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Medina JE, Castañeda S, Camargo M, Garcia-Corredor DJ, Muñoz M, Ramírez JD. Exploring viral diversity and metagenomics in livestock: insights into disease emergence and spillover risks in cattle. Vet Res Commun 2024:10.1007/s11259-024-10403-2. [PMID: 38865041 DOI: 10.1007/s11259-024-10403-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 05/01/2024] [Indexed: 06/13/2024]
Abstract
Cattle have a significant impact on human societies in terms of both economics and health. Viral infections pose a relevant problem as they directly or indirectly disrupt the balance within cattle populations. This has negative consequences at the economic level for producers and territories, and also jeopardizes human health through the transmission of zoonotic diseases that can escalate into outbreaks or pandemics. To establish prevention strategies and control measures at various levels (animal, farm, region, or global), it is crucial to identify the viral agents present in animals. Various techniques, including virus isolation, serological tests, and molecular techniques like PCR, are typically employed for this purpose. However, these techniques have two major drawbacks: they are ineffective for non-culturable viruses, and they only detect a small fraction of the viruses present. In contrast, metagenomics offers a promising approach by providing a comprehensive and unbiased analysis for detecting all viruses in a given sample. It has the potential to identify rare or novel infectious agents promptly and establish a baseline of healthy animals. Nevertheless, the routine application of viral metagenomics for epidemiological surveillance and diagnostics faces challenges related to socioeconomic variables, such as resource availability and space dedicated to metagenomics, as well as the lack of standardized protocols and resulting heterogeneity in presenting results. This review aims to provide an overview of the current knowledge and prospects for using viral metagenomics to detect and identify viruses in cattle raised for livestock, while discussing the epidemiological and clinical implications.
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Affiliation(s)
- Julián Esteban Medina
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Milena Camargo
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Centro de Tecnología en Salud (CETESA), Innovaseq SAS, Mosquera, Cundinamarca, Colombia
| | - Diego J Garcia-Corredor
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Grupo de Investigación en Medicina Veterinaria y Zootecnia, Facultad de Ciencias Agropecuarias, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Mark D, Tairo F, Ndunguru J, Kweka E, Saggaf M, Bachwenkizi H, Chiunga E, Lusana JL, Sikazwe G, Maghembe R. Assessing the effect of sample storage time on viral detection using a rapid and cost-effective CTAB-based extraction method. PLANT METHODS 2024; 20:64. [PMID: 38720311 PMCID: PMC11080235 DOI: 10.1186/s13007-024-01175-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/11/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Cassava leaf samples degrade quickly during storage and transportation from distant areas. Proper sampling and efficient, low-cost storage methods are critical for obtaining sufficient quality DNA and RNA for plant virus epidemiology and improving disease control understanding. This is useful when samples are collected from remote areas far from a laboratory or in developing countries where money and materials for virus diagnostics are scarce. RESULTS The effect of sample storage duration on nucleic acid (N.A.) quality on virus detection was investigated in this study. A simple, rapid, and cost-effective CTAB-based approach (M3) for single N.A. extraction was optimized and tested alongside two existing CTAB-based methods (M1 and M2) for N.A. extraction from fresh and herbarium cassava leaves stored for; 1, 8, 26, and 56 months. The amount and quality of DNA and RNA were determined using Nanodrop 2000 c U.V.-vis Spectrophotometer and agarose gel electrophoreses. The sample degradation rate was estimated using a simple mathematical model in Matlab computational software. The results show no significant difference in mean DNA concentration between M1 and M2 but a significant difference between M3 and the other two methods at p < 0.005. The mean DNA concentration extracted using M3 was higher for 1 and 8 months of leave storage. M3 and M2 produced high concentrations at 26 and 56 months of leave storage. Using a developed scale for quality score, M3 and M2 produced high-quality DNA from fresh samples. All methods produced poor-quality DNA and RNA at 8 and 26 months of leave storage and no visual bands at the age of 56 months. Statistically, there was a significant difference in the mean DNA quality between M1 and M2, but there was no significant difference between M3 and the other two methods at p < 0.005. However, Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) were readily detected by RT-PCR from RNA isolated using M3. The quality of DNA declined per storage time at 0.0493 and 0.0521/month, while RNA was 0.0678 and 0.0744/month. Compared to the existing two methods, modified CTAB extracted enough high-quality N.A. in one-third the time of the existing two methods. CONCLUSION Our method provides cost-effective, quick, and simple processing of fresh and dry samples, which will quicken and guide the decision on when and what type of sample to process for plant disease management and surveillance actions.
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Affiliation(s)
- Deogratius Mark
- Tanzania Agricultural Research Institute, 6226, Dar-es-Salaam, Tanzania.
| | - Fred Tairo
- Tanzania Agricultural Research Institute, 6226, Dar-es-Salaam, Tanzania
| | - Joseph Ndunguru
- Tanzania Agricultural Research Institute, 6226, Dar-es-Salaam, Tanzania
- Tanzania Plant Health and Pesticides Authority, Arusha, P.O.Box 3024, Tanzania
| | - Elisiana Kweka
- Tanzania Agricultural Research Institute, 6226, Dar-es-Salaam, Tanzania
| | - Maliha Saggaf
- Tanzania Agricultural Research Institute, 6226, Dar-es-Salaam, Tanzania
| | - Hilda Bachwenkizi
- Tanzania Agricultural Research Institute, 6226, Dar-es-Salaam, Tanzania
| | | | - James Leonard Lusana
- School of Aquatic Sciences and Fisheries Technology, University of Dar es Salaam, 60091, Dar es Salaam, Tanzania
| | - Geofrey Sikazwe
- Mkwawa University College of Education, University of Dar es Salaam, 2513, Iringa, Tanzania
| | - Reuben Maghembe
- Biological and Marine Sciences Unit, Faculty of Natural and Applied Sciences, Marian University College, 47, Bagamoyo, Tanzania
- Department of Biological Sciences, Faculty of Science, University of Botswana, Private Bag 0704, Gaborone, Botswana
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Soria-Villalba A, Pesantes N, Jiménez-Hernández N, Pons J, Moya A, Pérez-Brocal V. Comparison of Experimental Methodologies Based on Bulk-Metagenome and Virus-like Particle Enrichment: Pros and Cons for Representativeness and Reproducibility in the Study of the Fecal Human Virome. Microorganisms 2024; 12:162. [PMID: 38257988 PMCID: PMC10820677 DOI: 10.3390/microorganisms12010162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Studies on the human virome based on the application of metagenomic approaches involve overcoming a series of challenges and limitations inherent not only to the biological features of viruses, but also to methodological pitfalls which different approaches have tried to minimize. These approaches fall into two main categories: bulk-metagenomes and virus-like particle (VLP) enrichment. In order to address issues associated with commonly used experimental procedures to assess the degree of reliability, representativeness, and reproducibility, we designed a comparative analysis applied to three experimental protocols, one based on bulk-metagenomes and two based on VLP enrichment. These protocols were applied to stool samples from 10 adult participants, including two replicas per protocol and subject. We evaluated the performances of the three methods, not only through the analysis of the resulting composition, abundance, and diversity of the virome via taxonomical classification and type of molecule (DNA versus RNA, single stranded vs. double stranded), but also according to how the a priori identical replicas differed from each other according to the extraction methods used. Our results highlight the strengths and weaknesses of each approach, offering valuable insights and tailored recommendations for drawing reliable conclusions based on specific research goals.
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Affiliation(s)
| | - Nicole Pesantes
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), 46020 Valencia, Spain; (N.P.); (N.J.-H.); (J.P.); (A.M.)
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - Nuria Jiménez-Hernández
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), 46020 Valencia, Spain; (N.P.); (N.J.-H.); (J.P.); (A.M.)
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - Javier Pons
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), 46020 Valencia, Spain; (N.P.); (N.J.-H.); (J.P.); (A.M.)
| | - Andrés Moya
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), 46020 Valencia, Spain; (N.P.); (N.J.-H.); (J.P.); (A.M.)
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish National Research Council (CSIC), 46980 Valencia, Spain
| | - Vicente Pérez-Brocal
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), 46020 Valencia, Spain; (N.P.); (N.J.-H.); (J.P.); (A.M.)
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
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Mhamadi M, Mencattelli G, Gaye A, Ndiaye EH, Sow AA, Faye M, Ndione MHD, Diagne MM, Mhamadi M, Faye O, Weidmann M, Faye O, Diallo M, Diagne CT. Rapid On-Site Detection of Arboviruses by a Direct RT-qPCR Assay. BIOSENSORS 2023; 13:1035. [PMID: 38131795 PMCID: PMC10741549 DOI: 10.3390/bios13121035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 12/23/2023]
Abstract
Arthropod-borne diseases currently constitute a source of major health concerns worldwide. They account for about 50% of global infectious diseases and cause nearly 700,000 deaths every year. Their rapid increase and spread constitute a huge challenge for public health, highlighting the need for early detection during epidemics, to curtail the virus spread, and to enhance outbreak management. Here, we compared a standard quantitative polymerase chain reaction (RT-qPCR) and a direct RT-qPCR assay for the detection of Zika (ZIKV), Chikungunya (CHIKV), and Rift Valley Fever (RVFV) viruses from experimentally infected-mosquitoes. The direct RT-qPCR could be completed within 1.5 h and required 1 µL of viral supernatant from homogenized mosquito body pools. Results showed that the direct RT-qPCR can detect 85.71%, 89%, and 100% of CHIKV, RVFV, and ZIKV samples by direct amplifications compared to the standard method. The use of 1:10 diluted supernatant is suggested for CHIKV and RVFV direct RT-qPCR. Despite a slight drop in sensitivity for direct PCR, our technique is more affordable, less time-consuming, and provides a better option for qualitative field diagnosis during outbreak management. It represents an alternative when extraction and purification steps are not possible because of insufficient sample volume or biosecurity issues.
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Affiliation(s)
- Moufid Mhamadi
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Giulia Mencattelli
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Alioune Gaye
- Department of Medical Zoology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (A.G.); (E.H.N.)
| | - El Hadji Ndiaye
- Department of Medical Zoology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (A.G.); (E.H.N.)
| | - Aïssatou Aïcha Sow
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Martin Faye
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Marie Henriette Dior Ndione
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Moussa Moïse Diagne
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Moundhir Mhamadi
- DIATROPIX, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (M.M.); (M.D.)
| | - Ousmane Faye
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Manfred Weidmann
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, 01968 Senftenberg, Germany;
| | - Oumar Faye
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Mawlouth Diallo
- DIATROPIX, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (M.M.); (M.D.)
| | - Cheikh Tidiane Diagne
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
- DIATROPIX, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (M.M.); (M.D.)
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Evaluation of extraction and enrichment methods for recovery of respiratory RNA viruses in a metagenomics approach. J Virol Methods 2023; 314:114677. [PMID: 36657602 PMCID: PMC10009504 DOI: 10.1016/j.jviromet.2023.114677] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/09/2023] [Accepted: 01/14/2023] [Indexed: 01/18/2023]
Abstract
Viral metagenomics is increasingly applied in viral detection and virome characterization. Different extraction and enrichment techniques may be adopted, however, reports on their effective influence on viral recovery is often conflicting. Using a three step enrichment steps, the effect of three extraction kits and the influence of DNase treatment with or without rRNA removal for respiratory RNA virus recovery from nasopharyngeal swab samples was evaluated. The viral cocktail containing six different RNA viruses pooled in equal volume were subjected to the different extraction and enrichment methods, sequenced using the Illumina MiSeq, and analysed using Genome Detective. The PureLink® Viral RNA/DNA Mini Kit (PureLink) was highly efficient with better recovery of all the viral agents in the cocktail. The use of rRNA treatment resulted in increased viral recovery with PureLink and QIAamp® Viral RNA Mini kit, while having comparable recovery rate as DNase only with the QIAamp® MinElute Virus Spin Kit. The observed low reads and genome coverage of some of the viruses could be attributed to their low abundance. Depending on sample matrix, extraction choice and enrichment strategy may influence recovery of respiratory RNA virus in metagenomics studies, therefore individual evaluation and adoption may be necessary for a robust result.
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Colton H, Parker M, Stirrup O, Blackstone J, Loose M, McClure C, Roy S, Williams C, McLeod J, Smith D, Taha Y, Zhang P, Hsu S, Kele B, Harris K, Mapp F, Williams R, Flowers P, Breuer J, Partridge D, de Silva T. Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: analysis of data from the COG-UK HOCI study. J Hosp Infect 2023; 131:34-42. [PMID: 36228768 PMCID: PMC9550290 DOI: 10.1016/j.jhin.2022.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/13/2022] [Accepted: 09/22/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Barriers to rapid return of sequencing results can affect the utility of sequence data for infection prevention and control decisions. AIM To undertake a mixed-methods analysis to identify challenges that sites faced in achieving a rapid turnaround time (TAT) in the COVID-19 Genomics UK Hospital-Onset COVID-19 Infection (COG-UK HOCI) study. METHODS For the quantitative analysis, timepoints relating to different stages of the sequencing process were extracted from both the COG-UK HOCI study dataset and surveys of study sites. Qualitative data relating to the barriers and facilitators to achieving rapid TATs were included from thematic analysis. FINDINGS The overall TAT, from sample collection to receipt of sequence report by infection control teams, varied between sites (median 5.1 days, range 3.0-29.0 days). Most variation was seen between reporting of a positive COVID-19 polymerase chain reaction (PCR) result to sequence report generation (median 4.0 days, range 2.3-27.0 days). On deeper analysis, most of this variability was accounted for by differences in the delay between the COVID-19 PCR result and arrival of the sample at the sequencing laboratory (median 20.8 h, range 16.0-88.7 h). Qualitative analyses suggest that closer proximity of sequencing laboratories to diagnostic laboratories, increased staff flexibility and regular transport times facilitated a shorter TAT. CONCLUSION Integration of pathogen sequencing into diagnostic laboratories may help to improve sequencing TAT to allow sequence data to be of tangible value to infection control practice. Adding a quality control step upstream to increase capacity further down the workflow may also optimize TAT if lower quality samples are removed at an earlier stage.
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Affiliation(s)
- H. Colton
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK,Directorate of Laboratory Medicine, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK,Corresponding author. Address: Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry & Health, University of Sheffield, Medical School, Beech Hill Road, Sheffield S10 2RX, UK
| | - M.D. Parker
- Sheffield Biomedical Research Centre, University of Sheffield, Sheffield, UK,Sheffield Bioinformatics Core, University of Sheffield, Sheffield, UK
| | - O. Stirrup
- Institute for Global Health, University College London, London, UK
| | - J. Blackstone
- The Comprehensive Clinical Trials Unit, University College London, London, UK
| | - M. Loose
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - C.P. McClure
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - S. Roy
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK
| | - C. Williams
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK
| | - J. McLeod
- School of Psychological Sciences and Health, University of Strathclyde, Glasgow, UK
| | - D. Smith
- Department of Applied Biology, Cellular and Molecular Sciences/Microbiology Group, Northumbria University, Newcastle, UK
| | - Y. Taha
- Department of Infection and Tropical Medicine, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Royal Victoria Infirmary, Newcastle Upon Tyne, UK
| | - P. Zhang
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - S.N. Hsu
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK,Sheffield Bioinformatics Core, University of Sheffield, Sheffield, UK
| | - B. Kele
- Virology Department, East and South East London Pathology Partnership, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - K. Harris
- Virology Department, East and South East London Pathology Partnership, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - F. Mapp
- Institute for Global Health, University College London, London, UK
| | - R. Williams
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK
| | | | - P. Flowers
- School of Psychological Sciences and Health, University of Strathclyde, Glasgow, UK
| | - J. Breuer
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK
| | - D.G. Partridge
- Directorate of Laboratory Medicine, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - T.I. de Silva
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
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Schuele L, Cassidy H, Peker N, Rossen JWA, Couto N. Future potential of metagenomics in clinical laboratories. Expert Rev Mol Diagn 2021; 21:1273-1285. [PMID: 34755585 DOI: 10.1080/14737159.2021.2001329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Rapid and sensitive diagnostic strategies are necessary for patient care and public health. Most of the current conventional microbiological assays detect only a restricted panel of pathogens at a time or require a microbe to be successfully cultured from a sample. Clinical metagenomics next-generation sequencing (mNGS) has the potential to unbiasedly detect all pathogens in a sample, increasing the sensitivity for detection and enabling the discovery of unknown infectious agents. AREAS COVERED High expectations have been built around mNGS; however, this technique is far from widely available. This review highlights the advances and currently available options in terms of costs, turnaround time, sensitivity, specificity, validation, and reproducibility of mNGS as a diagnostic tool in clinical microbiology laboratories. EXPERT OPINION The need for a novel diagnostic tool to increase the sensitivity of microbial diagnostics is clear. mNGS has the potential to revolutionise clinical microbiology. However, its role as a diagnostic tool has yet to be widely established, which is crucial for successfully implementing the technique. A clear definition of diagnostic algorithms that include mNGS is vital to show clinical utility. Similarly to real-time PCR, mNGS will one day become a vital tool in any testing algorithm.
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Affiliation(s)
- Leonard Schuele
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Hayley Cassidy
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Nilay Peker
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - John W A Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Natacha Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands.,The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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Sylverken AA, El-Duah P, Owusu M, Schneider J, Yeboah R, Ayisi-Boateng NK, Gorman R, Adu E, Kwarteng A, Frimpong M, Binger T, Aryeetey S, Asamoah JA, Amoako YA, Amuasi JH, Beheim-Schwarzbach J, Owusu-Dabo E, Adu-Sarkodie Y, Obiri-Danso K, Corman VM, Drosten C, Phillips R. Transmission of SARS-CoV-2 in northern Ghana: insights from whole-genome sequencing. Arch Virol 2021; 166:1385-1393. [PMID: 33723631 PMCID: PMC7959303 DOI: 10.1007/s00705-021-04986-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 12/21/2020] [Indexed: 12/23/2022]
Abstract
Following the detection of the first imported case of COVID-19 in the northern sector of Ghana, we molecularly characterized and phylogenetically analysed sequences, including three complete genome sequences, of severe acute respiratory syndrome coronavirus 2 obtained from nine patients in Ghana. We performed high-throughput sequencing on nine samples that were found to have a high concentration of viral RNA. We also assessed the potential impact that long-distance transport of samples to testing centres may have on sequencing results. Here, two samples that were similar in terms of viral RNA concentration but were transported from sites that are over 400 km apart were analyzed. All sequences were compared to previous sequences from Ghana and representative sequences from regions where our patients had previously travelled. Three complete genome sequences and another nearly complete genome sequence with 95.6% coverage were obtained. Sequences with coverage in excess of 80% were found to belong to three lineages, namely A, B.1 and B.2. Our sequences clustered in two different clades, with the majority falling within a clade composed of sequences from sub-Saharan Africa. Less RNA fragmentation was seen in sample KATH23, which was collected 9 km from the testing site, than in sample TTH6, which was collected and transported over a distance of 400 km to the testing site. The clustering of several sequences from sub-Saharan Africa suggests regional circulation of the viruses in the subregion. Importantly, there may be a need to decentralize testing sites and build more capacity across Africa to boost the sequencing output of the subregion.
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Affiliation(s)
- Augustina Angelina Sylverken
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Philip El-Duah
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
- Institute of Virology, Charite, Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Owusu
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
- Department of Medical Diagnostics, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Julia Schneider
- Institute of Virology, Charite, Universitätsmedizin Berlin, Berlin, Germany
| | - Richmond Yeboah
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
| | | | - Richmond Gorman
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
| | - Eric Adu
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
| | - Alexander Kwarteng
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Michael Frimpong
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
- Department of Molecular Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Tabea Binger
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
| | - Sherihane Aryeetey
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
| | - Jesse Addo Asamoah
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
| | - Yaw Ampem Amoako
- Department of Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - John Humphrey Amuasi
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
- Department of Global and International Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Ellis Owusu-Dabo
- Department of Global and International Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Yaw Adu-Sarkodie
- Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Kwasi Obiri-Danso
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Victor Max Corman
- Institute of Virology, Charite, Universitätsmedizin Berlin, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charite, Universitätsmedizin Berlin, Berlin, Germany
| | - Richard Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
- Department of Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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9
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A Streamlined Approach to Rapidly Detect SARS-CoV-2 Infection Avoiding RNA Extraction: Workflow Validation. DISEASE MARKERS 2020; 2020:8869424. [PMID: 33343767 PMCID: PMC7727018 DOI: 10.1155/2020/8869424] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/28/2020] [Indexed: 01/21/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has rapidly spread worldwide from the beginning of 2020. The presence of viral RNA in samples by nucleic acid (NA) molecular analysis is the only method available to diagnose COVID-19 disease and to assess patients' viral load. Since the demand for laboratory reagents has increased, there has been a worldwide shortage of RNA extraction kits. We, therefore, developed a fast and cost-effective viral genome isolation method that, combined with quantitative RT-PCR assay, detects SARS-CoV-2 RNA in patient samples. The method relies on the addition of Proteinase K followed by a controlled heat-shock incubation and, then, E gene evaluation by RT-qPCR. It was validated for sensitivity, specificity, linearity, reproducibility, and precision. It detects as low as 10 viral copies/sample, is rapid, and has been characterized in 60 COVID-19-infected patients. Compared to automated extraction methods, our pretreatment guarantees the same positivity rate with the advantage of shortening the time of the analysis and reducing its cost. This is a rapid workflow meant to aid the healthcare system in the rapid identification of infected patients, such as during a pathogen-related outbreak. For its intrinsic characteristics, this workflow is suitable for large-scale screenings.
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10
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Sabatier M, Bal A, Destras G, Regue H, Quéromès G, Cheynet V, Lina B, Bardel C, Brengel-Pesce K, Navratil V, Josset L. Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses. Microorganisms 2020; 8:E1539. [PMID: 33036303 PMCID: PMC7601816 DOI: 10.3390/microorganisms8101539] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 12/25/2022] Open
Abstract
Viral metagenomics next-generation sequencing (mNGS) is increasingly being used to characterize the human virome. The impact of viral nucleic extraction on virome profiling has been poorly studied. Here, we aimed to compare the sensitivity and sample and reagent contamination of three extraction methods used for viral mNGS: two automated platforms (eMAG; MagNA Pure 24, MP24) and the manual QIAamp Viral RNA Mini Kit (QIAamp). Clinical respiratory samples (positive for Respiratory Syncytial Virus or Herpes Simplex Virus), one mock sample (including five viruses isolated from respiratory samples), and a no-template control (NTC) were extracted and processed through an mNGS workflow. QIAamp yielded a lower proportion of viral reads for both clinical and mock samples. The sample cross-contamination was higher when using MP24, with up to 36.09% of the viral reads mapping to mock viruses in the NTC (vs. 1.53% and 1.45% for eMAG and QIAamp, respectively). The highest number of viral reads mapping to bacteriophages in the NTC was found with QIAamp, suggesting reagent contamination. Our results highlight the importance of the extraction method choice for accurate virome characterization.
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Affiliation(s)
- Marina Sabatier
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Antonin Bal
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Grégory Destras
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Hadrien Regue
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
| | - Grégory Quéromès
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
| | - Valérie Cheynet
- Laboratoire Commun de Recherche Hospices Civils de Lyon—bioMérieux, Centre Hospitalier Lyon Sud, F-69310 Pierre-Bénite, France; (V.C.); (K.B.-P.)
| | - Bruno Lina
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Claire Bardel
- Université Lyon 1, Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, F-69100 Villeurbanne, France;
| | - Karen Brengel-Pesce
- Laboratoire Commun de Recherche Hospices Civils de Lyon—bioMérieux, Centre Hospitalier Lyon Sud, F-69310 Pierre-Bénite, France; (V.C.); (K.B.-P.)
| | - Vincent Navratil
- PRABI, Rhône Alpes Bioinformatics Center, UCBL, Université Claude Bernard Lyon 1, F-69000 Lyon, France;
- European Virus Bioinformatics Center, Leutragraben 1, D-07743 Jena, Germany
| | - Laurence Josset
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
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11
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RNA isolation efficacy of commercial and modified conventional methods for Citrus tristeza virus and mRNA internal control amplification. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-019-00405-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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12
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Implementation and Validation of the Roche Light Cycler 480 96-Well Plate Platform as a Real-Time PCR Assay for the Quantitative Detection of Cytomegalovirus (CMV) in Clinical Specimens Using the Luminex MultiCode ASRs System. Med Sci (Basel) 2020; 8:medsci8010014. [PMID: 32168800 PMCID: PMC7151591 DOI: 10.3390/medsci8010014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/03/2020] [Accepted: 03/07/2020] [Indexed: 11/16/2022] Open
Abstract
Allogenic stem-cell therapies benefit patients in the treatment of multiple diseases; however, the side effects of stem-cell therapies (SCT) derived from the concomitant use of immune suppression agents often include triggering infection diseases. Thus, analysis is required to improve the detection of pathogen infections in SCT. We develop a polymerase chain reaction (PCR)-based methodology for the qualitative real-time DNA detection of cytomegalovirus (CMV), with reference to herpes simplex virus types 1 (HSVI), Epstein–Barr virus (EBV), and varicella-zoster virus (VZV) in blood, urine, solid tissues, and cerebrospinal fluid. This real-time PCR of 96-well plate format provides a rapid framework as required by the Food and Drug Administration (FDA) for clinical settings, including the processing of specimens, reagent handling, special safety precautions, quality control criteria and analytical accuracy, precisely reportable range (analyst measurement range), reference range, limit of detection (LOD), analytical specificity established by interference study, and analyte stability. Specifically, we determined the reportable range (analyst measurement range) with the following criteria: CMV copies ≥200 copies/mL; report copy/mL value; CMV copies ≤199 copies/mL; report detected but below quantitative range; CMV copies = 0 with report <200 copies/mL. That is, with reference range, copy numbers (CN) per milliliter (mL) of the LOD were determined by standard curves that correlated Ct value and calibrated standard DNA panels. The three repeats determined that the measuring range was 1E2~1E6 copies/mL. The standard curves show the slopes were within the range −2.99 to −3.65 with R2 ≥ 0.98. High copy (HC) controls were within 0.17–0.18 log differences of DNA copy numbers; (2) low copy (LC) controls were within 0.17–0.18 log differences; (3) LOD was within 0.14–0.15 log differences. As such, we set up a fast, simple, inexpensive, sensitive, and reliable molecular approach for the qualitative detection of CMV pathogens. Conclusion: This real-time PCR of the 96-well plate format provides a rapid framework as required by the FDA for clinical settings.
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13
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Lewandowski K, Xu Y, Pullan ST, Lumley SF, Foster D, Sanderson N, Vaughan A, Morgan M, Bright N, Kavanagh J, Vipond R, Carroll M, Marriott AC, Gooch KE, Andersson M, Jeffery K, Peto TEA, Crook DW, Walker AS, Matthews PC. Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples. J Clin Microbiol 2019; 58:e00963-19. [PMID: 31666364 PMCID: PMC6935926 DOI: 10.1128/jcm.00963-19] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/21/2019] [Indexed: 01/11/2023] Open
Abstract
Influenza is a major global public health threat as a result of its highly pathogenic variants, large zoonotic reservoir, and pandemic potential. Metagenomic viral sequencing offers the potential for a diagnostic test for influenza virus which also provides insights on transmission, evolution, and drug resistance and simultaneously detects other viruses. We therefore set out to apply the Oxford Nanopore Technologies sequencing method to metagenomic sequencing of respiratory samples. We generated influenza virus reads down to a limit of detection of 102 to 103 genome copies/ml in pooled samples, observing a strong relationship between the viral titer and the proportion of influenza virus reads (P = 4.7 × 10-5). Applying our methods to clinical throat swabs, we generated influenza virus reads for 27/27 samples with mid-to-high viral titers (cycle threshold [CT ] values, <30) and 6/13 samples with low viral titers (CT values, 30 to 40). No false-positive reads were generated from 10 influenza virus-negative samples. Thus, Nanopore sequencing operated with 83% sensitivity (95% confidence interval [CI], 67 to 93%) and 100% specificity (95% CI, 69 to 100%) compared to the current diagnostic standard. Coverage of full-length virus was dependent on sample composition, being negatively influenced by increased host and bacterial reads. However, at high influenza virus titers, we were able to reconstruct >99% complete sequences for all eight gene segments. We also detected a human coronavirus coinfection in one clinical sample. While further optimization is required to improve sensitivity, this approach shows promise for the Nanopore platform to be used in the diagnosis and genetic analysis of influenza virus and other respiratory viruses.
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Affiliation(s)
- Kuiama Lewandowski
- Public Health England, National infection Service, Porton Down, Salisbury, United Kingdom
| | - Yifei Xu
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Steven T Pullan
- Public Health England, National infection Service, Porton Down, Salisbury, United Kingdom
| | - Sheila F Lumley
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Dona Foster
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Nicholas Sanderson
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Alison Vaughan
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Marcus Morgan
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Nicole Bright
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - James Kavanagh
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Richard Vipond
- Public Health England, National infection Service, Porton Down, Salisbury, United Kingdom
| | - Miles Carroll
- Public Health England, National infection Service, Porton Down, Salisbury, United Kingdom
| | - Anthony C Marriott
- Public Health England, National infection Service, Porton Down, Salisbury, United Kingdom
| | - Karen E Gooch
- Public Health England, National infection Service, Porton Down, Salisbury, United Kingdom
| | - Monique Andersson
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Katie Jeffery
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Timothy E A Peto
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Philippa C Matthews
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
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14
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Kafetzopoulou LE, Efthymiadis K, Lewandowski K, Crook A, Carter D, Osborne J, Aarons E, Hewson R, Hiscox JA, Carroll MW, Vipond R, Pullan ST. Assessment of metagenomic Nanopore and Illumina sequencing for recovering whole genome sequences of chikungunya and dengue viruses directly from clinical samples. ACTA ACUST UNITED AC 2019; 23. [PMID: 30563591 PMCID: PMC6299504 DOI: 10.2807/1560-7917.es.2018.23.50.1800228] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Background The recent global emergence and re-emergence of arboviruses has caused significant human disease. Common vectors, symptoms and geographical distribution make differential diagnosis both important and challenging. Aim To investigate the feasibility of metagenomic sequencing for recovering whole genome sequences of chikungunya and dengue viruses from clinical samples. Methods We performed metagenomic sequencing using both the Illumina MiSeq and the portable Oxford Nanopore MinION on clinical samples which were real-time reverse transcription-PCR (qRT-PCR) positive for chikungunya (CHIKV) or dengue virus (DENV), two of the most important arboviruses. A total of 26 samples with a range of representative clinical Ct values were included in the study. Results Direct metagenomic sequencing of nucleic acid extracts from serum or plasma without viral enrichment allowed for virus identification, subtype determination and elucidated complete or near-complete genomes adequate for phylogenetic analysis. One PCR-positive CHIKV sample was also found to be coinfected with DENV. Conclusions This work demonstrates that metagenomic whole genome sequencing is feasible for the majority of CHIKV and DENV PCR-positive patient serum or plasma samples. Additionally, it explores the use of Nanopore metagenomic sequencing for DENV and CHIKV, which can likely be applied to other RNA viruses, highlighting the applicability of this approach to front-line public health and potential portable applications using the MinION.
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Affiliation(s)
- Liana E Kafetzopoulou
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom.,Public Health England, National Infections Service, Porton Down, United Kingdom
| | - Kyriakos Efthymiadis
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, Brussels, Belgium
| | - Kuiama Lewandowski
- Public Health England, National Infections Service, Porton Down, United Kingdom
| | - Ant Crook
- Public Health England, National Infections Service, Porton Down, United Kingdom
| | - Dan Carter
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom.,Public Health England, National Infections Service, Porton Down, United Kingdom
| | - Jane Osborne
- Rare and Imported Pathogens Laboratory, Public Health England, Porton Down, United Kingdom
| | - Emma Aarons
- Rare and Imported Pathogens Laboratory, Public Health England, Porton Down, United Kingdom
| | - Roger Hewson
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom.,Public Health England, National Infections Service, Porton Down, United Kingdom
| | - Julian A Hiscox
- Institute of Infection and Global Health, University of Liverpool, United Kingdom.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
| | - Miles W Carroll
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom.,Public Health England, National Infections Service, Porton Down, United Kingdom
| | - Richard Vipond
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom.,Public Health England, National Infections Service, Porton Down, United Kingdom
| | - Steven T Pullan
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom.,Public Health England, National Infections Service, Porton Down, United Kingdom
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15
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Burton JE, Easterbrook L, Pitman J, Anderson D, Roddy S, Bailey D, Vipond R, Bruce CB, Roberts AD. The effect of a non-denaturing detergent and a guanidinium-based inactivation agent on the viability of Ebola virus in mock clinical serum samples. J Virol Methods 2017; 250:34-40. [PMID: 28941617 DOI: 10.1016/j.jviromet.2017.09.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/18/2017] [Accepted: 09/19/2017] [Indexed: 10/18/2022]
Abstract
The 2014 Ebola outbreak in West Africa required the rapid testing of clinical material for the presence of potentially high titre Ebola virus (EBOV). Safe, fast and effective methods for the inactivation of such clinical samples are required so that rapid diagnostic tests including downstream analysis by RT-qPCR or nucleotide sequencing can be carried out. One of the most commonly used guanidinium - based denaturing agents, AVL (Qiagen) has been shown to fully inactivate EBOV once ethanol is added, however this is not compatible with the use of automated nucleic acid extraction systems. Additional inactivation agents need to be identified that can be used in automated systems. A candidate inactivation agent is Triton X-100, a non-denaturing detergent that is frequently used in clinical nucleic acid extraction procedures and has previously been used for inactivation of EBOV. In this study the effect of 0.1% and 1.0% Triton X-100 (final concentration 0.08% and 0.8% respectively) alone and in combination with AVL on the viability of EBOV (106 TCID50/ml) spiked into commercially available pooled negative human serum was tested. The presence of viable EBOV in the treated samples was assessed by carrying out three serial passages of the samples in Vero E6 cells (37°C, 5% CO2, 1 week for each passage). At the end of each passage the cells were observed for evidence of cytopathic effect and samples were taken for rRT-PCR analysis for the presence of EBOV RNA. Before cell culture cytotoxic components of AVL and Triton X-100 were removed from the samples using size exclusion spin column technology or a hydrophobic adsorbent resin. The results of this study showed that EBOV spiked into human serum was not fully inactivated when treated with either 0.1% (v/v) Triton X-100 for 10 mins or 1.0% (v/v) Triton X-100 for 20 mins (final concentrations 0.08% and 0.8% Triton X-100 respectively). AVL alone also did not consistently provide complete inactivation. Samples treated with both AVL and 0.1% Triton X-100 for 10 or 20 mins were shown to be completely inactivated. This treatment is compatible with downstream analysis by RT-qPCR and next generation sequencing.
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Affiliation(s)
- J E Burton
- High Containment Microbiology, Public Health England, Porton Down, Salisbury, United Kingdom.
| | - L Easterbrook
- High Containment Microbiology, Public Health England, Porton Down, Salisbury, United Kingdom
| | - J Pitman
- High Containment Microbiology, Public Health England, Porton Down, Salisbury, United Kingdom
| | - D Anderson
- High Containment Microbiology, Public Health England, Porton Down, Salisbury, United Kingdom
| | - S Roddy
- High Containment Microbiology, Public Health England, Porton Down, Salisbury, United Kingdom
| | - D Bailey
- High Containment Microbiology, Public Health England, Porton Down, Salisbury, United Kingdom
| | - R Vipond
- High Containment Microbiology, Public Health England, Porton Down, Salisbury, United Kingdom
| | - C B Bruce
- High Containment Microbiology, Public Health England, Porton Down, Salisbury, United Kingdom
| | - A D Roberts
- High Containment Microbiology, Public Health England, Porton Down, Salisbury, United Kingdom
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