1
|
Dobner J, Nguyen T, Pavez-Giani MG, Cyganek L, Distelmaier F, Krutmann J, Prigione A, Rossi A. mtDNA analysis using Mitopore. Mol Ther Methods Clin Dev 2024; 32:101231. [PMID: 38572068 PMCID: PMC10988129 DOI: 10.1016/j.omtm.2024.101231] [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: 09/14/2023] [Accepted: 03/08/2024] [Indexed: 04/05/2024]
Abstract
Mitochondrial DNA (mtDNA) analysis is crucial for the diagnosis of mitochondrial disorders, forensic investigations, and basic research. Existing pipelines are complex, expensive, and require specialized personnel. In many cases, including the diagnosis of detrimental single nucleotide variants (SNVs), mtDNA analysis is still carried out using Sanger sequencing. Here, we developed a simple workflow and a publicly available webserver named Mitopore that allows the detection of mtDNA SNVs, indels, and haplogroups. To simplify mtDNA analysis, we tailored our workflow to process noisy long-read sequencing data for mtDNA analysis, focusing on sequence alignment and parameter optimization. We implemented Mitopore with eliBQ (eliminate bad quality reads), an innovative quality enhancement that permits the increase of per-base quality of over 20% for low-quality data. The whole Mitopore workflow and webserver were validated using patient-derived and induced pluripotent stem cells harboring mtDNA mutations. Mitopore streamlines mtDNA analysis as an easy-to-use fast, reliable, and cost-effective analysis method for both long- and short-read sequencing data. This significantly enhances the accessibility of mtDNA analysis and reduces the cost per sample, contributing to the progress of mtDNA-related research and diagnosis.
Collapse
Affiliation(s)
- Jochen Dobner
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Thach Nguyen
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Mario Gustavo Pavez-Giani
- Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany
| | - Lukas Cyganek
- Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Jean Krutmann
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
- Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Alessandro Prigione
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Andrea Rossi
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| |
Collapse
|
2
|
Makhoul M, Schlichtermann RH, Ugwuanyi S, Weber SE, Voss-Fels KP, Stahl A, Zetzsche H, Wittkop B, Snowdon RJ, Obermeier C. Novel PHOTOPERIOD-1 gene variants associate with yield-related and root-angle traits in European bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:125. [PMID: 38727862 PMCID: PMC11087350 DOI: 10.1007/s00122-024-04634-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/20/2024] [Indexed: 05/13/2024]
Abstract
KEY MESSAGE PHOTOPERIOD-1 homoeologous gene copies play a pivotal role in regulation of flowering time in wheat. Here, we show that their influence also extends to spike and shoot architecture and even impacts root development. The sequence diversity of three homoeologous copies of the PHOTOPERIOD-1 gene in European winter wheat was analyzed by Oxford Nanopore amplicon-based multiplex sequencing and molecular markers in a panel of 194 cultivars representing breeding progress over the past 5 decades. A strong, consistent association with an average 8% increase in grain yield was observed for the PpdA1-Hap1 haplotype across multiple environments. This haplotype was found to be linked in 51% of cultivars to the 2NS/2AS translocation, originally introduced from Aegilops ventricosa, which leads to an overestimation of its effect. However, even in cultivars without the 2NS/2AS translocation, PpdA1-Hap1 was significantly associated with increased grain yield, kernel per spike and kernel per m2 under optimal growth conditions, conferring a 4% yield advantage compared to haplotype PpdA1-Hap4. In contrast to Ppd-B1 and Ppd-D1, the Ppd-A1 gene exhibits novel structural variations and a high number of SNPs, highlighting the evolutionary changes that have occurred in this region over the course of wheat breeding history. Additionally, cultivars carrying the photoperiod-insensitive Ppd-D1a allele not only exhibit earlier heading, but also deeper roots compared to those with photoperiod-sensitive alleles under German conditions. PCR and KASP assays have been developed that can be effectively employed in marker-assisted breeding programs to introduce these favorable haplotypes.
Collapse
Affiliation(s)
- Manar Makhoul
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | | | - Samson Ugwuanyi
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Sven E Weber
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Kai P Voss-Fels
- Institute for Grapevine Breeding, Hochschule Geisenheim University, Geisenheim, Germany
| | - Andreas Stahl
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Holger Zetzsche
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Benjamin Wittkop
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Christian Obermeier
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany.
| |
Collapse
|
3
|
Hosch S, Wagner P, Giger JN, Dubach N, Saavedra E, Perno CF, Gody JC, Pagonendji MS, Ngoagouni C, Ndoua C, Nsanzabana C, Vickos U, Daubenberger C, Schindler T. PHARE: a bioinformatics pipeline for compositional profiling of multiclonal Plasmodium falciparum infections from long-read Nanopore sequencing data. J Antimicrob Chemother 2024; 79:987-996. [PMID: 38502783 PMCID: PMC11062946 DOI: 10.1093/jac/dkae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/14/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND The emergence of drug-resistant clones of Plasmodium falciparum is a major public health concern, and the ability to detect and track the spread of these clones is crucial for effective malaria control and treatment. However, in endemic settings, malaria infected people often carry multiple P. falciparum clones simultaneously making it likely to miss drug-resistant clones using traditional molecular typing methods. OBJECTIVES Our goal was to develop a bioinformatics pipeline for compositional profiling in multiclonal P. falciparum samples, sequenced using the Oxford Nanopore Technologies MinION platform. METHODS We developed the 'Finding P. falciparum haplotypes with resistance mutations in polyclonal infections' (PHARE) pipeline using existing bioinformatics tools and custom scripts written in python. PHARE was validated on three control datasets containing P. falciparum DNA of four laboratory strains at varying mixing ratios. Additionally, the pipeline was tested on clinical samples from children admitted to a paediatric hospital in the Central African Republic. RESULTS The PHARE pipeline achieved high recall and accuracy rates in all control datasets. The pipeline can be used on any gene and was tested with amplicons of the P. falciparum drug resistance marker genes pfdhps, pfdhfr and pfK13. CONCLUSIONS The PHARE pipeline helps to provide a more complete picture of drug resistance in the circulating P. falciparum population and can help to guide treatment recommendations. PHARE is freely available under the GNU Lesser General Public License v.3.0 on GitHub: https://github.com/Fippu/PHARE.
Collapse
Affiliation(s)
- Salome Hosch
- University of Basel, Petersplatz 1, 4001 Basel, Switzerland
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland
| | - Philipp Wagner
- University of Basel, Petersplatz 1, 4001 Basel, Switzerland
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland
| | - Johanna Nouria Giger
- University of Basel, Petersplatz 1, 4001 Basel, Switzerland
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland
| | - Nina Dubach
- University of Basel, Petersplatz 1, 4001 Basel, Switzerland
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland
| | - Elis Saavedra
- University of Basel, Petersplatz 1, 4001 Basel, Switzerland
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland
| | - Carlo Federico Perno
- Department of Microbiology, Ospedale Pediatrico Bambino Gesù, Piazza di Sant’Onofrio, 4, 00165 Roma, Italy
| | - Jean-Chrysostome Gody
- Department of Intensive Care, Pediatric University Hospital Centre of Bangui, Bangui, Central African Republic
| | | | - Carine Ngoagouni
- Medical Entomology Unit, Institut Pasteur of Bangui, Bangui, Central African Republic
| | - Christophe Ndoua
- National Malaria Control Program, Ministry of Health, Bangui, Central African Republic
| | - Christian Nsanzabana
- University of Basel, Petersplatz 1, 4001 Basel, Switzerland
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland
| | - Ulrich Vickos
- Department of Microbiology, Ospedale Pediatrico Bambino Gesù, Piazza di Sant’Onofrio, 4, 00165 Roma, Italy
| | - Claudia Daubenberger
- University of Basel, Petersplatz 1, 4001 Basel, Switzerland
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland
| | - Tobias Schindler
- University of Basel, Petersplatz 1, 4001 Basel, Switzerland
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland
| |
Collapse
|
4
|
Husser MC, Pham NP, Law C, Araujo FRB, Martin VJJ, Piekny A. Endogenous tagging using split mNeonGreen in human iPSCs for live imaging studies. eLife 2024; 12:RP92819. [PMID: 38652106 PMCID: PMC11037917 DOI: 10.7554/elife.92819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Abstract
Endogenous tags have become invaluable tools to visualize and study native proteins in live cells. However, generating human cell lines carrying endogenous tags is difficult due to the low efficiency of homology-directed repair. Recently, an engineered split mNeonGreen protein was used to generate a large-scale endogenous tag library in HEK293 cells. Using split mNeonGreen for large-scale endogenous tagging in human iPSCs would open the door to studying protein function in healthy cells and across differentiated cell types. We engineered an iPS cell line to express the large fragment of the split mNeonGreen protein (mNG21-10) and showed that it enables fast and efficient endogenous tagging of proteins with the short fragment (mNG211). We also demonstrate that neural network-based image restoration enables live imaging studies of highly dynamic cellular processes such as cytokinesis in iPSCs. This work represents the first step towards a genome-wide endogenous tag library in human stem cells.
Collapse
Affiliation(s)
| | - Nhat P Pham
- Biology Department, Concordia University, Montreal, Canada
| | - Chris Law
- Biology Department, Concordia University, Montreal, Canada
- Center for Microscopy and Cellular Imaging, Concordia University, Montreal, Canada
| | - Flavia R B Araujo
- Center for Applied Synthetic Biology, Concordia University, Montreal, Canada
| | - Vincent J J Martin
- Biology Department, Concordia University, Montreal, Canada
- Center for Applied Synthetic Biology, Concordia University, Montreal, Canada
| | - Alisa Piekny
- Biology Department, Concordia University, Montreal, Canada
- Center for Microscopy and Cellular Imaging, Concordia University, Montreal, Canada
- Center for Applied Synthetic Biology, Concordia University, Montreal, Canada
| |
Collapse
|
5
|
Francis EK, Antonopoulos A, Westman ME, McKay-Demeler J, Laing R, Šlapeta J. A mixed amplicon metabarcoding and sequencing approach for surveillance of drug resistance to levamisole and benzimidazole in Haemonchus spp. Int J Parasitol 2024; 54:55-64. [PMID: 37536387 DOI: 10.1016/j.ijpara.2023.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 08/05/2023]
Abstract
Anthelmintic-resistant parasitic nematodes present a significant threat to sustainable livestock production worldwide. The ability to detect the emergence of anthelmintic resistance at an early stage, and therefore determine which drugs remain most effective, is crucial for minimising production losses. Despite many years of research into the molecular basis of anthelmintic resistance, no molecular-based tools are commercially available for the diagnosis of resistance as it emerges in field settings. We describe a mixed deep amplicon sequencing approach to determine the frequency of the levamisole (LEV)-resistant single nucleotide polymorphism (SNP) within arc-8 exon 4 (S168T) in Haemonchus spp., coupled with benzimidazole (BZ)-resistant SNPs within β-tubulin isotype-1 and the internal transcribed spacer-2 (ITS-2) nemabiome. This constitutes the first known multi-drug and multi-species molecular diagnostic developed for helminths of veterinary importance. Of the ovine, bovine, caprine and camelid Australian field isolates we tested, S168T was detected in the majority of Haemonchus spp. populations from sheep and goats, but rarely at a frequency greater than 16%; an arbitrary threshold we set based on whole genome sequencing (WGS) of LEV-resistant Haemonchus contortus GWBII. Overall, BZ resistance was far more prevalent in Haemonchus spp. than LEV resistance, confirming that LEV is still an effective anthelmintic class for small ruminants in New South Wales, Australia. The mixed amplicon metabarcoding approach described herein paves the way towards the use of large scale sequencing as a surveillance technology in the field, the results of which can be translated into evidence-based recommendations for the livestock sector.
Collapse
Affiliation(s)
- Emily Kate Francis
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, New South Wales 2006, Australia
| | - Alistair Antonopoulos
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, G61 1QH Scotland, United Kingdom; Kreavet, Kruibeke, Belgium
| | - Mark Edward Westman
- Elizabeth Macarthur Agricultural Institute, New South Wales Department of Primary Industries, Menangle, New South Wales 2568, Australia
| | - Janina McKay-Demeler
- Elizabeth Macarthur Agricultural Institute, New South Wales Department of Primary Industries, Menangle, New South Wales 2568, Australia
| | - Roz Laing
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, G61 1QH Scotland, United Kingdom
| | - Jan Šlapeta
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, New South Wales 2006, Australia; The University of Sydney Institute for Infectious Diseases, New South Wales 2006, Australia.
| |
Collapse
|
6
|
Namias A, Sahlin K, Makoundou P, Bonnici I, Sicard M, Belkhir K, Weill M. Nanopore sequencing of PCR products enables multicopy gene family reconstruction. Comput Struct Biotechnol J 2023; 21:3656-3664. [PMID: 37533804 PMCID: PMC10393513 DOI: 10.1016/j.csbj.2023.07.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 08/04/2023] Open
Abstract
The importance of gene amplifications in evolution is more and more recognized. Yet, tools to study multi-copy gene families are still scarce, and many such families are overlooked using common sequencing methods. Haplotype reconstruction is even harder for polymorphic multi-copy gene families. Here, we show that all variants (or haplotypes) of a multi-copy gene family present in a single genome, can be obtained using Oxford Nanopore Technologies sequencing of PCR products, followed by steps of mapping, SNP calling and haplotyping. As a proof of concept, we acquired the sequences of highly similar variants of the cidA and cidB genes present in the genome of the Wolbachia wPip, a bacterium infecting Culex pipiens mosquitoes. Our method relies on a wide database of cid genes, previously acquired by cloning and Sanger sequencing. We addressed problems commonly faced when using mapping approaches for multi-copy gene families with highly similar variants. In addition, we confirmed that PCR amplification causes frequent chimeras which have to be carefully considered when working on families of recombinant genes. We tested the robustness of the method using a combination of bioinformatics (read simulations) and molecular biology approaches (sequence acquisitions through cloning and Sanger sequencing, specific PCRs and digital droplet PCR). When different haplotypes present within a single genome cannot be reconstructed from short reads sequencing, this pipeline confers a high throughput acquisition, gives reliable results as well as insights of the relative copy numbers of the different variants.
Collapse
Affiliation(s)
- Alice Namias
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Kristoffer Sahlin
- Department of Mathematics, Science for Life Laboratory, Stockholm University, 10691 Stockholm, Sweden
| | - Patrick Makoundou
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Iago Bonnici
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Mathieu Sicard
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Khalid Belkhir
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Mylène Weill
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| |
Collapse
|
7
|
Uematsu M, Baskin JM. Barcode-free multiplex plasmid sequencing using Bayesian analysis and nanopore sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536413. [PMID: 37090656 PMCID: PMC10120676 DOI: 10.1101/2023.04.12.536413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Plasmid construction is central to life science research, and sequence verification is arguably its costliest step. Long-read sequencing has emerged as a competitor to Sanger sequencing, with the principal benefit that whole plasmids can be sequenced in a single run. Nevertheless, the current cost of nanopore sequencing is still prohibitive for routine sequencing during plasmid construction. We develop a computational approach termed Simple Algorithm for Very Efficient Multiplexing of Oxford Nanopore Experiments for You (SAVEMONEY) that guides researchers to mix multiple plasmids and subsequently computationally de-mixes the resultant sequences. SAVEMONEY defines optimal mixtures in a pre-survey step, and following sequencing, executes a post-analysis workflow involving sequence classification, alignment, and consensus determination. By using Bayesian analysis with prior probability of expected plasmid construction error rate, high-confidence sequences can be obtained for each plasmid in the mixture. Plasmids differing by as little as two bases can be mixed for submission as a single sample for nanopore sequencing, and routine multiplexing of even six plasmids can still maintain high accuracy of consensus sequencing. SAVEMONEY should further democratize whole-plasmid sequencing by nanopore and related technologies, driving down the effective cost of whole-plasmid sequencing to lower than that of a single Sanger sequencing run.
Collapse
Affiliation(s)
- Masaaki Uematsu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Jeremy M. Baskin
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
8
|
Su J, Lui WW, Lee Y, Zheng Z, Siu GKH, Ng TTL, Zhang T, Lam TTY, Lao HY, Yam WC, Tam KKG, Leung KSS, Lam TW, Leung AWS, Luo R. Evaluation of Mycobacterium tuberculosis enrichment in metagenomic samples using ONT adaptive sequencing and amplicon sequencing for identification and variant calling. Sci Rep 2023; 13:5237. [PMID: 37002338 PMCID: PMC10066345 DOI: 10.1038/s41598-023-32378-x] [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: 12/20/2022] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Sensitive detection of Mycobacterium tuberculosis (TB) in small percentages in metagenomic samples is essential for microbial classification and drug resistance prediction. However, traditional methods, such as bacterial culture and microscopy, are time-consuming and sometimes have limited TB detection sensitivity. Oxford nanopore technologies (ONT) MinION sequencing allows rapid and simple sample preparation for sequencing. Its recently developed adaptive sequencing selects reads from targets while allowing real-time base-calling to achieve sequence enrichment or depletion during sequencing. Another common enrichment method is PCR amplification of the target TB genes. In this study, we compared both methods using ONT MinION sequencing for TB detection and variant calling in metagenomic samples using both simulation runs and those with synthetic and patient samples. We found that both methods effectively enrich TB reads from a high percentage of human (95%) and other microbial DNA. Adaptive sequencing with readfish and UNCALLDE achieved a 3.9-fold and 2.2-fold enrichment compared to the control run. We provide a simple automatic analysis framework to support the detection of TB for clinical use, openly available at https://github.com/HKU-BAL/ONT-TB-NF . Depending on the patient's medical condition and sample type, we recommend users evaluate and optimize their workflow for different clinical specimens to improve the detection limit.
Collapse
Affiliation(s)
- Junhao Su
- Department of Computer Science, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Wui Wang Lui
- Department of Computer Science, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - YanLam Lee
- Department of Computer Science, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Zhenxian Zheng
- Department of Computer Science, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China
| | - Timothy Ting-Leung Ng
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China
| | - Tong Zhang
- Department of Computer Science and Engineering, Department of Mathematics, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Pak Shek Kok, Hong Kong SAR, China
| | - Hiu-Yin Lao
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China
| | - Wing-Cheong Yam
- Department of Microbiology, Lee Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Kingsley King-Gee Tam
- Department of Microbiology, Lee Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Kenneth Siu-Sing Leung
- Department of Microbiology, Lee Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Tak-Wah Lam
- Department of Computer Science, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Amy Wing-Sze Leung
- Department of Computer Science, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China.
| | - Ruibang Luo
- Department of Computer Science, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China.
| |
Collapse
|
9
|
An Evaluation of Avian Influenza Virus Whole-Genome Sequencing Approaches Using Nanopore Technology. Microorganisms 2023; 11:microorganisms11020529. [PMID: 36838494 PMCID: PMC9967579 DOI: 10.3390/microorganisms11020529] [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: 01/20/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
As exemplified by the global response to the SARS-CoV-2 pandemic, whole-genome sequencing played an important role in monitoring the evolution of novel viral variants and provided guidance on potential antiviral treatments. The recent rapid and extensive introduction and spread of highly pathogenic avian influenza virus in Europe, North America, and elsewhere raises the need for similarly rapid sequencing to aid in appropriate response and mitigation activities. To facilitate this objective, we investigate a next-generation sequencing platform that uses a portable nanopore sequencing device to generate and present data in real time. This platform offers the potential to extend in-house sequencing capacities to laboratories that may otherwise lack resources to adopt sequencing technologies requiring large benchtop instruments. We evaluate this platform for routine use in a diagnostic laboratory. In this study, we evaluate different primer sets for the whole genome amplification of influenza A virus and evaluate five different library preparation approaches for sequencing on the nanopore platform using the MinION flow cell. A limited amplification procedure and a rapid procedure are found to be best among the approaches taken.
Collapse
|
10
|
Identification of Fish Species and Targeted Genetic Modifications Based on DNA Analysis: State of the Art. Foods 2023; 12:foods12010228. [PMID: 36613444 PMCID: PMC9818732 DOI: 10.3390/foods12010228] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/05/2023] Open
Abstract
Food adulteration is one of the most serious problems regarding food safety and quality worldwide. Besides misleading consumers, it poses a considerable health risk associated with the potential non-labeled allergen content. Fish and fish products are one of the most expensive and widely traded commodities, which predisposes them to being adulterated. Among all fraud types, replacing high-quality or rare fish with a less valuable species predominates. Because fish differ in their allergen content, specifically the main one, parvalbumin, their replacement can endanger consumers. This underlines the need for reliable, robust control systems for fish species identification. Various methods may be used for the aforementioned purpose. DNA-based methods are favored due to the characteristics of the target molecule, DNA, which is heat resistant, and the fact that through its sequencing, several other traits, including the recognition of genetic modifications, can be determined. Thus, they are considered to be powerful tools for identifying cases of food fraud. In this review, the major DNA-based methods applicable for fish meat and product authentication and their commercial applications are discussed, the possibilities of detecting genetic modifications in fish are evaluated, and future trends are highlighted, emphasizing the need for comprehensive and regularly updated online database resources.
Collapse
|
11
|
Leiva AM, Chittarath K, Lopez-Alvarez D, Vongphachanh P, Gomez MI, Sengsay S, Wang XW, Rodriguez R, Newby J, Cuellar WJ. Mitochondrial Genetic Diversity of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) Associated with Cassava in Lao PDR. INSECTS 2022; 13:861. [PMID: 36292809 PMCID: PMC9604212 DOI: 10.3390/insects13100861] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Cassava Mosaic Disease (CMD) caused by Sri Lankan cassava mosaic virus (SLCMV), has rapidly spread in Southeast Asia (SEA) since 2016. Recently it has been documented in Lao PDR. Previous reports have identified whitefly species of B. tabaci as potential vectors of CMD in SEA, but their occurrence and distribution in cassava fields is not well known. We conducted a countrywide survey in Lao PDR for adult whiteflies in cassava fields, and determined the abundance and genetic diversity of the B. tabaci species complex using mitochondrial cytochrome oxidase I (mtCOI) sequencing. In order to expedite the process, PCR amplifications were performed directly on whitefly adults without DNA extraction, and mtCOI sequences obtained using nanopore portable-sequencing technology. Low whitefly abundances and two cryptic species of the B. tabaci complex, Asia II 1 and Asia II 6, were identified. This is the first work on abundance and genetic identification of whiteflies associated with cassava in Lao PDR. This study indicates currently only a secondary role for Asia II in spreading CMD or as a pest. Routine monitoring and transmission studies on Asia II 6 should be carried out to establish its potential role as a vector of SLCMV in this region.
Collapse
Affiliation(s)
- Ana M. Leiva
- Cassava Program, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), The Americas Hub, Km 17 Recta Cali-Palmira, Cali 763537, Colombia
| | - Khonesavanh Chittarath
- Plant Protection Center (PPC), Department of Agriculture, Ministry of Agriculture and Forestry, Vientiane P.O. Box 811, Laos
| | - Diana Lopez-Alvarez
- Department of Biological Sciences, Universidad Nacional de Colombia UNAL-Palmira, Palmira 763533, Colombia
| | - Pinkham Vongphachanh
- Plant Protection Center (PPC), Department of Agriculture, Ministry of Agriculture and Forestry, Vientiane P.O. Box 811, Laos
| | - Maria Isabel Gomez
- Cassava Program, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), The Americas Hub, Km 17 Recta Cali-Palmira, Cali 763537, Colombia
| | - Somkhit Sengsay
- Plant Protection Center (PPC), Department of Agriculture, Ministry of Agriculture and Forestry, Vientiane P.O. Box 811, Laos
| | - Xiao-Wei Wang
- Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Rafael Rodriguez
- Cassava Program, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), The Americas Hub, Km 17 Recta Cali-Palmira, Cali 763537, Colombia
| | - Jonathan Newby
- Cassava Program Asia Office, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), Laos Country Office, Vientiane P.O. Box 783, Laos
| | - Wilmer J. Cuellar
- Cassava Program, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), The Americas Hub, Km 17 Recta Cali-Palmira, Cali 763537, Colombia
| |
Collapse
|