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Duan B, Zeng X, Peng J. Advances in genotypic antimicrobialresistance testing: a comprehensive review. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2570-4. [PMID: 39300049 DOI: 10.1007/s11427-023-2570-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/15/2024] [Indexed: 09/22/2024]
Abstract
Antimicrobial resistance (AMR) represents a substantial threat to global public health, complicating the treatment of common infections and leading to prolonged illness and escalated healthcare expenses. To effectively combat AMR, timely and accurate detection is crucial for AMR surveillance and individual-based therapy. Phenotypic antibiotic resistance testing (AST) has long been considered the gold standard in clinical applications, serving as the foundation for clinical AMR diagnosis and optimized therapy. It has significantly contributed to ensuring patients' health and the development of novel antimicrobials. Despite advancements in automated culture-based AST technologies, inherent limitations impede the widespread use of phenotypic AST in AMR surveillance. Genotypic AST technologies offer a promising alternative option, exhibiting advantages of rapidity, high sensitivity, and specificity. With the continuous advancement and expanding applications of genotypic AST technologies, such as microfluidics, mass spectrometry, and high-resolution melting curve analysis, new vigor has been injected into the development and clinical implementation of genotypic AST technologies. In this narrative review, we discuss the principles, applications, and advancements of emerging genotypic AST methods in clinical settings. The comprehensive review aims to highlight the significant scientific potential of emerging genotypic AST technologies in clinical AMR diagnosis, providing insights to enhance existing methods and explore novel approaches.
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Affiliation(s)
- Boheng Duan
- Huan Kui College of Nanchang University, Nanchang, 330031, China
| | - Xianjun Zeng
- Department of Imaging, The Second Affiliated Hospital of Nanchang University, Nanchang, 330038, China
| | - Junping Peng
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 102629, China.
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 102629, China.
- Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 102629, China.
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Quek ZBR, Ng SH. Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology. Pathogens 2024; 13:275. [PMID: 38668230 PMCID: PMC11054155 DOI: 10.3390/pathogens13040275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 04/29/2024] Open
Abstract
High-throughput sequencing (HTS) has revolutionised the field of pathogen genomics, enabling the direct recovery of pathogen genomes from clinical and environmental samples. However, pathogen nucleic acids are often overwhelmed by those of the host, requiring deep metagenomic sequencing to recover sufficient sequences for downstream analyses (e.g., identification and genome characterisation). To circumvent this, hybrid-capture target enrichment (HC) is able to enrich pathogen nucleic acids across multiple scales of divergences and taxa, depending on the panel used. In this review, we outline the applications of HC in human pathogens-bacteria, fungi, parasites and viruses-including identification, genomic epidemiology, antimicrobial resistance genotyping, and evolution. Importantly, we explored the applicability of HC to clinical metagenomics, which ultimately requires more work before it is a reliable and accurate tool for clinical diagnosis. Relatedly, the utility of HC was exemplified by COVID-19, which was used as a case study to illustrate the maturity of HC for recovering pathogen sequences. As we unravel the origins of COVID-19, zoonoses remain more relevant than ever. Therefore, the role of HC in biosurveillance studies is also highlighted in this review, which is critical in preparing us for the next pandemic. We also found that while HC is a popular tool to study viruses, it remains underutilised in parasites and fungi and, to a lesser extent, bacteria. Finally, weevaluated the future of HC with respect to bait design in the eukaryotic groups and the prospect of combining HC with long-read HTS.
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Affiliation(s)
- Z. B. Randolph Quek
- Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore
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Scheunert A, Lautenschlager U, Ott T, Oberprieler C. Nano-Strainer: A workflow for the identification of single-copy nuclear loci for plant systematic studies, using target capture kits and Oxford Nanopore long reads. Ecol Evol 2023; 13:e10190. [PMID: 37475726 PMCID: PMC10354226 DOI: 10.1002/ece3.10190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/18/2023] [Accepted: 06/01/2023] [Indexed: 07/22/2023] Open
Abstract
In modern plant systematics, target enrichment enables simultaneous analysis of hundreds of genes. However, when dealing with reticulate or polyploidization histories, few markers may suffice, but often are required to be single-copy, a condition that is not necessarily met with commercial capture kits. Also, large genome sizes can render target capture ineffective, so that amplicon sequencing would be preferable; however, knowledge about suitable loci is often missing. Here, we present a comprehensive workflow for the identification of putative single-copy nuclear markers in a genus of interest, by mining a small dataset from target capture using a few representative taxa. The proposed pipeline assesses sequence variability contained in the data from targeted loci and assigns reads to their respective genes, via a combined BLAST/clustering procedure. Cluster consensus sequences are then examined based on four pre-defined criteria presumably indicative for absence of paralogy. This is done by calculating four specialized indices; loci are ranked according to their performance in these indices, and top-scoring loci are considered putatively single- or low copy. The approach can be applied to any probe set. As it relies on long reads, the present contribution also provides template workflows for processing Nanopore-based target capture data. Obtained markers are further tested and then entered into amplicon sequencing. For the detection of possibly remaining paralogy in these data, which might occur in groups with rampant paralogy, we also employ the long-read assembly tool canu. In diploid representatives of the young Compositae genus Leucanthemum, characterized by high levels of polyploidy, our approach resulted in successful amplification of 13 loci. Modifications to remove traces of paralogy were made in seven of these. A species tree from the markers correctly reproduced main relationships in the genus, however, at low resolution. The presented workflow has the potential to valuably support phylogenetic research, for example in polyploid plant groups.
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Affiliation(s)
- Agnes Scheunert
- Evolutionary and Systematic Botany Group, Institute of Plant SciencesUniversity of RegensburgRegensburgGermany
| | - Ulrich Lautenschlager
- Evolutionary and Systematic Botany Group, Institute of Plant SciencesUniversity of RegensburgRegensburgGermany
| | - Tankred Ott
- Evolutionary and Systematic Botany Group, Institute of Plant SciencesUniversity of RegensburgRegensburgGermany
| | - Christoph Oberprieler
- Evolutionary and Systematic Botany Group, Institute of Plant SciencesUniversity of RegensburgRegensburgGermany
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Sadasivan H, Wadden J, Goliya K, Ranjan P, Dickson RP, Blaauw D, Das R, Narayanasamy S. Rapid Real-time Squiggle Classification for Read until using RawMap. ARCHIVES OF CLINICAL AND BIOMEDICAL RESEARCH 2023; 7:45-57. [PMID: 36938368 PMCID: PMC10022530 DOI: 10.26502/acbr.50170318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
ReadUntil enables Oxford Nanopore Technology's (ONT) sequencers to selectively sequence reads of target species in real-time. This enables efficient microbial enrichment for applications such as microbial abundance estimation and is particularly beneficial for metagenomic samples with a very high fraction of non-target reads (> 99% can be human reads). However, read-until requires a fast and accurate software filter that analyzes a short prefix of a read and determines if it belongs to a microbe of interest (target) or not. The baseline Read Until pipeline uses a deep neural network-based basecaller called Guppy and is slow and inaccurate for this task (~60% of bases sequenced are unclassified). We present RawMap, an efficient CPU-only microbial species-agnostic Read Until classifier for filtering non-target human reads in the squiggle space. RawMap uses a Support Vector Machine (SVM), which is trained to distinguish human from microbe using non-linear and non-stationary characteristics of ONT's squiggle output (continuous electrical signals). Compared to the baseline Read Until pipeline, RawMap is a 1327X faster classifier and significantly improves the sequencing time and cost, and compute time savings. We show that RawMap augmented pipelines reduce sequencing time and cost by ~24% and computing cost by 22%. Additionally, since RawMap is agnostic to microbial species, it can also classify microbial species it is not trained on. We also discuss how RawMap may be used as an alternative to the RT-PCR test for viral load quantification of SARS-CoV-2.
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Affiliation(s)
- Harisankar Sadasivan
- Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, 48109, USA
| | - Jack Wadden
- Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, 48109, USA
| | - Kush Goliya
- Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, 48109, USA
| | - Piyush Ranjan
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, 48109, USA
| | - Robert P Dickson
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, 48109, USA
| | - David Blaauw
- Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, 48109, USA
| | - Reetuparna Das
- Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, 48109, USA
| | - Satish Narayanasamy
- Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, 48109, USA
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Dippenaar A, Goossens SN, Grobbelaar M, Oostvogels S, Cuypers B, Laukens K, Meehan CJ, Warren RM, van Rie A. Nanopore Sequencing for Mycobacterium tuberculosis: a Critical Review of the Literature, New Developments, and Future Opportunities. J Clin Microbiol 2022; 60:e0064621. [PMID: 34133895 PMCID: PMC8769739 DOI: 10.1128/jcm.00646-21] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The next-generation, short-read sequencing technologies that generate comprehensive, whole-genome data with single nucleotide resolution have already advanced tuberculosis diagnosis, treatment, surveillance, and source investigation. Their high costs, tedious and lengthy processes, and large equipment remain major hurdles for research use in high tuberculosis burden countries and implementation into routine care. The portable next-generation sequencing devices developed by Oxford Nanopore Technologies (ONT) are attractive alternatives due to their long-read sequence capability, compact low-cost hardware, and continued improvements in accuracy and throughput. A systematic review of the published literature demonstrated limited uptake of ONT sequencing in tuberculosis research and clinical care. Of the 12 eligible articles presenting ONT sequencing data on at least one Mycobacterium tuberculosis sample, four addressed software development for long-read ONT sequencing data with potential applications for M. tuberculosis. Only eight studies presented results of ONT sequencing of M. tuberculosis, of which five performed whole-genome and three did targeted sequencing. Based on these findings, we summarize the standard processes, reflect on the current limitations of ONT sequencing technology, and the research needed to overcome the main hurdles. The low capital cost, portable nature and continued improvement in the performance of ONT sequencing make it an attractive option for sequencing for research and clinical care, but limited data are available on its application in the tuberculosis field. Important research investment is needed to unleash the full potential of ONT sequencing for tuberculosis research and care.
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Affiliation(s)
- Anzaan Dippenaar
- Tuberculosis Omics Research Consortium, Family Medicine and Population Health, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Sander N. Goossens
- Tuberculosis Omics Research Consortium, Family Medicine and Population Health, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Melanie Grobbelaar
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Selien Oostvogels
- Tuberculosis Omics Research Consortium, Family Medicine and Population Health, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Bart Cuypers
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Molecular Parasitology Group, Institute of Tropical Medicine, Antwerp, Belgium
| | - Kris Laukens
- Molecular Parasitology Group, Institute of Tropical Medicine, Antwerp, Belgium
| | - Conor J. Meehan
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
- School of Chemistry and Bioscience, Faculty of Life Science, University of Bradford, Bradford, West Yorkshire, United Kingdom
| | - Robin M. Warren
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Annelies van Rie
- Tuberculosis Omics Research Consortium, Family Medicine and Population Health, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
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Wu YC, Chen CI, Chen PY, Kuo CH, Hung YH, Peng KY, Wu VC, Tsai-Wu JJ, Hsu CL. GRAde: a long-read sequencing approach to efficiently identifying the CYP11B1/CYP11B2 chimeric form in patients with glucocorticoid-remediable aldosteronism. BMC Bioinformatics 2022; 22:613. [PMID: 35012455 PMCID: PMC8750845 DOI: 10.1186/s12859-022-04561-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glucocorticoid-remediable aldosteronism (GRA) is a form of heritable hypertension caused by a chimeric fusion resulting from unequal crossing over between 11β-hydroxylase (CYP11B1) and aldosterone synthase (CYP11B2), which are two genes with similar sequences. Different crossover patterns of the CYP11B1 and CYP11B2 chimeric genes may be associated with a variety of clinical presentations. It is therefore necessary to develop an efficient approach for identifying the differences between the hybrid genes of a patient with GRA. RESULTS We developed a long-read analysis pipeline named GRAde (GRA deciphering), which utilizes the nonidentical bases in the CYP11B1 and CYP11B2 genomic sequences to identify and visualize the chimeric form. We sequenced the polymerase chain reaction (PCR) products of the CYP11B1/CYP11B2 chimeric gene from 36 patients with GRA using the Nanopore MinION device and analyzed the sequences using GRAde. Crossover events were identified for 30 out of the 36 samples. The crossover sites appeared in the region exhibiting high sequence similarity between CYP11B1 and CYP11B2, and 53.3% of the cases were identified as having a gene conversion in intron 2. More importantly, there were six cases for whom the PCR products indicated a chimeric gene, but the GRAde results revealed no crossover pattern. The crossover regions were further verified by Sanger sequencing analysis. CONCLUSIONS PCR-based target enrichment followed by long-read sequencing is an efficient and precise approach to dissecting complex genomic regions, such as those involved in GRA mutations, which could be directly applied to clinical diagnosis. The scripts of GRAde are available at https://github.com/hsu-binfo/GRAde .
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Affiliation(s)
- Yu-Ching Wu
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Chia-I Chen
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Peng-Ying Chen
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chun-Hung Kuo
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Hsuan Hung
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Kang-Yung Peng
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Vin-Cent Wu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Jyy-Jih Tsai-Wu
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Chia-Lang Hsu
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - TAIPAI group
- TAIPAI, Taiwan Primary Aldosteronism Investigator Group and TSA, Taiwan Society of Aldosteronism, Taipei, Taiwan
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Brait N, Külekçi B, Goerzer I. Long range PCR-based deep sequencing for haplotype determination in mixed HCMV infections. BMC Genomics 2022; 23:31. [PMID: 34991471 PMCID: PMC8735729 DOI: 10.1186/s12864-021-08272-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 12/03/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Short read sequencing has been used extensively to decipher the genome diversity of human cytomegalovirus (HCMV) strains, but falls short to reveal individual genomes in mixed HCMV strain populations. Novel third-generation sequencing platforms offer an extended read length and promise to resolve how distant polymorphic sites along individual genomes are linked. In the present study, we established a long amplicon PacBio sequencing workflow to identify the absolute and relative quantities of unique HCMV haplotypes spanning over multiple hypervariable sites in mixtures. Initial validation of this approach was performed with defined HCMV DNA templates derived from cell-culture enriched viruses and was further tested for its suitability on patient samples carrying mixed HCMV infections. RESULTS Total substitution and indel error rate of mapped reads ranged from 0.17 to 0.43% depending on the stringency of quality trimming. Artificial HCMV DNA mixtures were correctly determined down to 1% abundance of the minor DNA source when the total HCMV DNA input was 4 × 104 copies/ml. PCR products of up to 7.7 kb and a GC content < 55% were efficiently generated when DNA was directly isolated from patient samples. In a single sample, up to three distinct haplotypes were identified showing varying relative frequencies. Alignments of distinct haplotype sequences within patient samples showed uneven distribution of sequence diversity, interspersed by long identical stretches. Moreover, diversity estimation at single polymorphic regions as assessed by short amplicon sequencing may markedly underestimate the overall diversity of mixed haplotype populations. CONCLUSIONS Quantitative haplotype determination by long amplicon sequencing provides a novel approach for HCMV strain characterisation in mixed infected samples which can be scaled up to cover the majority of the genome by multi-amplicon panels. This will substantially improve our understanding of intra-host HCMV strain diversity and its dynamic behaviour.
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Affiliation(s)
- Nadja Brait
- Center for Virology, Medical University of Vienna, Vienna, Austria
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Büşra Külekçi
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Irene Goerzer
- Center for Virology, Medical University of Vienna, Vienna, Austria.
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Schuele L, Cassidy H, Lizarazo E, Strutzberg-Minder K, Schuetze S, Loebert S, Lambrecht C, Harlizius J, Friedrich AW, Peter S, Niesters HGM, Rossen JWA, Couto N. Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples. Viruses 2020; 12:E1358. [PMID: 33260903 PMCID: PMC7759923 DOI: 10.3390/v12121358] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 12/18/2022] Open
Abstract
Shotgun metagenomic sequencing (SMg) enables the simultaneous detection and characterization of viruses in human, animal and environmental samples. However, lack of sensitivity still poses a challenge and may lead to poor detection and data acquisition for detailed analysis. To improve sensitivity, we assessed a broad scope targeted sequence capture (TSC) panel (ViroCap) in both human and animal samples. Moreover, we adjusted TSC for the Oxford Nanopore MinION and compared the performance to an SMg approach. TSC on the Illumina NextSeq served as the gold standard. Overall, TSC increased the viral read count significantly in challenging human samples, with the highest genome coverage achieved using the TSC on the MinION. TSC also improved the genome coverage and sequencing depth in clinically relevant viruses in the animal samples, such as influenza A virus. However, SMg was shown to be adequate for characterizing a highly diverse animal virome. TSC on the MinION was comparable to the NextSeq and can provide a valuable alternative, offering longer reads, portability and lower initial cost. Developing new viral enrichment approaches to detect and characterize significant human and animal viruses is essential for the One Health Initiative.
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Affiliation(s)
- Leonard Schuele
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 RC Groningen, The Netherlands; (H.C.); (E.L.); (A.W.F.); (H.G.M.N.); (J.W.A.R.); (N.C.)
- Institute of Medical Microbiology and Hygiene, University of Tübingen, 72076 Tübingen, Germany;
| | - Hayley Cassidy
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 RC Groningen, The Netherlands; (H.C.); (E.L.); (A.W.F.); (H.G.M.N.); (J.W.A.R.); (N.C.)
| | - Erley Lizarazo
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 RC Groningen, The Netherlands; (H.C.); (E.L.); (A.W.F.); (H.G.M.N.); (J.W.A.R.); (N.C.)
| | | | - Sabine Schuetze
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, 59505 Bad Sassendorf, Germany; (S.S.); (S.L.); (C.L.); (J.H.)
| | - Sandra Loebert
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, 59505 Bad Sassendorf, Germany; (S.S.); (S.L.); (C.L.); (J.H.)
| | - Claudia Lambrecht
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, 59505 Bad Sassendorf, Germany; (S.S.); (S.L.); (C.L.); (J.H.)
| | - Juergen Harlizius
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, 59505 Bad Sassendorf, Germany; (S.S.); (S.L.); (C.L.); (J.H.)
| | - Alex W. Friedrich
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 RC Groningen, The Netherlands; (H.C.); (E.L.); (A.W.F.); (H.G.M.N.); (J.W.A.R.); (N.C.)
| | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University of Tübingen, 72076 Tübingen, Germany;
| | - Hubert G. M. Niesters
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 RC Groningen, The Netherlands; (H.C.); (E.L.); (A.W.F.); (H.G.M.N.); (J.W.A.R.); (N.C.)
| | - John W. A. Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 RC Groningen, The Netherlands; (H.C.); (E.L.); (A.W.F.); (H.G.M.N.); (J.W.A.R.); (N.C.)
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
| | - Natacha Couto
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 RC Groningen, The Netherlands; (H.C.); (E.L.); (A.W.F.); (H.G.M.N.); (J.W.A.R.); (N.C.)
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
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Grädel C, Terrazos Miani MA, Baumann C, Barbani MT, Neuenschwander S, Leib SL, Suter-Riniker F, Ramette A. Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing. Viruses 2020; 12:v12080841. [PMID: 32752120 PMCID: PMC7472277 DOI: 10.3390/v12080841] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 12/14/2022] Open
Abstract
Enteroviruses are small RNA viruses that affect millions of people each year by causing an important burden of disease with a broad spectrum of symptoms. In routine diagnostic laboratories, enteroviruses are identified by PCR-based methods, often combined with partial sequencing for genotyping. In this proof-of-principle study, we assessed direct RNA sequencing (DRS) using nanopore sequencing technology for fast whole-genome sequencing of viruses directly from clinical samples. The approach was complemented by sequencing the corresponding viral cDNA via Illumina MiSeq sequencing. DRS of total RNA extracted from three different enterovirus-positive stool samples produced long RNA fragments, covering between 59% and 99.6% of the most similar reference genome sequences. The identification of the enterovirus sequences in the samples was confirmed by short-read cDNA sequencing. Sequence identity between DRS and Illumina MiSeq enterovirus consensus sequences ranged between 94% and 97%. Here, we show that nanopore DRS can be used to correctly identify enterovirus genotypes from patient stool samples with high viral load and that the approach also provides rich metatranscriptomic information on sample composition for all life domains.
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Affiliation(s)
- Carole Grädel
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland; (C.G.); (M.A.T.M.); (C.B.); (M.T.B.); (S.N.); (S.L.L.); (F.S.-R.)
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Miguel A. Terrazos Miani
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland; (C.G.); (M.A.T.M.); (C.B.); (M.T.B.); (S.N.); (S.L.L.); (F.S.-R.)
| | - Christian Baumann
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland; (C.G.); (M.A.T.M.); (C.B.); (M.T.B.); (S.N.); (S.L.L.); (F.S.-R.)
| | - Maria Teresa Barbani
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland; (C.G.); (M.A.T.M.); (C.B.); (M.T.B.); (S.N.); (S.L.L.); (F.S.-R.)
| | - Stefan Neuenschwander
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland; (C.G.); (M.A.T.M.); (C.B.); (M.T.B.); (S.N.); (S.L.L.); (F.S.-R.)
| | - Stephen L. Leib
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland; (C.G.); (M.A.T.M.); (C.B.); (M.T.B.); (S.N.); (S.L.L.); (F.S.-R.)
| | - Franziska Suter-Riniker
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland; (C.G.); (M.A.T.M.); (C.B.); (M.T.B.); (S.N.); (S.L.L.); (F.S.-R.)
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland; (C.G.); (M.A.T.M.); (C.B.); (M.T.B.); (S.N.); (S.L.L.); (F.S.-R.)
- Correspondence: ; Tel.: +41-31-632-9540
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10
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Van Poelvoorde LA, Saelens X, Thomas I, Roosens NH. Next-Generation Sequencing: An Eye-Opener for the Surveillance of Antiviral Resistance in Influenza. Trends Biotechnol 2020; 38:360-367. [DOI: 10.1016/j.tibtech.2019.09.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/24/2019] [Accepted: 09/25/2019] [Indexed: 12/14/2022]
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11
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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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12
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Nanopore Targeted Sequencing for Rapid Gene Mutations Detection in Acute Myeloid Leukemia. Genes (Basel) 2019; 10:genes10121026. [PMID: 31835432 PMCID: PMC6947272 DOI: 10.3390/genes10121026] [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: 11/12/2019] [Revised: 12/05/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023] Open
Abstract
Acute myeloid leukemia (AML) clinical settings cannot do without molecular testing to confirm or rule out predictive biomarkers for prognostic stratification, in order to initiate or withhold targeted therapy. Next generation sequencing offers the advantage of the simultaneous investigation of numerous genes, but these methods remain expensive and time consuming. In this context, we present a nanopore-based assay for rapid (24 h) sequencing of six genes (NPM1, FLT3, CEBPA, TP53, IDH1 and IDH2) that are recurrently mutated in AML. The study included 22 AML patients at diagnosis; all data were compared with the results of S5 sequencing, and discordant variants were validated by Sanger sequencing. Nanopore approach showed substantial advantages in terms of speed and low cost. Furthermore, the ability to generate long reads allows a more accurate detection of longer FLT3 internal tandem duplications and phasing double CEBPA mutations. In conclusion, we propose a cheap, rapid workflow that can potentially enable all basic molecular biology laboratories to perform detailed targeted gene sequencing analysis in AML patients, in order to define their prognosis and the appropriate treatment.
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13
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Houldcroft CJ. Human Herpesvirus Sequencing in the Genomic Era: The Growing Ranks of the Herpetic Legion. Pathogens 2019; 8:E186. [PMID: 31614759 PMCID: PMC6963362 DOI: 10.3390/pathogens8040186] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/10/2019] [Accepted: 10/11/2019] [Indexed: 12/19/2022] Open
Abstract
The nine human herpesviruses are some of the most ubiquitous pathogens worldwide, causing life-long latent infection in a variety of different tissues. Human herpesviruses range from mild childhood infections to known tumour viruses and 'trolls of transplantation'. Epstein-Barr virus was the first human herpesvirus to have its whole genome sequenced; GenBank now includes thousands of herpesvirus genomes. This review will cover some of the recent advances in our understanding of herpesvirus diversity and disease that have come about as a result of new sequencing technologies, such as target enrichment and long-read sequencing. It will also look at the problem of resolving mixed-genotype infections, whether with short or long-read sequencing methods; and conclude with some thoughts on the future of the field as herpesvirus population genomics becomes a reality.
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Affiliation(s)
- Charlotte J Houldcroft
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambs CB2 0QQ UK.
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambs CB10 1SA, UK.
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14
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Bethune K, Mariac C, Couderc M, Scarcelli N, Santoni S, Ardisson M, Martin J, Montúfar R, Klein V, Sabot F, Vigouroux Y, Couvreur TLP. Long-fragment targeted capture for long-read sequencing of plastomes. APPLICATIONS IN PLANT SCIENCES 2019; 7:e1243. [PMID: 31139509 PMCID: PMC6526642 DOI: 10.1002/aps3.1243] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/21/2019] [Indexed: 05/09/2023]
Abstract
PREMISE Third-generation sequencing methods generate significantly longer reads than those produced using alternative sequencing methods. This provides increased possibilities for the study of biodiversity, phylogeography, and population genetics. We developed a protocol for in-solution enrichment hybridization capture of long DNA fragments applicable to complete plastid genomes. METHODS AND RESULTS The protocol uses cost-effective in-house probes developed via long-range PCR and was used in six non-model monocot species (Poaceae: African rice, pearl millet, fonio; and three palm species). DNA was extracted from fresh and silica gel-dried leaves. Our protocol successfully captured long-read plastome fragments (3151 bp median on average), with an enrichment rate ranging from 15% to 98%. DNA extracted from silica gel-dried leaves led to low-quality plastome assemblies when compared to DNA extracted from fresh tissue. CONCLUSIONS Our protocol could also be generalized to capture long sequences from specific nuclear fragments.
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Affiliation(s)
| | | | | | | | - Sylvain Santoni
- UMR AGAP, Equipe Diversité et Adaptation de la Vigne et des Espèces MéditerranéennesINRA2 Place Viala34060MontpellierFrance
| | - Morgane Ardisson
- UMR AGAP, Equipe Diversité et Adaptation de la Vigne et des Espèces MéditerranéennesINRA2 Place Viala34060MontpellierFrance
| | | | - Rommel Montúfar
- Facultad de Ciencias Exactas y NaturalesPontificia Universidad Católica del EcuadorQuitoEcuador
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15
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Stevens RC, Steele JL, Glover WR, Sanchez-Garcia JF, Simpson SD, O’Rourke D, Ramsdell JS, MacManes MD, Thomas WK, Shuber AP. A novel CRISPR/Cas9 associated technology for sequence-specific nucleic acid enrichment. PLoS One 2019; 14:e0215441. [PMID: 30998719 PMCID: PMC6472885 DOI: 10.1371/journal.pone.0215441] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 04/03/2019] [Indexed: 01/08/2023] Open
Abstract
Massively parallel sequencing technologies have made it possible to generate large quantities of sequence data. However, as research-associated information is transferred into clinical practice, cost and throughput constraints generally require sequence-specific targeted analyses. Therefore, sample enrichment methods have been developed to meet the needs of clinical sequencing applications. However, current amplification and hybrid capture enrichment methods are limited in the contiguous length of sequences for which they are able to enrich. PCR based amplification also loses methylation data and other native DNA features. We have developed a novel technology (Negative Enrichment) where we demonstrate targeting long (>10 kb) genomic regions of interest. We use the specificity of CRISPR-Cas9 single guide RNA (Cas9/sgRNA) complexes to define 5' and 3' termini of sequence-specific loci in genomic DNA, targeting 10 to 36 kb regions. The complexes were found to provide protection from exonucleases, by protecting the targeted sequences from degradation, resulting in enriched, double-strand, non-amplified target sequences suitable for next-generation sequencing library preparation or other downstream analyses.
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Affiliation(s)
- Richard C. Stevens
- Genetics Research LLC, Wakefield, Massachusetts, United States of America
| | - Jennifer L. Steele
- Genetics Research LLC, Wakefield, Massachusetts, United States of America
| | - William R. Glover
- Genetics Research LLC, Wakefield, Massachusetts, United States of America
| | | | - Stephen D. Simpson
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, United States of America
| | - Devon O’Rourke
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, United States of America
- Department of Molecular Cellular and Developmental Biology, University of New Hampshire, Durham, New Hampshire, United States of America
| | - Jordan S. Ramsdell
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, United States of America
| | - Matthew D. MacManes
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, United States of America
- Department of Molecular Cellular and Developmental Biology, University of New Hampshire, Durham, New Hampshire, United States of America
| | - W. Kelley Thomas
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, United States of America
| | - Anthony P. Shuber
- Genetics Research LLC, Wakefield, Massachusetts, United States of America
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16
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Martí-Carreras J, Maes P. Human cytomegalovirus genomics and transcriptomics through the lens of next-generation sequencing: revision and future challenges. Virus Genes 2019; 55:138-164. [PMID: 30604286 PMCID: PMC6458973 DOI: 10.1007/s11262-018-1627-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/14/2018] [Indexed: 12/13/2022]
Abstract
The human cytomegalovirus (HCMV) genome was sequenced by hierarchical shotgun almost 30 years ago. Over these years, low and high passaged strains have been sequenced, improving, albeit still far from complete, the understanding of the coding potential, expression dynamics and diversity of wild-type HCMV strains. Next-generation sequencing (NGS) platforms have enabled a huge advancement, facilitating the comparison of differentially passaged strains, challenging diagnostics and research based on a single or reduced gene set genotyping. In addition, it allowed to link genetic features to different viral phenotypes as for example, correlating large genomic re-arrangements to viral attenuation or different mutations to antiviral resistance and cell tropism. NGS platforms provided the first high-resolution experiments to HCMV dynamics, allowing the study of intra-host viral population structures and the description of rare transcriptional events. Long-read sequencing has recently become available, helping to identify new genomic re-arrangements, partially accounting for the genetic variability displayed in clinical isolates, as well as, in changing the understanding of the HCMV transcriptome. Better knowledge of the transcriptome resulted in a vast number of new splicing events and alternative transcripts, although most of them still need additional validation. This review summarizes the sequencing efforts reached so far, discussing its approaches and providing a revision and new nuances on HCMV sequence variability in the sequencing field.
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Affiliation(s)
- Joan Martí-Carreras
- Zoonotic Infectious Diseases Unit, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, Box 1040, 3000, Leuven, Belgium
| | - Piet Maes
- Zoonotic Infectious Diseases Unit, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, Box 1040, 3000, Leuven, Belgium.
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17
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Wongsurawat T, Jenjaroenpun P, Taylor MK, Lee J, Tolardo AL, Parvathareddy J, Kandel S, Wadley TD, Kaewnapan B, Athipanyasilp N, Skidmore A, Chung D, Chaimayo C, Whitt M, Kantakamalakul W, Sutthent R, Horthongkham N, Ussery DW, Jonsson CB, Nookaew I. Rapid Sequencing of Multiple RNA Viruses in Their Native Form. Front Microbiol 2019; 10:260. [PMID: 30858830 PMCID: PMC6398364 DOI: 10.3389/fmicb.2019.00260] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 01/31/2019] [Indexed: 12/14/2022] Open
Abstract
Long-read nanopore sequencing by a MinION device offers the unique possibility to directly sequence native RNA. We combined an enzymatic poly-A tailing reaction with the native RNA sequencing to (i) sequence complex population of single-stranded (ss)RNA viruses in parallel, (ii) detect genome, subgenomic mRNA/mRNA simultaneously, (iii) detect a complex transcriptomic architecture without the need for assembly, (iv) enable real-time detection. Using this protocol, positive-ssRNA, negative-ssRNA, with/without a poly(A)-tail, segmented/non-segmented genomes were mixed and sequenced in parallel. Mapping of the generated sequences on the reference genomes showed 100% length recovery with up to 97% identity. This work provides a proof of principle and the validity of this strategy, opening up a wide range of applications to study RNA viruses.
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Affiliation(s)
- Thidathip Wongsurawat
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Piroon Jenjaroenpun
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Mariah K. Taylor
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Jasper Lee
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Aline Lavado Tolardo
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Jyothi Parvathareddy
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Sangam Kandel
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
- Department of Bioinformatics, University of Arkansas at Little Rock, Little Rock, AR, United States
| | - Taylor D. Wadley
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Bualan Kaewnapan
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Niracha Athipanyasilp
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Andrew Skidmore
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, United States
| | - Donghoon Chung
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, United States
| | - Chutikarn Chaimayo
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Michael Whitt
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Wannee Kantakamalakul
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Ruengpung Sutthent
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Navin Horthongkham
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - David W. Ussery
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
- Department of Physiology and Biophysics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Colleen B. Jonsson
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
- Department of Physiology and Biophysics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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18
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Karamitros T, van Wilgenburg B, Wills M, Klenerman P, Magiorkinis G. Nanopore sequencing and full genome de novo assembly of human cytomegalovirus TB40/E reveals clonal diversity and structural variations. BMC Genomics 2018; 19:577. [PMID: 30068288 PMCID: PMC6090854 DOI: 10.1186/s12864-018-4949-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 07/19/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Human cytomegalovirus (HCMV) has a double-stranded DNA genome of approximately 235 Kbp that is structurally complex including extended GC-rich repeated regions. Genomic recombination events are frequent in HCMV cultures but have also been observed in vivo. Thus, the assembly of HCMV whole genomes from technologies producing shorter than 500 bp sequences is technically challenging. Here we improved the reconstruction of HCMV full genomes by means of a hybrid, de novo genome-assembly bioinformatics pipeline upon data generated from the recently released MinION MkI B sequencer from Oxford Nanopore Technologies. RESULTS The MinION run of the HCMV (strain TB40/E) library resulted in ~ 47,000 reads from a single R9 flowcell and in ~ 100× average read depth across the virus genome. We developed a novel, self-correcting bioinformatics algorithm to assemble the pooled HCMV genomes in three stages. In the first stage of the bioinformatics algorithm, long contigs (N50 = 21,892) of lower accuracy were reconstructed. In the second stage, short contigs (N50 = 5686) of higher accuracy were assembled, while in the final stage the high quality contigs served as template for the correction of the longer contigs resulting in a high-accuracy, full genome assembly (N50 = 41,056). We were able to reconstruct a single representative haplotype without employing any scaffolding steps. The majority (98.8%) of the genomic features from the reference strain were accurately annotated on this full genome construct. Our method also allowed the detection of multiple alternative sub-genomic fragments and non-canonical structures suggesting rearrangement events between the unique (UL /US) and the repeated (T/IRL/S) genomic regions. CONCLUSIONS Third generation high-throughput sequencing technologies can accurately reconstruct full-length HCMV genomes including their low-complexity and highly repetitive regions. Full-length HCMV genomes could prove crucial in understanding the genetic determinants and viral evolution underpinning drug resistance, virulence and pathogenesis.
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Affiliation(s)
- Timokratis Karamitros
- Department of Zoology, University of Oxford, Oxford, United Kingdom. .,Public Health Laboratories, Department of Microbiology, Hellenic Pasteur Institute, 127 Vas Sofias Ave, 11527, Athens, Greece.
| | - Bonnie van Wilgenburg
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Mark Wills
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Paul Klenerman
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom.,NIHR Biomedical Research Centre, Oxford, United Kingdom
| | - Gkikas Magiorkinis
- Department of Zoology, University of Oxford, Oxford, United Kingdom. .,Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, M. Asias 75 str., 11527, Athens, Greece.
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19
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Roosenhoff R, van der Vries E, van der Linden A, van Amerongen G, Stittelaar KJ, Smits SL, Schutten M, Fouchier RAM. Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. PLoS One 2018; 13:e0200849. [PMID: 30024940 PMCID: PMC6053203 DOI: 10.1371/journal.pone.0200849] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/28/2018] [Indexed: 12/13/2022] Open
Abstract
Influenza viruses can cause severe life threatening infections in high-risk patients, including young children, the elderly and patients with compromised immunity due to underlying medical conditions or immunosuppressive treatment. The impaired immunity of these patients causes prolonged virus infection and combined with antiviral treatment facilitates the emergence of viruses with resistance mutations. The diverse nature of their immune status makes them a challenging group to study the impact of influenza virus infection and the efficacy of antiviral therapy. Immunocompromised ferrets may represent a suitable animal model to assess influenza virus infection and antiviral treatment strategies in immunocompromised hosts. Here, ferrets were given a daily oral solution of mycophenolate mofetil, tacrolimus and prednisolone sodium phosphate to suppress their immune system. Groups of immunocompromised and immunocompetent ferrets were inoculated with an A/H3N2 influenza virus and were subsequently treated with Oseltamivir or left untreated. Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) was performed on the throat and nose specimens to study virus replication during the course of infection. All immunocompromised ferrets had prolonged presence of viral RNA and a higher total amount of virus shedding compared to the immunocompetent ferrets. Although Oseltamivir reduced the total amount of virus shedding from the nose and throat of treated ferrets, it also resulted in the emergence of the neuraminidase R292K resistance substitution in all these animals, as determined by mutation specific RT-PCR and next-generation sequencing. No additional mutations that could be associated with the emergence of the R292K resistance mutation were detected. The immunocompromised ferret model can be used to study A/H3N2 virus shedding and is a promising model to study new antiviral strategies and the emergence of antiviral resistance in immunocompromised hosts.
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Affiliation(s)
| | - Erhard van der Vries
- Department of Infectious Diseases & Immunology, Division of Virology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Utrecht, The Netherlands
| | - Anne van der Linden
- Department of Viroscience, Erasmus MC, Rotterdam, Zuid- Holland, The Netherlands
| | | | | | - Saskia L. Smits
- Viroclinics Biosciences BV, Rotterdam, Zuid-Holland, The Netherlands
| | - Martin Schutten
- Clinical Virology and Diagnostics, Alkmaar, Noord-Holland, The Netherlands
| | - Ron A. M. Fouchier
- Department of Viroscience, Erasmus MC, Rotterdam, Zuid- Holland, The Netherlands
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20
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Chen X, Ni G, He K, Ding ZL, Li GM, Adeola AC, Murphy RW, Wang WZ, Zhang YP. Capture Hybridization of Long-Range DNA Fragments for High-Throughput Sequencing. Methods Mol Biol 2018. [PMID: 29536436 DOI: 10.1007/978-1-4939-7717-8_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Capture hybridization coupled with high-throughput sequencing (HTS) has become one of the most popular approaches to address some scientific problems not only for fundamental evolution but also for ecology and human disease in recent years. However, the technical problem of limited probe capture ability affects its widespread application. Here, we propose to capture hybridize long-range DNA fragments for HTS (termed LR-LCH). We provide a case of three amphibian samples to examine LR-LCH with 2 kb libraries and comparison of standard capture hybridization with 480 bp libraries. Capture sensitivity increased from an average 13.57% of standard capture hybridization to an average 19.80% of LR-LCH; capture efficiency also increased from an average 72.56% of standard capture hybridization to an average 97.71% of LR-LCH. These indicate that longer fragments in the library generally contain both relatively variable regions and relatively conservative regions. The divergent parts of target DNA are enriched along with conservative parts of DNA sequence that effectively captured during hybridization. We present a protocol that allows users to overcome the low capture sensitivity problem for high divergent regions.
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Affiliation(s)
- Xing Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming, Yunnan, China
| | - Gang Ni
- State Key Laboratory of Genetic Resources and Evolution, Kunming, Yunnan, China.,Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming, Yunnan, China
| | - Kai He
- State Key Laboratory of Genetic Resources and Evolution, Kunming, Yunnan, China
| | - Zhao-Li Ding
- Kunming Biological Diversity Regional Centre of Large Apparatus and Equipments, Kunming, Yunnan, China.,Public Technology Service Centre, Kunming, Yunnan, China
| | - Gui-Mei Li
- Kunming Biological Diversity Regional Centre of Large Apparatus and Equipments, Kunming, Yunnan, China.,Public Technology Service Centre, Kunming, Yunnan, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Kunming, Yunnan, China.,China-Africa Centre for Research and Education & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming, Yunnan, China.,Animal Branch of the Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming, Yunnan, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada
| | - Wen-Zhi Wang
- Wildlife Forensics Science Services, Kunming, Yunnan, China. .,Guizhou Academy of Testing and Analysis, Guiyang, Guizhou, China. .,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China. .,Animal Branch of the Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming, Yunnan, China. .,Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming, Yunnan, China. .,Animal Branch of the Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China. .,Laboratory for Conservation and Utilization of Bio-resource and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan, China.
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21
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George S, Pankhurst L, Hubbard A, Votintseva A, Stoesser N, Sheppard AE, Mathers A, Norris R, Navickaite I, Eaton C, Iqbal Z, Crook DW, Phan HTT. Resolving plasmid structures in Enterobacteriaceae using the MinION nanopore sequencer: assessment of MinION and MinION/Illumina hybrid data assembly approaches. Microb Genom 2017; 3:e000118. [PMID: 29026658 PMCID: PMC5610714 DOI: 10.1099/mgen.0.000118] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 04/28/2017] [Indexed: 01/31/2023] Open
Abstract
This study aimed to assess the feasibility of using the Oxford Nanopore Technologies (ONT) MinION long-read sequencer in reconstructing fully closed plasmid sequences from eight Enterobacteriaceae isolates of six different species with plasmid populations of varying complexity. Species represented were Escherichia coli, Klebsiella pneumoniae, Citrobacter freundii, Enterobacter cloacae, Serratia marcescens and Klebsiella oxytoca, with plasmid populations ranging from 1–11 plasmids with sizes of 2–330 kb. Isolates were sequenced using Illumina (short-read) and ONT’s MinION (long-read) platforms, and compared with fully resolved PacBio (long-read) sequence assemblies for the same isolates. We compared the performance of different assembly approaches including SPAdes, plasmidSPAdes, hybridSPAdes, Canu, Canu+Pilon (canuPilon) and npScarf in recovering the plasmid structures of these isolates by comparing with the gold-standard PacBio reference sequences. Overall, canuPilon provided consistently good quality assemblies both in terms of assembly statistics (N50, number of contigs) and assembly accuracy [presence of single nucleotide polymorphisms (SNPs)/indels with respect to the reference sequence]. For plasmid reconstruction, Canu recovered 70 % of the plasmids in complete contigs, and combining three assembly approaches (Canu or canuPilon, hybridSPAdes and plasmidSPAdes) resulted in a total 78 % recovery rate for all the plasmids. The analysis demonstrated the potential of using MinION sequencing technology to resolve important plasmid structures in Enterobacteriaceae species independent of and in conjunction with Illumina sequencing data. A consensus assembly derived from several assembly approaches could present significant benefit in accurately resolving the greatest number of plasmid structures.
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Affiliation(s)
- Sophie George
- 1Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Louise Pankhurst
- 1Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Alasdair Hubbard
- 1Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Antonia Votintseva
- 1Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Nicole Stoesser
- 1Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Anna E Sheppard
- 1Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Amy Mathers
- 2Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA
| | - Rachel Norris
- 3The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Indre Navickaite
- 1Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | | | - Zamin Iqbal
- 3The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Derrick W Crook
- 1Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Hang T T Phan
- 1Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
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22
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Quick J, Grubaugh ND, Pullan ST, Claro IM, Smith AD, Gangavarapu K, Oliveira G, Robles-Sikisaka R, Rogers TF, Beutler NA, Burton DR, Lewis-Ximenez LL, de Jesus JG, Giovanetti M, Hill SC, Black A, Bedford T, Carroll MW, Nunes M, Alcantara LC, Sabino EC, Baylis SA, Faria NR, Loose M, Simpson JT, Pybus OG, Andersen KG, Loman NJ. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nat Protoc 2017; 12:1261-1276. [PMID: 28538739 PMCID: PMC5902022 DOI: 10.1038/nprot.2017.066] [Citation(s) in RCA: 708] [Impact Index Per Article: 101.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genome sequencing has become a powerful tool for studying emerging infectious diseases; however, genome sequencing directly from clinical samples (i.e., without isolation and culture) remains challenging for viruses such as Zika, for which metagenomic sequencing methods may generate insufficient numbers of viral reads. Here we present a protocol for generating coding-sequence-complete genomes, comprising an online primer design tool, a novel multiplex PCR enrichment protocol, optimized library preparation methods for the portable MinION sequencer (Oxford Nanopore Technologies) and the Illumina range of instruments, and a bioinformatics pipeline for generating consensus sequences. The MinION protocol does not require an Internet connection for analysis, making it suitable for field applications with limited connectivity. Our method relies on multiplex PCR for targeted enrichment of viral genomes from samples containing as few as 50 genome copies per reaction. Viral consensus sequences can be achieved in 1-2 d by starting with clinical samples and following a simple laboratory workflow. This method has been successfully used by several groups studying Zika virus evolution and is facilitating an understanding of the spread of the virus in the Americas. The protocol can be used to sequence other viral genomes using the online Primal Scheme primer designer software. It is suitable for sequencing either RNA or DNA viruses in the field during outbreaks or as an inexpensive, convenient method for use in the lab.
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Affiliation(s)
- Joshua Quick
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | | | - Steven T Pullan
- Public Health England, National Infection Service, Porton Down, Salisbury, UK
| | - Ingra M Claro
- Department of Infectious Disease and Institute of Tropical Medicine, University of Saõ Paulo, Saõ Paulo, Brazil
| | - Andrew D Smith
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | | | - Glenn Oliveira
- Scripps Translational Science Institute, La Jolla, California, USA
| | | | - Thomas F Rogers
- The Scripps Research Institute, La Jolla, California, USA
- Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | | | | | | | - Marta Giovanetti
- Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Brazil
- University of Rome, Tor Vergata, Italy
| | - Sarah C Hill
- Department of Zoology, University of Oxford, Oxford, UK
| | - Allison Black
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Miles W Carroll
- Public Health England, National Infection Service, Porton Down, Salisbury, UK
- University of Southampton, South General Hospital, Southampton, UK
| | | | | | - Ester C Sabino
- Department of Infectious Disease and Institute of Tropical Medicine, University of Saõ Paulo, Saõ Paulo, Brazil
| | | | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
| | - Matthew Loose
- DeepSeq, School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | | | - Kristian G Andersen
- The Scripps Research Institute, La Jolla, California, USA
- Scripps Translational Science Institute, La Jolla, California, USA
| | - Nicholas J Loman
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
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