both periods exhibited conserved amino acid changes in the known antigenic epitopes, suggesting that replacement of the predominant G2P[4] cluster was unlikely a result of immune escape. Our findings demonstrate that the pre- and post-vaccine G2P[4] strains circulating in Kilifi, coastal Kenya, differed genetically but likely were antigenically similar. This information informs the discussion on the consequences of rotavirus vaccination on rotavirus diversity.
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Affiliation(s)
- Timothy O Makori
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Kalimoni, PO Box 62000-00200, Juja, Kenya
| | - Joel L Bargul
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Kalimoni, PO Box 62000-00200, Juja, Kenya
- International Centre of Insect Physiology and Ecology, Animal Health Theme, ICIPE Road Kasarani, P.O BOX 30772-00100, Nairobi, Kenya
| | - Arnold W Lambisia
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
| | - Mike J Mwanga
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
| | - Nickson Murunga
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
| | - Zaydah R de Laurent
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
| | - Clement S Lewa
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
| | - Martin Mutunga
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
| | - Paul Kellam
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, Exhibition Road, London SW7 2AZ, UK
- Kymab Ltd, The Bennet Building (B930), Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Matthew Cotten
- Medical Research Centre (MRC)/Uganda Virus Research Institute, Plot No: 51-59 Nakiwogo Road, P.O.Box 49, Entebbe, Uganda
- MRC-University of Glasgow, Centre for Virus Research Glasgow, 464 Bearsden Road, Glasgow G61 1QH UK
| | - D James Nokes
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute (SBIDER), The University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK
| | - My Phan
- Medical Research Centre (MRC)/Uganda Virus Research Institute, Plot No: 51-59 Nakiwogo Road, P.O.Box 49, Entebbe, Uganda
- MRC-University of Glasgow, Centre for Virus Research Glasgow, 464 Bearsden Road, Glasgow G61 1QH UK
| | - Charles N Agoti
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
- School of Health and Human Sciences, Pwani University, Kilifi-Malindi Road, P.O BOX 195-80108, Kilifi, Kenya
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Hill SC, François S, Thézé J, Smith AL, Simmonds P, Perrins CM, van der Hoek L, Pybus OG. Impact of host age on viral and bacterial communities in a waterbird population. THE ISME JOURNAL 2023; 17:215-226. [PMID: 36319706 PMCID: PMC9860062 DOI: 10.1038/s41396-022-01334-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022]
Abstract
Wildlife harbour pathogens that can harm human or livestock health and are the source of most emerging infectious diseases. It is rarely considered how changes in wildlife population age-structures or how age-stratified behaviours might alter the level of pathogen detection within a species, or risk of spillover to other species. Micro-organisms that occur in healthy animals can be an important model for understanding and predicting the dynamics of pathogens of greater health concern, which are hard to study in wild populations due to their relative rarity. We therefore used a metagenomic approach to jointly characterise viral and prokaryotic carriage in faeces collected from a healthy wild bird population (Cygnus olor; mute swan) that has been subject to long-term study. Using 223 samples from known individuals allowed us to compare differences in prokaryotic and eukaryotic viral carriage between adults and juveniles at an unprecedented level of detail. We discovered and characterised 77 novel virus species, of which 21% belong putatively to bird-infecting families, and described the core prokaryotic microbiome of C. olor. Whilst no difference in microbiota diversity was observed between juveniles and adult individuals, 50% (4/8) of bird-infecting virus families (picornaviruses, astroviruses, adenoviruses and bornaviruses) and 3.4% (9/267) of prokaryotic families (including Helicobacteraceae, Spirochaetaceae and Flavobacteriaceae families) were differentially abundant and/or prevalent between juveniles and adults. This indicates that perturbations that affect population age-structures of wildlife could alter circulation dynamics and spillover risk of microbes, potentially including pathogens.
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Affiliation(s)
- Sarah C Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK.
- Department of Biology, University of Oxford, Oxford, UK.
| | - Sarah François
- Department of Biology, University of Oxford, Oxford, UK.
| | - Julien Thézé
- Department of Biology, University of Oxford, Oxford, UK
- UMR EPIA, Université Clermont Auvergne, INRAE, VetAgro Sup, Saint-Genès-Champanelle, France
| | - Adrian L Smith
- Department of Biology, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, UK
| | | | - Lia van der Hoek
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Oliver G Pybus
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK.
- Department of Biology, University of Oxford, Oxford, UK.
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Araujo NM, Osiowy C. Hepatitis B Virus Genotype G: The Odd Cousin of the Family. Front Microbiol 2022; 13:872766. [PMID: 35432294 PMCID: PMC9009205 DOI: 10.3389/fmicb.2022.872766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
With a widespread distribution but low prevalence worldwide, the hepatitis B virus (HBV) genotype G (HBV/G) is a recently described genotype for which the origin and biology are poorly understood. Some unique features make HBV/G the most peculiar of all genotypes. In this review, we reflect on the major milestones in HBV/G research, highlighting the main aspects of its discovery, molecular epidemiology, and virological and clinical characteristics. We also illustrate common pitfalls in the routine detection, which may lead to underestimated rates of HBV/G infection. Large-scale analysis of data from dozens of articles was further performed, with the aim of gaining comprehensive insights into the epidemiological aspects of HBV/G. Finally, we point out recent findings on HBV/G origins and discuss new perspectives regarding the evolutionary history of HBV/G and the plausibility of an African geographic re-emergence of this genotype.
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Affiliation(s)
- Natalia M. Araujo
- Laboratory of Molecular Virology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Carla Osiowy
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- *Correspondence: Carla Osiowy,
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8
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Lu L, Ashworth J, Nguyen D, Li K, Smith DB, Woolhouse M. No Exchange of Picornaviruses in Vietnam between Humans and Animals in a High-Risk Cohort with Close Contact despite High Prevalence and Diversity. Viruses 2021; 13:v13091709. [PMID: 34578290 PMCID: PMC8473303 DOI: 10.3390/v13091709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 02/03/2023] Open
Abstract
Hospital-based and community-based 'high-risk cohort' studies investigating humans at risk of zoonotic infection due to occupational or residential exposure to animals were conducted in Vietnam, with diverse viruses identified from faecal samples collected from humans, domestic and wild animals. In this study, we focus on the positive-sense RNA virus family Picornaviridae, investigating the prevalence, diversity, and potential for cross-species transmission. Through metagenomic sequencing, we found picornavirus contigs in 23% of samples, belonging to 15 picornavirus genera. Prevalence was highest in bats (67%) while diversity was highest in rats (nine genera). In addition, 22% of the contigs were derived from novel viruses: Twelve phylogenetically distinct clusters were observed in rats of which seven belong to novel species or types in the genera Hunnivirus, Parechovirus, Cardiovirus, Mosavirus and Mupivirus; four distinct clusters were found in bats, belonging to one novel parechovirus species and one related to an unclassified picornavirus. There was no evidence for zoonotic transmission in our data. Our study provides an improved knowledge of the diversity and prevalence of picornaviruses, including a variety of novel picornaviruses in rats and bats. We highlight the importance of monitoring the human-animal interface for possible spill-over events.
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Affiliation(s)
- Lu Lu
- Usher Institute, University of Edinburgh, Edinburgh EH9 3FL, UK; (J.A.); (M.W.)
- Correspondence:
| | - Jordan Ashworth
- Usher Institute, University of Edinburgh, Edinburgh EH9 3FL, UK; (J.A.); (M.W.)
| | - Dung Nguyen
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; (D.N.); (D.B.S.)
| | - Kejin Li
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK;
| | - Donald B. Smith
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; (D.N.); (D.B.S.)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK;
| | - Mark Woolhouse
- Usher Institute, University of Edinburgh, Edinburgh EH9 3FL, UK; (J.A.); (M.W.)
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9
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Roach M, Cantu A, Vieri MK, Cotten M, Kellam P, Phan M, van der Hoek L, Mandro M, Tepage F, Mambandu G, Musinya G, Laudisoit A, Colebunders R, Edwards R, Mokili JL. No Evidence Known Viruses Play a Role in the Pathogenesis of Onchocerciasis-Associated Epilepsy. An Explorative Metagenomic Case-Control Study. Pathogens 2021; 10:pathogens10070787. [PMID: 34206564 PMCID: PMC8308762 DOI: 10.3390/pathogens10070787] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/11/2021] [Accepted: 06/17/2021] [Indexed: 11/16/2022] Open
Abstract
Despite the increasing epidemiological evidence that the Onchocerca volvulus parasite is strongly associated with epilepsy in children, hence the name onchocerciasis-associated epilepsy (OAE), the pathophysiological mechanism of OAE remains to be elucidated. In June 2014, children with unprovoked convulsive epilepsy and healthy controls were enrolled in a case control study in Titule, Bas-Uélé Province in the Democratic Republic of the Congo (DRC) to identify risk factors for epilepsy. Using a subset of samples collected from individuals enrolled in this study (16 persons with OAE and 9 controls) plasma, buffy coat, and cerebrospinal fluid (CSF) were subjected to random-primed next-generation sequencing. The resulting sequences were analyzed using sensitive computational methods to identify viral DNA and RNA sequences. Anneloviridae, Flaviviridae, Hepadnaviridae (Hepatitis B virus), Herpesviridae, Papillomaviridae, Polyomaviridae (Human polyomavirus), and Virgaviridae were identified in cases and in controls. Not unexpectedly, a variety of bacteriophages were also detected in all cases and controls. However, none of the identified viral sequences were found enriched in OAE cases, which was our criteria for agents that might play a role in the etiology or pathogenesis of OAE.
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Affiliation(s)
- Michael Roach
- College of Science and Engineering, Flinders University, Adelaide, SA 5001, Australia; (M.R.); (R.E.)
| | - Adrian Cantu
- Computational Sciences Research Center, Biology Department, San Diego State University, San Diego, CA 92182, USA;
| | - Melissa Krizia Vieri
- Global Health Institute, University of Antwerp, 2160 Antwerp, Belgium; (M.K.V.); (R.C.)
| | - Matthew Cotten
- Wellcome Trust Sanger Institute, Hinxton CB10 1RQ, UK;
- MRC/UVRI and London School of Hygiene and Tropical Medicine, Entebbe, Uganda; (P.K.); (M.P.)
- Centre for Virus Research, MRC-University of Glasgow, Glasgow G61 1QH, UK
| | - Paul Kellam
- MRC/UVRI and London School of Hygiene and Tropical Medicine, Entebbe, Uganda; (P.K.); (M.P.)
| | - My Phan
- MRC/UVRI and London School of Hygiene and Tropical Medicine, Entebbe, Uganda; (P.K.); (M.P.)
- Centre for Virus Research, MRC-University of Glasgow, Glasgow G61 1QH, UK
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1012 WX Amsterdam, The Netherlands;
| | - Michel Mandro
- Provincial Health Division Ituri, Ministry of Health, Ituri, Congo;
| | - Floribert Tepage
- Provincial Health Division Bas Uélé, Ministry of Health, Bas Uélé, Congo;
| | - Germain Mambandu
- Provincial Health Division Tshopo, Ministry of Health, Tshopo, Congo;
| | | | | | - Robert Colebunders
- Global Health Institute, University of Antwerp, 2160 Antwerp, Belgium; (M.K.V.); (R.C.)
| | - Robert Edwards
- College of Science and Engineering, Flinders University, Adelaide, SA 5001, Australia; (M.R.); (R.E.)
- Computational Sciences Research Center, Biology Department, San Diego State University, San Diego, CA 92182, USA;
- Viral Information Institute, Biology Department, San Diego State University, San Diego, CA 92182, USA
| | - John L. Mokili
- Viral Information Institute, Biology Department, San Diego State University, San Diego, CA 92182, USA
- Correspondence:
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10
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Allesøe RL, Lemvigh CK, Phan MVT, Clausen PTLC, Florensa AF, Koopmans MPG, Lund O, Cotten M. Automated download and clean-up of family-specific databases for kmer-based virus identification. Bioinformatics 2021; 37:705-710. [PMID: 33031509 PMCID: PMC8097684 DOI: 10.1093/bioinformatics/btaa857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 09/09/2020] [Accepted: 09/23/2020] [Indexed: 12/17/2022] Open
Abstract
SUMMARY Here, we present an automated pipeline for Download Of NCBI Entries (DONE) and continuous updating of a local sequence database based on user-specified queries. The database can be created with either protein or nucleotide sequences containing all entries or complete genomes only. The pipeline can automatically clean the database by removing entries with matches to a database of user-specified sequence contaminants. The default contamination entries include sequences from the UniVec database of plasmids, marker genes and sequencing adapters from NCBI, an E.coli genome, rRNA sequences, vectors and satellite sequences. Furthermore, duplicates are removed and the database is automatically screened for sequences from green fluorescent protein, luciferase and antibiotic resistance genes that might be present in some GenBank viral entries, and could lead to false positives in virus identification. For utilizing the database, we present a useful opportunity for dealing with possible human contamination. We show the applicability of DONE by downloading a virus database comprising 37 virus families. We observed an average increase of 16 776 new entries downloaded per month for the 37 families. In addition, we demonstrate the utility of a custom database compared to a standard reference database for classifying both simulated and real sequence data. AVAILABILITYAND IMPLEMENTATION The DONE pipeline for downloading and cleaning is deposited in a publicly available repository (https://bitbucket.org/genomicepidemiology/done/src/master/). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rosa L Allesøe
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Camilla K Lemvigh
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.,Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - My V T Phan
- Department of Viroscience, Erasmus University Medical Centre, 3000 CA Rotterdam, The Netherlands
| | - Philip T L C Clausen
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Alfred F Florensa
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Centre, 3000 CA Rotterdam, The Netherlands
| | - Ole Lund
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Matthew Cotten
- Department of Viroscience, Erasmus University Medical Centre, 3000 CA Rotterdam, The Netherlands.,MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda.,MRC-University of Glasgow Centre for Virus Research, G61 1QH Scotland, UK
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11
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Fitzpatrick AH, Rupnik A, O'Shea H, Crispie F, Keaveney S, Cotter P. High Throughput Sequencing for the Detection and Characterization of RNA Viruses. Front Microbiol 2021; 12:621719. [PMID: 33692767 PMCID: PMC7938315 DOI: 10.3389/fmicb.2021.621719] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
This review aims to assess and recommend approaches for targeted and agnostic High Throughput Sequencing of RNA viruses in a variety of sample matrices. HTS also referred to as deep sequencing, next generation sequencing and third generation sequencing; has much to offer to the field of environmental virology as its increased sequencing depth circumvents issues with cloning environmental isolates for Sanger sequencing. That said however, it is important to consider the challenges and biases that method choice can impart to sequencing results. Here, methodology choices from RNA extraction, reverse transcription to library preparation are compared based on their impact on the detection or characterization of RNA viruses.
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Affiliation(s)
- Amy H. Fitzpatrick
- Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland
- Shellfish Microbiology, Marine Institute, Oranmore, Ireland
- Biological Sciences, Munster Technological University, Cork, Ireland
| | | | - Helen O'Shea
- Biological Sciences, Munster Technological University, Cork, Ireland
| | - Fiona Crispie
- Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland
| | | | - Paul Cotter
- Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland
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12
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Nantel-Fortier N, Gauthier M, L'Homme Y, Fravalo P, Brassard J. Treatments of porcine fecal samples affect high-throughput virome sequencing results. J Virol Methods 2020; 289:114045. [PMID: 33333107 DOI: 10.1016/j.jviromet.2020.114045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 12/17/2022]
Abstract
The porcine enteric microbiota is currently extensively studied, taking advantage of developments in high-throughput sequencing technologies. However, the viral part of the microbiota, the virome, is being lightly explored, and the impact of the pretreatments used before sequencing the viruses is barely considered. In this study, the impacts of filtration, RNase and DNase treatments on virus reads recovery and diversity after sequencing on a MiSeq platform were assessed on fecal samples individually taken at <3, 5, 12 and 20 weeks from two piglets. None of the four pretreatment series affected the virus read averages or influenced diversity, but the samples with the higher proportion of reads corresponding to an entry in the "nt" database were those receiving the least number of pretreatments. The enzymatic pretreatments affected the detection of the single-stranded RNA viruses of Aichivirus C, porcine astrovirus, Sapovirus and posavirus, which is worrisome, as these viruses can be involved in swine diarrhea. If enzymatic pretreatments are used when sequencing using a high-throughput method, it may impact single-stranded RNA virus recovery, but not the overall virome diversity. Therefore, filtrated samples may be the better option, reducing the amount of bacterial genetic material while preserving the virus reads.
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Affiliation(s)
- Nicolas Nantel-Fortier
- Research Chair in Meat Safety, Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Quebec, Canada; Swine and Poultry Infections Disease Research Center (CRIPA-FRQNT), University of Montreal, Canada
| | - Martin Gauthier
- Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Hyacinthe, Quebec, Canada
| | - Yvan L'Homme
- Swine and Poultry Infections Disease Research Center (CRIPA-FRQNT), University of Montreal, Canada; CEGEP Garneau, Quebec City, Quebec, Canada
| | - Philippe Fravalo
- Research Chair in Meat Safety, Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Quebec, Canada; Swine and Poultry Infections Disease Research Center (CRIPA-FRQNT), University of Montreal, Canada
| | - Julie Brassard
- Swine and Poultry Infections Disease Research Center (CRIPA-FRQNT), University of Montreal, Canada; Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Hyacinthe, Quebec, Canada.
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13
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Metagenomic Analysis of the Enteric RNA Virome of Infants from the Oukasie Clinic, North West Province, South Africa, Reveals Diverse Eukaryotic Viruses. Viruses 2020; 12:v12111260. [PMID: 33167516 PMCID: PMC7694487 DOI: 10.3390/v12111260] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 12/25/2022] Open
Abstract
Establishing a diverse gut microbiota after birth is essential for preventing illnesses later in life. However, little knowledge exists about the total viral population (virome) present in the gut of infants during the early developmental stage, with RNA viruses being generally overlooked. Therefore, this small pilot longitudinal study investigated the diversity and changes in the enteric RNA virome in healthy infants from South Africa. Faecal samples (n = 12) were collected from four infants at three time points (on average at 8, 13, and 25 weeks), and then sequenced on an Illumina MiSeq platform. The genomic analysis revealed a diverse population of human enteric viruses from the infants’ stools, and changes in the enteric virome composition were observed over time. The Reoviridae family, more specifically the Rotavirus genus, was the most common and could be linked to viral shedding due to the administration of live-attenuated oral vaccines in South Africa, followed by the Picornaviridae family including parechoviruses, echoviruses, coxsackieviruses, enteroviruses, and polioviruses. Polioviruses were also linked to vaccine-related shedding. Astroviridae (astroviruses) and Caliciviridae (noroviruses) were present at low abundance. It is evident that an infant’s gut is colonized by distinct viral populations irrespective of their health state. Further characterization of the human virome (with a larger participant pool) is imperative to provide more conclusive insights into the viral community structure and diversity that has been shown in the current study, despite the smaller sample size.
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14
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Kinsella CM, Bart A, Deijs M, Broekhuizen P, Kaczorowska J, Jebbink MF, van Gool T, Cotten M, van der Hoek L. Entamoeba and Giardia parasites implicated as hosts of CRESS viruses. Nat Commun 2020; 11:4620. [PMID: 32934242 PMCID: PMC7493932 DOI: 10.1038/s41467-020-18474-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 08/25/2020] [Indexed: 12/13/2022] Open
Abstract
Metagenomic techniques have enabled genome sequencing of unknown viruses without isolation in cell culture, but information on the virus host is often lacking, preventing viral characterisation. High-throughput methods capable of identifying virus hosts based on genomic data alone would aid evaluation of their medical or biological relevance. Here, we address this by linking metagenomic discovery of three virus families in human stool samples with determination of probable hosts. Recombination between viruses provides evidence of a shared host, in which genetic exchange occurs. We utilise networks of viral recombination to delimit virus-host clusters, which are then anchored to specific hosts using (1) statistical association to a host organism in clinical samples, (2) endogenous viral elements in host genomes, and (3) evidence of host small RNA responses to these elements. This analysis suggests two CRESS virus families (Naryaviridae and Nenyaviridae) infect Entamoeba parasites, while a third (Vilyaviridae) infects Giardia duodenalis. The trio supplements five CRESS virus families already known to infect eukaryotes, extending the CRESS virus host range to protozoa. Phylogenetic analysis implies CRESS viruses infecting multicellular life have evolved independently on at least three occasions.
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Affiliation(s)
- Cormac M Kinsella
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
| | - Aldert Bart
- Laboratory of Clinical Parasitology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Patricia Broekhuizen
- Laboratory of Clinical Parasitology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Joanna Kaczorowska
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Maarten F Jebbink
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Tom van Gool
- Laboratory of Clinical Parasitology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Matthew Cotten
- MRC/UVRI & LSHTM Uganda Research Unit, 3FC6+Q3, Entebbe, Uganda.,MRC-University of Glasgow Centre for Virus Research, G61 1QH, Glasgow, UK
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
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15
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Strubbia S, Schaeffer J, Besnard A, Wacrenier C, Le Mennec C, Garry P, Desdouits M, Le Guyader FS. Metagenomic to evaluate norovirus genomic diversity in oysters: Impact on hexamer selection and targeted capture-based enrichment. Int J Food Microbiol 2020; 323:108588. [PMID: 32200157 DOI: 10.1016/j.ijfoodmicro.2020.108588] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 02/08/2023]
Abstract
Human virus transmission through food consumption has been identified since many years and the international trade increases the risk of dissemination of viral pathogens. The development of metagenomic approach holds many promises for the surveillance of viruses in food and water. This work aimed to analyze norovirus diversity and to evaluate strain-dependent accumulation patterns in three oyster types by using a metagenomic approach. Different hexamer sets to prime cDNA were evaluated before capture-based approach to enhance virus reads recovery during deep sequencing. The study includes the use of technical replicates of artificially contaminated oysters and the analysis of multiple negatives controls. Results showed a clear impact of the hexamer set used for cDNA synthesis. A set of In-house designed (I-HD) hexamers, selected to lower mollusk amplification, gave promising results in terms of viral reads abundancy. However, the best correlation between CT values, thus concentrations, and number of reads was observed using random hexamers. Random hexamers also provided the highest numbers of reads and allowed the identification of sequence of different human enteric viruses. Regarding human norovirus, different genogroups and genotypes were identified among contigs longer than 500 bp. Two full genomes and six sequences longer than 3600 bases were obtained allowing a precise strain identification. The use of technical triplicates was found valuable to increase the chances to sequence viral strains present at low concentrations. Analyzing viral contamination in shellfish samples is quite challenging, however this work demonstrates that the recovery of full genome or long contigs, allowing clear identification of viral strains is possible.
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Affiliation(s)
| | | | - Alban Besnard
- Ifremer, Laboratoire de Microbiologie LSEM-SG2M, France
| | | | | | - Pascal Garry
- Ifremer, Laboratoire de Microbiologie LSEM-SG2M, France
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16
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Wainaina E, Otieno CA, Kamau J, Nyachieo A, Lowther SA. Norovirus infections and knowledge, attitudes and practices in food safety among food handlers in an informal urban settlement, Kenya 2017. BMC Public Health 2020; 20:474. [PMID: 32276622 PMCID: PMC7146951 DOI: 10.1186/s12889-020-8401-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/24/2020] [Indexed: 01/18/2023] Open
Abstract
Introduction A leading cause of acute gastroenteritis, norovirus can be transmitted by infected food handlers but norovirus outbreaks are not routinely investigated in Kenya. We estimated norovirus prevalence and associated factors among food handlers in an informal urban settlement in Nairobi, Kenya. Methods We conducted a cross-sectional survey among food handlers using pretested questionnaires and collected stool specimens from food handlers which were analyzed for norovirus by conventional PCR. We observed practices that allow norovirus transmission and surveyed respondents on knowledge, attitudes, and practices in food safety. We calculated odd ratios (OR) with 95% confidence intervals (CI) to identify factors associated with norovirus infection. Variables with p < 0.05 were included in multivariate logistic regression analysis to calculate adjusted OR and 95% CI. Results Of samples from 283 respondents, 43 (15.2%) tested positive for norovirus. Factors associated with norovirus detection were: reporting diarrhea and vomiting within the previous month (AOR = 5.7, 95% CI = 1.2–27.4), not knowing aerosols from infected persons can contaminate food (AOR = 6.5, 95% CI = 1.1–37.5), not knowing that a dirty chopping board can contaminate food (AOR = 26.1, 95% CI = 1.6–416.7), observing respondents touching food bare-handed (AOR = 3.7, 95% CI = 1.5–11.1), and working in premises without hand washing services (AOR = 20, 95% CI = 3.4–100.0). Conclusion The norovirus infection was prevalent amongst food handlers and factors associated with infection were based on knowledge and practices of food hygiene. We recommend increased hygiene training and introduce more routine inclusion of norovirus testing in outbreaks in Kenya.
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Affiliation(s)
- Eliud Wainaina
- Moi University, Eldoret, Kenya. .,Field Epidemiology and Laboratory Training Program, Ministry of Health Program, Kenyatta National Hospital Grounds, P.O Box 22313-00100, Nairobi, Kenya.
| | | | - Joseph Kamau
- Institute of Primate Research, Karen, Kenya.,University of Nairobi, Nairobi, Kenya
| | - Atunga Nyachieo
- Institute of Primate Research, Karen, Kenya.,University of Nairobi, Nairobi, Kenya
| | - Sara A Lowther
- Centers for Disease Control and Prevention, Atlanta, GA, USA
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17
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Artika IM, Wiyatno A, Ma'roef CN. Pathogenic viruses: Molecular detection and characterization. INFECTION GENETICS AND EVOLUTION 2020; 81:104215. [PMID: 32006706 PMCID: PMC7106233 DOI: 10.1016/j.meegid.2020.104215] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 01/23/2020] [Accepted: 01/28/2020] [Indexed: 12/14/2022]
Abstract
Pathogenic viruses are viruses that can infect and replicate within human cells and cause diseases. The continuous emergence and re-emergence of pathogenic viruses has become a major threat to public health. Whenever pathogenic viruses emerge, their rapid detection is critical to enable implementation of specific control measures and the limitation of virus spread. Further molecular characterization to better understand these viruses is required for the development of diagnostic tests and countermeasures. Advances in molecular biology techniques have revolutionized the procedures for detection and characterization of pathogenic viruses. The development of PCR-based techniques together with DNA sequencing technology, have provided highly sensitive and specific methods to determine virus circulation. Pathogenic viruses potentially having global catastrophic consequences may emerge in regions where capacity for their detection and characterization is limited. Development of a local capacity to rapidly identify new viruses is therefore critical. This article reviews the molecular biology of pathogenic viruses and the basic principles of molecular techniques commonly used for their detection and characterization. The principles of good laboratory practices for handling pathogenic viruses are also discussed. This review aims at providing researchers and laboratory personnel with an overview of the molecular biology of pathogenic viruses and the principles of molecular techniques and good laboratory practices commonly implemented for their detection and characterization. The continous emergence and re-emergence of pathogenic viruses has become a major threat to public health. PCR-based techniques together with DNA sequencing technology have provided highly sensitive and specific methods to determine virus circulation. Southeast Asia is considered to be vulnerable to potential outbreaks of pathogenic viruses. A number of pathogenic viruses have been reported to circulate in this region. The 2019 novel coronavirus has also been identified in Southeast Asia. Development of local capacity to rapidly identify new viruses is very important.
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Affiliation(s)
- I Made Artika
- Biosafety Level 3 Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia; Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Darmaga Campus, Bogor 16680, Indonesia.
| | - Ageng Wiyatno
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia
| | - Chairin Nisa Ma'roef
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia
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18
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Strubbia S, Phan MVT, Schaeffer J, Koopmans M, Cotten M, Le Guyader FS. Characterization of Norovirus and Other Human Enteric Viruses in Sewage and Stool Samples Through Next-Generation Sequencing. FOOD AND ENVIRONMENTAL VIROLOGY 2019; 11:400-409. [PMID: 31446609 PMCID: PMC6848244 DOI: 10.1007/s12560-019-09402-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 08/17/2019] [Indexed: 05/06/2023]
Abstract
This study aimed to optimize a method to identify human enteric viruses in sewage and stool samples using random primed next-generation sequencing. We tested three methods, two employed virus enrichment based on the binding properties of the viral capsid using pig-mucin capture or by selecting viral RNA prior to library preparation through a capture using the SureSelect target enrichment. The third method was based on a non-specific biophysical precipitation with polyethylene glycol. Full genomes of a number of common human enteric viruses including norovirus, rotavirus, husavirus, enterovirus and astrovirus were obtained. In stool samples full norovirus genome were detected as well as partial enterovirus genome. A variety of norovirus sequences was detected in sewage samples, with genogroup II being more prevalent. Interestingly, the pig-mucin capture enhanced not only the recovery of norovirus and rotavirus but also recovery of astrovirus, sapovirus and husavirus. Documenting sewage virome using these methods provides information for molecular epidemiology and may be useful in developing strategies to prevent further spread of viruses.
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Affiliation(s)
- Sofia Strubbia
- Ifremer, Laboratoire de Microbiologie, LSEM-SG2M, BP 21105, 44311, Nantes Cedex 3, France
| | - My V T Phan
- Department of Viroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Julien Schaeffer
- Ifremer, Laboratoire de Microbiologie, LSEM-SG2M, BP 21105, 44311, Nantes Cedex 3, France
| | - Marion Koopmans
- Department of Viroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Matthew Cotten
- Department of Viroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- London School of Hygiene and Tropical Medicine, London, UK
- Uganda Virus Research Institute, Entebbe, Uganda
- MRC-Centre for Virus Research, Glasgow, UK
| | - Françoise S Le Guyader
- Ifremer, Laboratoire de Microbiologie, LSEM-SG2M, BP 21105, 44311, Nantes Cedex 3, France.
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19
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Strubbia S, Schaeffer J, Oude Munnink BB, Besnard A, Phan MVT, Nieuwenhuijse DF, de Graaf M, Schapendonk CME, Wacrenier C, Cotten M, Koopmans MPG, Le Guyader FS. Metavirome Sequencing to Evaluate Norovirus Diversity in Sewage and Related Bioaccumulated Oysters. Front Microbiol 2019; 10:2394. [PMID: 31681246 PMCID: PMC6811496 DOI: 10.3389/fmicb.2019.02394] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/03/2019] [Indexed: 12/20/2022] Open
Abstract
Metagenomic sequencing is a promising method to determine the virus diversity in environmental samples such as sewage or shellfish. However, to identify the short RNA genomes of human enteric viruses among the large diversity of nucleic acids present in such complex matrices, method optimization is still needed. This work presents methodological developments focused on norovirus, a small ssRNA non-enveloped virus known as the major cause of human gastroenteritis worldwide and frequently present in human excreta and sewage. Different elution protocols were applied and Illumina MiSeq technology were used to study norovirus diversity. A double approach, agnostic deep sequencing and a capture-based approach (VirCapSeq-VERT) was used to identify norovirus in environmental samples. Family-specific viral contigs were classified and sorted by SLIM and final norovirus contigs were genotyped using the online Norovirus genotyping tool v2.0. From sewage samples, 14 norovirus genogroup I sequences were identified of which six were complete genomes. For norovirus genogroup II, nine sequences were identified and three of them comprised more than half of the genome. In oyster samples bioaccumulated with these sewage samples, only the use of an enrichment step during library preparation allowed successful identification of nine different sequences of norovirus genogroup I and four for genogroup II (>500 bp). This study demonstrates the importance of method development to increase virus recovery, and the interest of a capture-based approach to be able to identify viruses present at low concentrations.
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Affiliation(s)
- Sofia Strubbia
- Laboratoire de Microbiologie, LSEM-SG2M-RBE, Ifremer, Nantes, France
| | - Julien Schaeffer
- Laboratoire de Microbiologie, LSEM-SG2M-RBE, Ifremer, Nantes, France
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Alban Besnard
- Laboratoire de Microbiologie, LSEM-SG2M-RBE, Ifremer, Nantes, France
| | - My V T Phan
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - David F Nieuwenhuijse
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | - Candice Wacrenier
- Laboratoire de Microbiologie, LSEM-SG2M-RBE, Ifremer, Nantes, France
| | - Matthew Cotten
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
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20
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Woolhouse M, Ashworth J, Bogaardt C, Tue NT, Baker S, Thwaites G, Phuc TM. Sample descriptors linked to metagenomic sequencing data from human and animal enteric samples from Vietnam. Sci Data 2019; 6:202. [PMID: 31615980 PMCID: PMC6794271 DOI: 10.1038/s41597-019-0215-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 08/21/2019] [Indexed: 11/09/2022] Open
Abstract
There is still limited information on the diversity of viruses co-circulating in humans and animals. Here, we report data obtained from a large field collection of enteric samples taken from humans, pigs, rodents and other mammal hosts in Vietnam between 2012 and 2016. Each of 2100 stool or rectal swab samples was subjected to virally-enriched agnostic metagenomic sequencing; the short read sequence data are accessible from the European Nucleotide Archive (ENA). We link the sequence data to metadata on host type and demography and geographic location, distinguishing hospital patients, members of a cohort identified as a high risk of zoonotic infections (e.g. abattoir workers, rat traders) and animals. These data are suitable for further studies of virus diversity and virus discovery in humans and animals from Vietnam and to identify viruses found in multiple hosts that are potentially zoonotic.
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Affiliation(s)
- Mark Woolhouse
- Usher Institute, University of Edinburgh, Edinburgh, UK.
| | | | | | - Ngo Tri Tue
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam
| | - Steve Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID) Department of Medicine, University of Cambridge, Cambridge, UK
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam
| | - Tran My Phuc
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam
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21
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Detection of human immunodeficiency virus (HIV) RNA in the sweat of HIV-infected patients. North Clin Istanb 2019; 7:6-10. [PMID: 32232197 PMCID: PMC7103743 DOI: 10.14744/nci.2019.56255] [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: 10/23/2019] [Accepted: 05/23/2019] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVE: Human immunodeficiency virus (HIV) infection is a significant health problem. Many studies reported that HIV was mainly transmitted through parenteral exposure, sexual activity, and body secretions, such as saliva and semen. Many people, including health-care providers and patient relatives, may easily contact with the sweat of HIV-infected patients. Although reference books assert that HIV does not transmit through sweat, to our knowledge, there is no systemic study which this statement is based upon. This study aims to investigate the potential of sweat to transmit HIV infection. METHODS: This study included 31 treatment-naive HIV RNA-positive patients who were in the acute phase of the infection and 26 subjects with a negative HIV RNA test who had received antiviral treatment. A total of 57 sweat samples collected from intact skin areas were prospectively evaluated by polymerase chain reaction (PCR) for the presence of HIV RNA. HIV RNA levels in the blood samples were also noted. RESULTS: HIV RNA was not detected by PCR in any sweat sample taken from HIV-infected HIV RNA-negative and -positive subjects. CONCLUSION: The findings obtained in this study suggest that sweat by itself has no potential for transmitting HIV infection.
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22
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van Beek J, de Graaf M, Smits S, Schapendonk CME, Verjans GMGM, Vennema H, van der Eijk AA, Phan MVT, Cotten M, Koopmans M. Whole-Genome Next-Generation Sequencing to Study Within-Host Evolution of Norovirus (NoV) Among Immunocompromised Patients With Chronic NoV Infection. J Infect Dis 2019; 216:1513-1524. [PMID: 29029115 DOI: 10.1093/infdis/jix520] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 09/22/2017] [Indexed: 01/29/2023] Open
Abstract
Background The genus Norovirus comprises large genetic diversity, and new GII.4 variants emerge every 2-3 years. It is unknown in which host these new variants originate. Here we study whether prolonged shedders within the immunocompromised population could be a reservoir for newly emerging strains. Methods Sixty-five fecal samples from 16 immunocompromised patients were retrospectively selected. Isolated viral RNA was enriched by hybridization with a custom norovirus whole-genome RNA bait set and deep sequenced on the Illumina MiSeq platform. Results Patients shed virus for average 352 days (range, 76-716 days). Phylogenetic analysis showed distinct GII.4 variants in 3 of 13 patients (23%). The viral mutation rates were variable between patients but did not differ between various immune status groups. All within-host GII.4 viral populations showed amino acid changes at blocking epitopes over time, and the majority of VP1 amino acid mutations were located at the capsid surface. Conclusions This study found viruses in immunocompromised hosts that are genetically distinct from viruses circulating in the general population, and these patients therefore may contain a reservoir for newly emerging strains. Future studies need to determine whether these new strains are of risk to other immunocompromised patients and the general population.
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Affiliation(s)
- Janko van Beek
- Department of Viroscience, Erasmus Medical Center, Bilthoven, the Netherlands.,Center for Infectious Diseases Research, Diagnostics, and Screening, National Institute of Public Health and the Environment, Bilthoven, the Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus Medical Center, Bilthoven, the Netherlands
| | - Saskia Smits
- Department of Viroscience, Erasmus Medical Center, Bilthoven, the Netherlands.,Viroclinics Biosciences, Rotterdam, Bilthoven, the Netherlands
| | | | | | - Harry Vennema
- Center for Infectious Diseases Research, Diagnostics, and Screening, National Institute of Public Health and the Environment, Bilthoven, the Netherlands
| | | | - My V T Phan
- Department of Viroscience, Erasmus Medical Center, Bilthoven, the Netherlands
| | - Matthew Cotten
- Department of Viroscience, Erasmus Medical Center, Bilthoven, the Netherlands
| | - Marion Koopmans
- Department of Viroscience, Erasmus Medical Center, Bilthoven, the Netherlands
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23
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Fernández-Orth D, Miró E, Brown-Jaque M, Rodríguez-Rubio L, Espinal P, Rodriguez-Navarro J, González-López JJ, Muniesa M, Navarro F. Faecal phageome of healthy individuals: presence of antibiotic resistance genes and variations caused by ciprofloxacin treatment. J Antimicrob Chemother 2019; 74:854-864. [DOI: 10.1093/jac/dky540] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/19/2018] [Accepted: 11/26/2018] [Indexed: 12/12/2022] Open
Affiliation(s)
| | - Elisenda Miró
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, Barcelona, Spain
| | - Maryury Brown-Jaque
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Diagonal 643, Annex, Floor 0, Barcelona, Spain
| | - Lorena Rodríguez-Rubio
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Diagonal 643, Annex, Floor 0, Barcelona, Spain
| | - Paula Espinal
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, Barcelona, Spain
| | - Judith Rodriguez-Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Juan José González-López
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Clinical Microbiology, Hospital Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Pg Vall d’Hebron 119-129, Barcelona, Spain
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Diagonal 643, Annex, Floor 0, Barcelona, Spain
| | - Ferran Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
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24
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Kamau E, Agoti CN, Ngoi JM, de Laurent ZR, Gitonga J, Cotten M, Phan MVT, Nokes DJ, Delwart E, Sanders E, Warimwe GM. Complete Genome Sequences of Dengue Virus Type 2 Strains from Kilifi, Kenya. Microbiol Resour Announc 2019; 8:e01566-18. [PMID: 30701251 PMCID: PMC6346200 DOI: 10.1128/mra.01566-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 01/02/2019] [Indexed: 12/16/2022] Open
Abstract
Dengue infection remains poorly characterized in Africa and little is known regarding its associated viral genetic diversity. Here, we report dengue virus type 2 (DENV-2) sequence data from 10 clinical samples, including 5 complete genome sequences of the cosmopolitan genotype, obtained from febrile adults seeking outpatient care in coastal Kenya.
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Affiliation(s)
- Everlyn Kamau
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Joyce M Ngoi
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - John Gitonga
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Matthew Cotten
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - My V T Phan
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - D James Nokes
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences, Zeeman Institute, University of Warwick, Coventry, United Kingdom
| | - Eric Delwart
- Blood Systems Research Institute, University of California, San Francisco, California, USA
| | - Eduard Sanders
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - George M Warimwe
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
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25
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Virus discovery reveals frequent infection by diverse novel members of the Flaviviridae in wild lemurs. Arch Virol 2018; 164:509-522. [PMID: 30460488 DOI: 10.1007/s00705-018-4099-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 10/31/2018] [Indexed: 12/13/2022]
Abstract
Lemurs are highly endangered mammals inhabiting the forests of Madagascar. In this study, we performed virus discovery on serum samples collected from 84 wild lemurs and identified viral sequence fragments from 4 novel viruses within the family Flaviviridae, including members of the genera Hepacivirus and Pegivirus. The sifaka hepacivirus (SifHV, two genotypes) and pegivirus (SifPgV, two genotypes) were discovered in the diademed sifaka (Propithecus diadema), while other pegiviral fragments were detected in samples from the indri (Indri indri, IndPgV) and the weasel sportive lemur (Lepilemur mustelinus, LepPgV). Although data are preliminary, each viral species appeared host species-specific and frequent infection was detected (18 of 84 individuals were positive for at least one virus). The complete coding sequence and partial 5' and 3' untranslated regions (UTRs) were obtained for SifHV and its genomic organization was consistent with that of other hepaciviruses, with one unique polyprotein and highly structured UTRs. Phylogenetic analyses showed the SifHV belonged to a clade that includes several viral species identified in rodents from Asia and North America, while SifPgV and IndPgV were more closely related to pegiviral species A and C, that include viruses found in humans as well as New- and Old-World monkeys. Our results support the current proposed model of virus-host co-divergence with frequent occurrence of cross-species transmission for these genera and highlight how the discovery of more members of the Flaviviridae can help clarify the ecology and evolutionary history of these viruses. Furthermore, this knowledge is important for conservation and captive management of lemurs.
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26
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Phan MVT, Ngo Tri T, Hong Anh P, Baker S, Kellam P, Cotten M. Identification and characterization of Coronaviridae genomes from Vietnamese bats and rats based on conserved protein domains. Virus Evol 2018; 4:vey035. [PMID: 30568804 PMCID: PMC6295324 DOI: 10.1093/ve/vey035] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The Coronaviridae family of viruses encompasses a group of pathogens with a zoonotic potential as observed from previous outbreaks of the severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus. Accordingly, it seems important to identify and document the coronaviruses in animal reservoirs, many of which are uncharacterized and potentially missed by more standard diagnostic assays. A combination of sensitive deep sequencing technology and computational algorithms is essential for virus surveillance, especially for characterizing novel- or distantly related virus strains. Here, we explore the use of profile Hidden Markov Model-defined Pfam protein domains (Pfam domains) encoded by new sequences as a Coronaviridae sequence classification tool. The encoded domains are used first in a triage to identify potential Coronaviridae sequences and then processed using a Random Forest method to classify the sequences to the Coronaviridae genus level. The application of this algorithm on Coronaviridae genomes assembled from agnostic deep sequencing data from surveillance of bats and rats in Dong Thap province (Vietnam) identified thirty-four Alphacoronavirus and eleven Betacoronavirus genomes. This collection of bat and rat coronaviruses genomes provided essential information on the local diversity of coronaviruses and substantially expanded the number of coronavirus full genomes available from bat and rats and may facilitate further molecular studies on this group of viruses.
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Affiliation(s)
- My V T Phan
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Tue Ngo Tri
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Pham Hong Anh
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Paul Kellam
- Department of Infection and Immunity, Imperial College London, London, UK
- Kymab Ltd, Babraham Research Campus, Cambridge, UK
| | - Matthew Cotten
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
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27
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Kiyuka PK, Agoti CN, Munywoki PK, Njeru R, Bett A, Otieno JR, Otieno GP, Kamau E, Clark TG, van der Hoek L, Kellam P, Nokes DJ, Cotten M. Human Coronavirus NL63 Molecular Epidemiology and Evolutionary Patterns in Rural Coastal Kenya. J Infect Dis 2018; 217:1728-1739. [PMID: 29741740 PMCID: PMC6037089 DOI: 10.1093/infdis/jiy098] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 02/27/2018] [Indexed: 11/13/2022] Open
Abstract
Background Human coronavirus NL63 (HCoV-NL63) is a globally endemic pathogen causing mild and severe respiratory tract infections with reinfections occurring repeatedly throughout a lifetime. Methods Nasal samples were collected in coastal Kenya through community-based and hospital-based surveillance. HCoV-NL63 was detected with multiplex real-time reverse transcription PCR, and positive samples were targeted for nucleotide sequencing of the spike (S) protein. Additionally, paired samples from 25 individuals with evidence of repeat HCoV-NL63 infection were selected for whole-genome virus sequencing. Results HCoV-NL63 was detected in 1.3% (75/5573) of child pneumonia admissions. Two HCoV-NL63 genotypes circulated in Kilifi between 2008 and 2014. Full genome sequences formed a monophyletic clade closely related to contemporary HCoV-NL63 from other global locations. An unexpected pattern of repeat infections was observed with some individuals showing higher viral titers during their second infection. Similar patterns for 2 other endemic coronaviruses, HCoV-229E and HCoV-OC43, were observed. Repeat infections by HCoV-NL63 were not accompanied by detectable genotype switching. Conclusions In this coastal Kenya setting, HCoV-NL63 exhibited low prevalence in hospital pediatric pneumonia admissions. Clade persistence with low genetic diversity suggest limited immune selection, and absence of detectable clade switching in reinfections indicates initial exposure was insufficient to elicit a protective immune response.
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Affiliation(s)
- Patience K Kiyuka
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
| | - Charles N Agoti
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
- School of Health and Human Sciences, Pwani University, Kilifi, Kenya
| | - Patrick K Munywoki
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
| | - Regina Njeru
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
| | - Anne Bett
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
| | - James R Otieno
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
| | - Grieven P Otieno
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
| | - Everlyn Kamau
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Academic Medical Center of the University of Amsterdam, the Netherlands
| | - Paul Kellam
- Department of Medicine, Division of Infectious Diseases, Imperial College London
- Kymab Ltd., Babraham Research Campus, Cambridge
| | - D James Nokes
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
- School of Life Sciences and Zeeman Institute, University of Warwick, Coventry
| | - Matthew Cotten
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
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28
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Nooij S, Schmitz D, Vennema H, Kroneman A, Koopmans MPG. Overview of Virus Metagenomic Classification Methods and Their Biological Applications. Front Microbiol 2018; 9:749. [PMID: 29740407 PMCID: PMC5924777 DOI: 10.3389/fmicb.2018.00749] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 04/03/2018] [Indexed: 12/20/2022] Open
Abstract
Metagenomics poses opportunities for clinical and public health virology applications by offering a way to assess complete taxonomic composition of a clinical sample in an unbiased way. However, the techniques required are complicated and analysis standards have yet to develop. This, together with the wealth of different tools and workflows that have been proposed, poses a barrier for new users. We evaluated 49 published computational classification workflows for virus metagenomics in a literature review. To this end, we described the methods of existing workflows by breaking them up into five general steps and assessed their ease-of-use and validation experiments. Performance scores of previous benchmarks were summarized and correlations between methods and performance were investigated. We indicate the potential suitability of the different workflows for (1) time-constrained diagnostics, (2) surveillance and outbreak source tracing, (3) detection of remote homologies (discovery), and (4) biodiversity studies. We provide two decision trees for virologists to help select a workflow for medical or biodiversity studies, as well as directions for future developments in clinical viral metagenomics.
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Affiliation(s)
- Sam Nooij
- Emerging and Endemic Viruses, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands.,Viroscience Laboratory, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Dennis Schmitz
- Emerging and Endemic Viruses, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands.,Viroscience Laboratory, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Harry Vennema
- Emerging and Endemic Viruses, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Annelies Kroneman
- Emerging and Endemic Viruses, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Marion P G Koopmans
- Emerging and Endemic Viruses, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands.,Viroscience Laboratory, Erasmus University Medical Centre, Rotterdam, Netherlands
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29
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D'arc M, Furtado C, Siqueira JD, Seuánez HN, Ayouba A, Peeters M, Soares MA. Assessment of the gorilla gut virome in association with natural simian immunodeficiency virus infection. Retrovirology 2018; 15:19. [PMID: 29402305 PMCID: PMC5800045 DOI: 10.1186/s12977-018-0402-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 01/28/2018] [Indexed: 01/10/2023] Open
Abstract
Background Simian immunodeficiency viruses (SIVs) of chimpanzees and gorillas from Central Africa crossed the species barrier at least four times giving rise to human immunodeficiency virus type 1 (HIV-1) groups M, N, O and P. The paradigm of non-pathogenic lentiviral infections has been challenged by observations of naturally infected chimpanzees with SIVcpz associated with a negative impact on their life span and reproduction, CD4+ T-lymphocyte loss and lymphoid tissue destruction. With the advent and dissemination of new generation sequencing technologies, novel promising markers of immune deficiency have been explored in human and nonhuman primate species, showing changes in the microbiome (dysbiosis) that might be associated with pathogenic conditions. The aim of the present study was to identify and compare enteric viromes of SIVgor-infected and uninfected gorillas using noninvasive sampling and ultradeep sequencing, and to assess the association of virome composition with potential SIVgor pathogenesis in their natural hosts. Results We analyzed both RNA and DNA virus libraries of 23 fecal samples from 11 SIVgor-infected (two samples from one animal) and 11 uninfected western lowland gorillas from Campo-Ma’an National Park (CP), in southwestern Cameroon. Three bacteriophage families (Siphoviridae, Myoviridae and Podoviridae) represented 67.5 and 68% of the total annotated reads in SIVgor-infected and uninfected individuals, respectively. Conversely, mammalian viral families, such as Herpesviridae and Reoviridae, previously associated with gut- and several mammalian diseases were significantly more abundant (p < 0.003) in the SIVgor-infected group. In the present study, we analyzed, for the first time, the enteric virome of gorillas and their association with SIVgor status. This also provided the first evidence of association of specific mammalian viral families and SIVgor in a putative dysbiosis context. Conclusions Our results suggested that viromes might be potentially used as markers of lentiviral disease progression in wild gorilla populations. The diverse mammalian viral families, herein described in SIVgor-infected gorillas, may play a pivotal role in a disease progression still unclear in these animals but already well characterized in pathogenic lentiviral infections in other organisms. Larger sample sets should be further explored to reduce intrinsic sampling variation.
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Affiliation(s)
- Mirela D'arc
- Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil.,Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | | | - Héctor N Seuánez
- Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil.,Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Ahidjo Ayouba
- UMI233/INSERM1175 Institut de Recherche pour le Développement (IRD), University of Montpellier, Montpellier, France
| | - Martine Peeters
- UMI233/INSERM1175 Institut de Recherche pour le Développement (IRD), University of Montpellier, Montpellier, France
| | - Marcelo A Soares
- Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil. .,Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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30
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François S, Filloux D, Frayssinet M, Roumagnac P, Martin DP, Ogliastro M, Froissart R. Increase in taxonomic assignment efficiency of viral reads in metagenomic studies. Virus Res 2017; 244:230-234. [PMID: 29154906 DOI: 10.1016/j.virusres.2017.11.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/10/2017] [Accepted: 11/10/2017] [Indexed: 12/17/2022]
Abstract
Metagenomics studies have revolutionized the field of biology by revealing the presence of many previously unisolated and uncultured micro-organisms. However, one of the main problems encountered in metagenomic studies is the high percentage of sequences that cannot be assigned taxonomically using commonly used similarity-based approaches (e.g. BLAST or HMM). These unassigned sequences are allegorically called « dark matter » in the metagenomic literature and are often referred to as being derived from new or unknown organisms. Here, based on published and original metagenomic datasets coming from virus-like particle enriched samples, we present and quantify the improvement of viral taxonomic assignment that is achievable with a new similarity-based approach. Indeed, prior to any use of similarity based taxonomic assignment methods, we propose assembling contigs from short reads as is currently routinely done in metagenomic studies, but then to further map unassembled reads to the assembled contigs. This additional mapping step increases significantly the proportions of taxonomically assignable sequence reads from a variety -plant, insect and environmental (estuary, lakes, soil, feces) - of virome studies.
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Affiliation(s)
- S François
- INRA-Université de Montpellier UMR DGIMI 34095 Montpellier, France
| | - D Filloux
- CIRAD-INRA-Supagro, UMR BGPI, Campus International de Baillarguet, 34398 Montpellier, France
| | - M Frayssinet
- INRA-Université de Montpellier UMR DGIMI 34095 Montpellier, France
| | - P Roumagnac
- CIRAD-INRA-Supagro, UMR BGPI, Campus International de Baillarguet, 34398 Montpellier, France
| | - D P Martin
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
| | - M Ogliastro
- INRA-Université de Montpellier UMR DGIMI 34095 Montpellier, France
| | - R Froissart
- CNRS-IRD-Université de Montpellier, UMR MIVEGEC, 911 avenue Agropolis, 34394, Montpellier, France.
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31
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Carding SR, Davis N, Hoyles L. Review article: the human intestinal virome in health and disease. Aliment Pharmacol Ther 2017; 46:800-815. [PMID: 28869283 PMCID: PMC5656937 DOI: 10.1111/apt.14280] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 04/07/2017] [Accepted: 08/07/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND The human virome consists of animal-cell viruses causing transient infections, bacteriophage (phage) predators of bacteria and archaea, endogenous retroviruses and viruses causing persistent and latent infections. High-throughput, inexpensive, sensitive sequencing methods and metagenomics now make it possible to study the contribution dsDNA, ssDNA and RNA virus-like particles make to the human virome, and in particular the intestinal virome. AIM To review and evaluate the pioneering studies that have attempted to characterise the human virome and generated an increased interest in understanding how the intestinal virome might contribute to maintaining health, and the pathogenesis of chronic diseases. METHODS Relevant virome-related articles were selected for review following extensive language- and date-unrestricted, electronic searches of the literature. RESULTS The human intestinal virome is personalised and stable, and dominated by phages. It develops soon after birth in parallel with prokaryotic communities of the microbiota, becoming established during the first few years of life. By infecting specific populations of bacteria, phages can alter microbiota structure by killing host cells or altering their phenotype, enabling phages to contribute to maintaining intestinal homeostasis or microbial imbalance (dysbiosis), and the development of chronic infectious and autoimmune diseases including HIV infection and Crohn's disease, respectively. CONCLUSIONS Our understanding of the intestinal virome is fragmented and requires standardised methods for virus isolation and sequencing to provide a more complete picture of the virome, which is key to explaining the basis of virome-disease associations, and how enteric viruses can contribute to disease aetiologies and be rationalised as targets for interventions.
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Affiliation(s)
- S. R. Carding
- Norwich Medical SchoolUniversity of East AngliaNorwichUK,The Gut Health and Food Safety Research ProgrammeThe Quadram InstituteNorwich Research ParkNorwichUK
| | - N. Davis
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
| | - L. Hoyles
- Department of Surgery and CancerImperial College LondonLondonUK
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Oude Munnink BB, Phan MVT, Simmonds P, Koopmans MPG, Kellam P, van der Hoek L, Cotten M. Characterization of Posa and Posa-like virus genomes in fecal samples from humans, pigs, rats, and bats collected from a single location in Vietnam. Virus Evol 2017; 3:vex022. [PMID: 28948041 PMCID: PMC5597861 DOI: 10.1093/ve/vex022] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Porcine stool-associated RNA virus (posavirus), and Human stool-associated RNA virus
(husavirus) are viruses in the order Picornavirales recently described in
porcine and human fecal samples. The tentative group (Posa and Posa-like viruses: PPLVs)
also includes fish stool-associated RNA virus (fisavirus) as well as members detected in
insects (Drosophila subobscura and Anopheles sinensis)
and parasites (Ascaris suum). As part of an agnostic deep sequencing
survey of animal and human viruses in Vietnam, we detected three husaviruses in human
fecal samples, two of which share 97–98% amino acid identity to Dutch husavirus strains
and one highly divergent husavirus with only 25% amino acid identity to known husaviruses.
In addition, the current study found forty-seven complete posavirus genomes from pigs, ten
novel rat stool-associated RNA virus genomes (tentatively named rasavirus), and sixteen
novel bat stool-associated RNA virus genomes (tentatively named basavirus). The five
expected Picornavirales protein domains (helicase, 3C-protease,
RNA-dependent RNA polymerase, and two Picornavirus capsid domain) were found to be encoded
by all PPLV genomes. In addition, a nucleotide composition analysis revealed that the
PPLVs shared compositional properties with arthropod viruses and predicted non-mammalian
hosts for all PPLV lineages. The study adds seventy-six genomes to the twenty-nine PPLV
genomes currently available and greatly extends our sequence knowledge of this group of
viruses within the Picornavirales order.
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Affiliation(s)
- Bas B Oude Munnink
- Department of Virus Genomics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.,Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - My V T Phan
- Department of Virus Genomics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.,Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Paul Kellam
- Department of Virus Genomics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.,Department of Infectious Diseases and Immunity, Imperial College London, London, UK
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Matthew Cotten
- Department of Virus Genomics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.,Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
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Lewandowska DW, Zagordi O, Geissberger FD, Kufner V, Schmutz S, Böni J, Metzner KJ, Trkola A, Huber M. Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples. MICROBIOME 2017; 5:94. [PMID: 28789678 PMCID: PMC5549297 DOI: 10.1186/s40168-017-0317-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/25/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Sequence-specific PCR is the most common approach for virus identification in diagnostic laboratories. However, as specific PCR only detects pre-defined targets, novel virus strains or viruses not included in routine test panels will be missed. Recently, advances in high-throughput sequencing allow for virus-sequence-independent identification of entire virus populations in clinical samples, yet standardized protocols are needed to allow broad application in clinical diagnostics. Here, we describe a comprehensive sample preparation protocol for high-throughput metagenomic virus sequencing using random amplification of total nucleic acids from clinical samples. RESULTS In order to optimize metagenomic sequencing for application in virus diagnostics, we tested different enrichment and amplification procedures on plasma samples spiked with RNA and DNA viruses. A protocol including filtration, nuclease digestion, and random amplification of RNA and DNA in separate reactions provided the best results, allowing reliable recovery of viral genomes and a good correlation of the relative number of sequencing reads with the virus input. We further validated our method by sequencing a multiplexed viral pathogen reagent containing a range of human viruses from different virus families. Our method proved successful in detecting the majority of the included viruses with high read numbers and compared well to other protocols in the field validated against the same reference reagent. Our sequencing protocol does work not only with plasma but also with other clinical samples such as urine and throat swabs. CONCLUSIONS The workflow for virus metagenomic sequencing that we established proved successful in detecting a variety of viruses in different clinical samples. Our protocol supplements existing virus-specific detection strategies providing opportunities to identify atypical and novel viruses commonly not accounted for in routine diagnostic panels.
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Affiliation(s)
- Dagmara W Lewandowska
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Osvaldo Zagordi
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | | | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Karin J Metzner
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Rämistrasse 100, 8091, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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34
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Membrane Bioreactor-Based Wastewater Treatment Plant in Saudi Arabia: Reduction of Viral Diversity, Load, and Infectious Capacity. WATER 2017. [DOI: 10.3390/w9070534] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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35
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Lin HH, Liao YC. drVM: a new tool for efficient genome assembly of known eukaryotic viruses from metagenomes. Gigascience 2017; 6:1-10. [PMID: 28369462 PMCID: PMC5466706 DOI: 10.1093/gigascience/gix003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 01/15/2017] [Indexed: 11/29/2022] Open
Abstract
Background: Virus discovery using high-throughput next-generation sequencing has become more commonplace. However, although analysis of deep next-generation sequencing data allows us to identity potential pathogens, the entire analytical procedure requires competency in the bioinformatics domain, which includes implementing proper software packages and preparing prerequisite databases. Simple and user-friendly bioinformatics pipelines are urgently required to obtain complete viral genome sequences from metagenomic data. Results: This manuscript presents a pipeline, drVM (detect and reconstruct known viral genomes from metagenomes), for rapid viral read identification, genus-level read partition, read normalization, de novo assembly, sequence annotation, and coverage profiling. The first two procedures and sequence annotation rely on known viral genomes as a reference database. drVM was validated via the analysis of over 300 sequencing runs generated by Illumina and Ion Torrent platforms to provide complete viral genome assemblies for a variety of virus types including DNA viruses, RNA viruses, and retroviruses. drVM is available for free download at: https://sourceforge.net/projects/sb2nhri/files/drVM/ and is also assembled as a Docker container, an Amazon machine image, and a virtual machine to facilitate seamless deployment. Conclusions: drVM was compared with other viral detection tools to demonstrate its merits in terms of viral genome completeness and reduced computation time. This substantiates the platform's potential to produce prompt and accurate viral genome sequences from clinical samples.
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36
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Achinko D, Dormer A, Narayanan M, Norman E, Abbas M. Regulatory patterns of differentially expressed genes in Ebola and related viruses are critical for viral screening and diagnosis. F1000Res 2017. [DOI: 10.12688/f1000research.10597.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background Viral detection techniques and applications are a critical first step to pathogen detection within a given population, especially during outbreaks. Common viral tests currently used are direct specimen examination, indirect examination and serological tests. Serological tests have gained intense interest because they are rapidly performed with patient blood samples for quick diagnosis and treatment. The diagnostic techniques developed around serology are often expensive, require expertise to use and cannot be afforded by developing countries with recurrent viral outbreaks. Therefore exploiting the huge amount of viral data available in various databases is critical to develop affordable and easy-to-use diagnostic tools. Methods This study obtained viral sample data from Gene Expression Omnibus database with focus on use of viral glycoprotein for host penetration. Gene relative mean across 34 obtained viral samples were extracted into data tables and used with edgeR statistical software in R version 3.3.1. Results Three clusters previously known to be LCK specific (Ebola virus relative viral cluster, EBOVC), CD209 specific (Mean differentiation cluster, MDC) and both LCK and CD209 specific (Kurtosis group cluster, KGC), expressed unique patterns of four proteins of interest (CD209, LCK, IL-2 and MYB). Differential expression analysis showed two cluster patterns on heatmaps, with differentially expressed proteins down-regulated in MDC but up-regulated in KGC and EBOVC for all pairwise cluster comparative analyses performed. Heatmaps showed two distinct immune related patterns, identifying MDC as B-lymphotropic while KGC and EBOVC as T-lymphotropic. Identified pathways were dominantly involved with homeostasis of immune cells and viral cell surface receptors involved in protein kinase activities. Conclusions Regulatory proteomic variants identified in clusters suggest transcription repression of HLA class I alleles. This study identified viral expression patterns with screening and therapeutic applications. Given that the viral pathogenetic pathway for Ebola has not been clearly identified yet, assembling its components is vital for vaccine development.
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Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res 2017; 27:824-834. [PMID: 28298430 PMCID: PMC5411777 DOI: 10.1101/gr.213959.116] [Citation(s) in RCA: 1993] [Impact Index Per Article: 284.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 03/13/2017] [Indexed: 01/25/2023]
Abstract
While metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly of metagenomic data remains challenging, thus stifling biological discoveries. Moreover, recent studies revealed that complex bacterial populations may be composed from dozens of related strains, thus further amplifying the challenge of metagenomic assembly. metaSPAdes addresses various challenges of metagenomic assembly by capitalizing on computational ideas that proved to be useful in assemblies of single cells and highly polymorphic diploid genomes. We benchmark metaSPAdes against other state-of-the-art metagenome assemblers and demonstrate that it results in high-quality assemblies across diverse data sets.
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Affiliation(s)
- Sergey Nurk
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia 199004
| | - Dmitry Meleshko
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia 199004
| | - Anton Korobeynikov
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia 199004.,Department of Statistical Modelling, St. Petersburg State University, St. Petersburg, Russia 198515
| | - Pavel A Pevzner
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia 199004.,Department of Computer Science and Engineering, University of California, San Diego, California 92093-0404, USA
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38
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Nieuwenhuijse DF, Koopmans MPG. Metagenomic Sequencing for Surveillance of Food- and Waterborne Viral Diseases. Front Microbiol 2017; 8:230. [PMID: 28261185 PMCID: PMC5309255 DOI: 10.3389/fmicb.2017.00230] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 02/01/2017] [Indexed: 12/25/2022] Open
Abstract
A plethora of viruses can be transmitted by the food- and waterborne route. However, their recognition is challenging because of the variety of viruses, heterogeneity of symptoms, the lack of awareness of clinicians, and limited surveillance efforts. Classical food- and waterborne viral disease outbreaks are mainly caused by caliciviruses, but the source of the virus is often not known and the foodborne mode of transmission is difficult to discriminate from human-to-human transmission. Atypical food- and waterborne viral disease can be caused by viruses such as hepatitis A and hepatitis E. In addition, a source of novel emerging viruses with a potential to spread via the food- and waterborne route is the repeated interaction of humans with wildlife. Wildlife-to-human adaptation may give rise to self- limiting outbreaks in some cases, but when fully adjusted to the human host can be devastating. Metagenomic sequencing has been investigated as a promising solution for surveillance purposes as it detects all viruses in a single protocol, delivers additional genomic information for outbreak tracing, and detects novel unknown viruses. Nevertheless, several issues must be addressed to apply metagenomic sequencing in surveillance. First, sample preparation is difficult since the genomic material of viruses is generally overshadowed by host- and bacterial genomes. Second, several data analysis issues hamper the efficient, robust, and automated processing of metagenomic data. Third, interpretation of metagenomic data is hard, because of the lack of general knowledge of the virome in the food chain and the environment. Further developments in virus-specific nucleic acid extraction methods, bioinformatic data processing applications, and unifying data visualization tools are needed to gain insightful surveillance knowledge from suspect food samples.
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39
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Abstract
To document the viral zoonotic risks in Vietnam, fecal samples were systematically collected from a number of mammals in southern Vietnam and subjected to agnostic deep sequencing. We describe here novel Vietnamese bunyavirus sequences detected in bat feces. The complete L and S segments from 14 viruses were determined.
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40
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Cotten M, Koopmans M. Next-generation sequencing and norovirus. Future Virol 2016; 11:719-722. [PMID: 28757893 DOI: 10.2217/fvl-2016-0099] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 09/23/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Matthew Cotten
- Virosciences Department, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Marion Koopmans
- Virosciences Department, Erasmus Medical Center, Rotterdam, The Netherlands
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41
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Phan MVT, Anh PH, Cuong NV, Munnink BBO, van der Hoek L, My PT, Tri TN, Bryant JE, Baker S, Thwaites G, Woolhouse M, Kellam P, Rabaa MA, Cotten M. Unbiased whole-genome deep sequencing of human and porcine stool samples reveals circulation of multiple groups of rotaviruses and a putative zoonotic infection. Virus Evol 2016; 2:vew027. [PMID: 28748110 PMCID: PMC5522372 DOI: 10.1093/ve/vew027] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Coordinated and synchronous surveillance for zoonotic viruses in both human clinical cases and animal reservoirs provides an opportunity to identify interspecies virus movement. Rotavirus (RV) is an important cause of viral gastroenteritis in humans and animals. In this study, we document the RV diversity within co-located humans and animals sampled from the Mekong delta region of Vietnam using a primer-independent, agnostic, deep sequencing approach. A total of 296 stool samples (146 from diarrhoeal human patients and 150 from pigs living in the same geographical region) were directly sequenced, generating the genomic sequences of sixty human rotaviruses (all group A) and thirty-one porcine rotaviruses (thirteen group A, seven group B, six group C, and five group H). Phylogenetic analyses showed the co-circulation of multiple distinct RV group A (RVA) genotypes/strains, many of which were divergent from the strain components of licensed RVA vaccines, as well as considerable virus diversity in pigs including full genomes of rotaviruses in groups B, C, and H, none of which have been previously reported in Vietnam. Furthermore, the detection of an atypical RVA genotype constellation (G4-P[6]-I1-R1-C1-M1-A8-N1-T7-E1-H1) in a human patient and a pig from the same region provides some evidence for a zoonotic event.
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Affiliation(s)
- My V T Phan
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Pham Hong Anh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Van Cuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Bas B Oude Munnink
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Phuc Tran My
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tue Ngo Tri
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Juliet E Bryant
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Stephen Baker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,London School of Tropical Medicine and Hygiene, London, UK
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mark Woolhouse
- Centre for Immunity, Infection & Evolution, University of Edinburgh, Edinburgh, UK
| | - Paul Kellam
- Kymab Inc., Cambridge, UK.,Imperial College, London, UK
| | - Maia A Rabaa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Matthew Cotten
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.,Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
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Sano K, Naoi Y, Kishimoto M, Masuda T, Tanabe H, Ito M, Niira K, Haga K, Asano K, Tsuchiaka S, Omatsu T, Furuya T, Katayama Y, Oba M, Ouchi Y, Yamasato H, Ishida M, Shirai J, Katayama K, Mizutani T, Nagai M. Identification of further diversity among posaviruses. Arch Virol 2016; 161:3541-3548. [PMID: 27619795 DOI: 10.1007/s00705-016-3048-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/01/2016] [Indexed: 02/06/2023]
Abstract
Recently, there have been reports of new members of posavirus-like viruses in the order Picornavirales. In this study, using a metagenomics approach, 11 posavirus-like sequences (>7,000 nucleotides) were detected in 155 porcine fecal samples. Phylogenetic analysis revealed that the newly identified virus sequences, together with other posavirus-like viruses, form distinct clusters within the order Picornavirales, composed of eight genogroups and unassigned sequences based on amino acid sequences of the helicase and RNA-dependent RNA polymerase regions, with <40 % and <50 % sequence identity, respectively. We propose further classifications of highly diverse posavirus populations based on newly identified sequences from Japanese pig feces.
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Affiliation(s)
- Kaori Sano
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Yuki Naoi
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Mai Kishimoto
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Tsuneyuki Masuda
- Kurayoshi Livestock Hygiene Service Center, Kurayoshi, Tottori, 683-0017, Japan
| | - Hitomi Tanabe
- Rokko Livestock Hygiene Service Center, Hokota, Ibaraki, 311-1593, Japan
| | - Mika Ito
- Ishikawa Nanbu Livestock Hygiene Service Center, Kanazawa, Ishikawa, 920-3101, Japan
| | - Kazutaka Niira
- Tochigi Prefectural South District Animal Hygiene Service Center, Tochigi, Tochigi, 328-0002, Japan
| | - Kei Haga
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo, 208-0011, Japan
| | - Keigo Asano
- Department of Bioproduction Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836, Japan
| | - Shinobu Tsuchiaka
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Tsutomu Omatsu
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Tetsuya Furuya
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Yukie Katayama
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Mami Oba
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Yoshinao Ouchi
- Kenhoku Livestock Hygiene Service Center, Mito, Ibaraki, 310-0002, Japan
| | - Hiroshi Yamasato
- Kurayoshi Livestock Hygiene Service Center, Kurayoshi, Tottori, 683-0017, Japan
| | - Motohiko Ishida
- Department of Bioproduction Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836, Japan
| | - Junsuke Shirai
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Kazuhiko Katayama
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo, 208-0011, Japan
| | - Tetsuya Mizutani
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Makoto Nagai
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan. .,Department of Bioproduction Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836, Japan.
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Abstract
Primer-independent agnostic deep sequencing was used to generate three human rhinovirus (HRV) B genomes and one HRV C genome from samples collected in a household respiratory survey in rural coastal Kenya. The study provides the first rhinovirus genomes from Kenya and will help improve the sensitivity of local molecular diagnostics.
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44
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Hasing ME, Hazes B, Lee BE, Preiksaitis JK, Pang XL. A next generation sequencing-based method to study the intra-host genetic diversity of norovirus in patients with acute and chronic infection. BMC Genomics 2016; 17:480. [PMID: 27363999 PMCID: PMC4929757 DOI: 10.1186/s12864-016-2831-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 06/12/2016] [Indexed: 12/12/2022] Open
Abstract
Background Immunocompromised individuals with chronic norovirus (NoV) infection and elderly patients are hypothesized to be reservoirs where NoV might accumulate mutations and evolve into pandemic strains. Next generation sequencing (NGS) methods can monitor the intra-host diversity of NoV and its evolution but low abundance of viral RNA results in sub-optimal efficiency. In this study, we: 1) established a next generation sequencing-based method for NoV using bacterial rRNA depletion as a viral RNA enrichment strategy, and 2) measured the intra-host genetic diversity of NoV in specimens of patients with acute NoV infection (n = 4) and in longitudinal specimens of an immunocompromised patient with chronic NoV infection (n = 2). Results A single Illumina MiSeq dataset resulted in near full-length genome sequences for 5 out of 6 multiplexed samples. Experimental depletion of bacterial rRNA in stool RNA provided up to 1.9 % of NoV reads. The intra-host viral population in patients with acute NoV infection was homogenous and no single nucleotide variants (SNVs) were detected. In contrast, the NoV population from the immunocompromised patient was highly diverse and accumulated SNVs over time (51 SNVs in the first sample and 122 SNVs in the second sample collected 4 months later). The percentages of SNVs causing non-synonymous mutations were 27.5 % and 20.5 % for the first and second samples, respectively. The majority of non-synonymous mutations occurred, in increasing order of frequency, in p22, the major capsid (VP1) and minor capsid (VP2) genes. Conclusions The results provide data useful for the selection and improvement of NoV RNA enrichment strategies for NGS. Whole genome analysis using next generation sequencing confirmed that the within-host population of NoV in an immunocompromised individual with chronic NoV infection was more diverse compared to that in individuals with acute infection. We also observed an accumulation of non-synonymous mutations at the minor capsid gene that has not been reported in previous studies and might have a role in NoV adaptation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2831-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maria E Hasing
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, T6G 2B7, Canada
| | - Bart Hazes
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Bonita E Lee
- Department of Pediatrics, University of Alberta, Edmonton, AB, T6G 1C9, Canada
| | - Jutta K Preiksaitis
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2B7, Canada
| | - Xiaoli L Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, T6G 2B7, Canada. .,Provincial Laboratory for Public Health (ProvLab), Edmonton, AB, T6G 2 J2, Canada.
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Oude Munnink BB, Cotten M, Deijs M, Jebbink MF, Bakker M, Jazaeri Farsani SM, Canuti M, Kellam P, van der Hoek L. A novel genus in the order Picornavirales detected in human stool. J Gen Virol 2016; 96:3440-3443. [PMID: 26354795 DOI: 10.1099/jgv.0.000279] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recently, four new viruses belonging to an unassigned family within the order Picornavirales were identified in excrements of healthy carp (fisavirus) and pigs (posavirus 1, 2 and 3). We report the detection and characterization of a fifth virus present in human faeces. The virus, named human stool-associated RNA virus (husavirus), contains a single ORF encoding a putative 2993 AA polyprotein, with a Hel-Pro-Pol replication block, typical for the Picornavirales. Phylogenetic analysis revealed that the closest relative to husavirus is posavirus 1, and together they cluster with fisavirus, posavirus 2 and 3 and a roundworm (Ascaris suum) derived virus. Husavirus was detected in eight human stool samples collected in 1984 (n52), 1985 (n54), 1995 (n51) and 2014 (n51). From three strains of husavirus from 1984 and 1985 the full genome sequence was determined, showing less than 5% intraspecies variation in the nucleotide composition. The host of this virus remains to be determined.
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Affiliation(s)
- Bas B Oude Munnink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | | | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Maarten F Jebbink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Seyed Mohammad Jazaeri Farsani
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Marta Canuti
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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46
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Complete Genome Characterization of Two Wild-Type Measles Viruses from Vietnamese Infants during the 2014 Outbreak. GENOME ANNOUNCEMENTS 2016; 4:4/2/e00250-16. [PMID: 27081130 PMCID: PMC4832158 DOI: 10.1128/genomea.00250-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A large measles virus outbreak occurred across Vietnam in 2014. We identified and obtained complete measles virus genomes in stool samples collected from two diarrheal pediatric patients in Dong Thap Province. These are the first complete genome sequences of circulating measles viruses in Vietnam during the 2014 measles outbreak.
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47
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Oude Munnink BB, Cotten M, Canuti M, Deijs M, Jebbink MF, van Hemert FJ, Phan MVT, Bakker M, Jazaeri Farsani SM, Kellam P, van der Hoek L. A Novel Astrovirus-Like RNA Virus Detected in Human Stool. Virus Evol 2016; 2:vew005. [PMID: 27774298 PMCID: PMC4989881 DOI: 10.1093/ve/vew005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Several novel clades of astroviruses have recently been identified in human faecal samples. Here, we describe a novel astrovirus-like RNA virus detected in human stools, which we have tentatively named bastrovirus. The genome of this novel virus consists of 6,300 nucleotides organized in three open reading frames. Several sequence divergent strains were detected sharing 67–93 per cent nucleotide identity. Bastrovirus encodes a putative structural protein that is homologous to the capsid protein found in members of the Astroviridae family (45% amino acid identity). The virus also encodes a putative non-structural protein that is genetically distant from astroviruses but shares some homology to the non-structural protein encoded by members of the Hepeviridae family (28% amino acid identity). This novel bastrovirus is present in 8.7 per cent (35/400) of faecal samples collected from 300 HIV-1-positive and 100 HIV-1-negative individuals suggesting common occurrence of the virus. However, whether the source of the virus is infected human cells or other, for example, dietary, remains to be determined.
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Affiliation(s)
- Bas B. Oude Munnink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Matthew Cotten
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK and
| | - Marta Canuti
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Maarten F. Jebbink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Formijn J. van Hemert
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - My V. T. Phan
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK and
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Seyed Mohammad Jazaeri Farsani
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK and
- Division of Infection and Immunity, University College London, WC1E 6BT London, UK
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
- *Corresponding author: E-mail:
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48
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Friis-Nielsen J, Kjartansdóttir KR, Mollerup S, Asplund M, Mourier T, Jensen RH, Hansen TA, Rey-Iglesia A, Richter SR, Nielsen IB, Alquezar-Planas DE, Olsen PVS, Vinner L, Fridholm H, Nielsen LP, Willerslev E, Sicheritz-Pontén T, Lund O, Hansen AJ, Izarzugaza JMG, Brunak S. Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers. Viruses 2016; 8:E53. [PMID: 26907326 PMCID: PMC4776208 DOI: 10.3390/v8020053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/29/2016] [Accepted: 02/05/2016] [Indexed: 12/17/2022] Open
Abstract
Virus discovery from high throughput sequencing data often follows a bottom-up approach where taxonomic annotation takes place prior to association to disease. Albeit effective in some cases, the approach fails to detect novel pathogens and remote variants not present in reference databases. We have developed a species independent pipeline that utilises sequence clustering for the identification of nucleotide sequences that co-occur across multiple sequencing data instances. We applied the workflow to 686 sequencing libraries from 252 cancer samples of different cancer and tissue types, 32 non-template controls, and 24 test samples. Recurrent sequences were statistically associated to biological, methodological or technical features with the aim to identify novel pathogens or plausible contaminants that may associate to a particular kit or method. We provide examples of identified inhabitants of the healthy tissue flora as well as experimental contaminants. Unmapped sequences that co-occur with high statistical significance potentially represent the unknown sequence space where novel pathogens can be identified.
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Affiliation(s)
- Jens Friis-Nielsen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Kristín Rós Kjartansdóttir
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Sarah Mollerup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Maria Asplund
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Randi Holm Jensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Thomas Arn Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Alba Rey-Iglesia
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Stine Raith Richter
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Ida Broman Nielsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - David E Alquezar-Planas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Pernille V S Olsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Helena Fridholm
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Lars Peter Nielsen
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, DK-2300 Copenhagen S, Denmark.
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Thomas Sicheritz-Pontén
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Ole Lund
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Anders Johannes Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Jose M G Izarzugaza
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Søren Brunak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
- NNF Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark.
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49
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Development of a candidate reference material for adventitious virus detection in vaccine and biologicals manufacturing by deep sequencing. Vaccine 2015; 34:2035-43. [PMID: 26709640 PMCID: PMC4823300 DOI: 10.1016/j.vaccine.2015.12.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/30/2015] [Accepted: 12/05/2015] [Indexed: 02/05/2023]
Abstract
Deep sequencing has potential as an improved adventitious virus screening method. 15 laboratories sequenced a common reagent containing 25 target viruses. 6 viruses were detected by all lab, the remainder were detected by 4–14 labs. A wide range of sample preparation and bioinformatics methods is currently used. A common reference material is essential to enable results to be compared.
Background Unbiased deep sequencing offers the potential for improved adventitious virus screening in vaccines and biotherapeutics. Successful implementation of such assays will require appropriate control materials to confirm assay performance and sensitivity. Methods A common reference material containing 25 target viruses was produced and 16 laboratories were invited to process it using their preferred adventitious virus detection assay. Results Fifteen laboratories returned results, obtained using a wide range of wet-lab and informatics methods. Six of 25 target viruses were detected by all laboratories, with the remaining viruses detected by 4–14 laboratories. Six non-target viruses were detected by three or more laboratories. Conclusion The study demonstrated that a wide range of methods are currently used for adventitious virus detection screening in biological products by deep sequencing and that they can yield significantly different results. This underscores the need for common reference materials to ensure satisfactory assay performance and enable comparisons between laboratories.
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50
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Rabaa MA, Tue NT, Phuc TM, Carrique-Mas J, Saylors K, Cotten M, Bryant JE, Nghia HDT, Cuong NV, Pham HA, Berto A, Phat VV, Dung TTN, Bao LH, Hoa NT, Wertheim H, Nadjm B, Monagin C, van Doorn HR, Rahman M, Tra MPV, Campbell JI, Boni MF, Tam PTT, van der Hoek L, Simmonds P, Rambaut A, Toan TK, Van Vinh Chau N, Hien TT, Wolfe N, Farrar JJ, Thwaites G, Kellam P, Woolhouse MEJ, Baker S. The Vietnam Initiative on Zoonotic Infections (VIZIONS): A Strategic Approach to Studying Emerging Zoonotic Infectious Diseases. ECOHEALTH 2015; 12:726-35. [PMID: 26403795 PMCID: PMC4700077 DOI: 10.1007/s10393-015-1061-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 05/20/2015] [Accepted: 08/24/2015] [Indexed: 06/05/2023]
Abstract
The effect of newly emerging or re-emerging infectious diseases of zoonotic origin in human populations can be potentially catastrophic, and large-scale investigations of such diseases are highly challenging. The monitoring of emergence events is subject to ascertainment bias, whether at the level of species discovery, emerging disease events, or disease outbreaks in human populations. Disease surveillance is generally performed post hoc, driven by a response to recent events and by the availability of detection and identification technologies. Additionally, the inventory of pathogens that exist in mammalian and other reservoirs is incomplete, and identifying those with the potential to cause disease in humans is rarely possible in advance. A major step in understanding the burden and diversity of zoonotic infections, the local behavioral and demographic risks of infection, and the risk of emergence of these pathogens in human populations is to establish surveillance networks in populations that maintain regular contact with diverse animal populations, and to simultaneously characterize pathogen diversity in human and animal populations. Vietnam has been an epicenter of disease emergence over the last decade, and practices at the human/animal interface may facilitate the likelihood of spillover of zoonotic pathogens into humans. To tackle the scientific issues surrounding the origins and emergence of zoonotic infections in Vietnam, we have established The Vietnam Initiative on Zoonotic Infections (VIZIONS). This countrywide project, in which several international institutions collaborate with Vietnamese organizations, is combining clinical data, epidemiology, high-throughput sequencing, and social sciences to address relevant one-health questions. Here, we describe the primary aims of the project, the infrastructure established to address our scientific questions, and the current status of the project. Our principal objective is to develop an integrated approach to the surveillance of pathogens circulating in both human and animal populations and assess how frequently they are exchanged. This infrastructure will facilitate systematic investigations of pathogen ecology and evolution, enhance understanding of viral cross-species transmission events, and identify relevant risk factors and drivers of zoonotic disease emergence.
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Affiliation(s)
- Maia A Rabaa
- Centre for Immunity, Infection & Evolution, The University of Edinburgh, Edinburgh, UK
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Ngo Tri Tue
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Tran My Phuc
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Juan Carrique-Mas
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | | | | | - Juliet E Bryant
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hanoi, Vietnam
| | - Ho Dang Trung Nghia
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- The Hospital for Tropical Diseases, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam
| | - Nguyen Van Cuong
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Hong Anh Pham
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Alessandra Berto
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Voong Vinh Phat
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Tran Thi Ngoc Dung
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Long Hoang Bao
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hanoi, Vietnam
| | - Ngo Thi Hoa
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Heiman Wertheim
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hanoi, Vietnam
| | - Behzad Nadjm
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hanoi, Vietnam
| | | | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Motiur Rahman
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | | | - James I Campbell
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Maciej F Boni
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Pham Thi Thanh Tam
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Peter Simmonds
- Centre for Immunity, Infection & Evolution, The University of Edinburgh, Edinburgh, UK
| | - Andrew Rambaut
- Centre for Immunity, Infection & Evolution, The University of Edinburgh, Edinburgh, UK
| | | | - Nguyen Van Vinh Chau
- The Hospital for Tropical Diseases, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam
| | - Tran Tinh Hien
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | | | - Jeremy J Farrar
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Paul Kellam
- The Wellcome Trust Sanger Institute, Cambridge, UK
| | - Mark E J Woolhouse
- Centre for Immunity, Infection & Evolution, The University of Edinburgh, Edinburgh, UK
| | - Stephen Baker
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam.
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK.
- The Hospital for Tropical Diseases, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam.
- The London School of Hygiene and Tropical Medicine, London, UK.
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