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Onywera H, Ondoa P, Nfii F, Ogwell A, Kebede Y, Christoffels A, Tessema SK. Boosting pathogen genomics and bioinformatics workforce in Africa. Lancet Infect Dis 2024; 24:e106-e112. [PMID: 37778362 DOI: 10.1016/s1473-3099(23)00394-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 06/02/2023] [Accepted: 06/16/2023] [Indexed: 10/03/2023]
Abstract
Next-generation sequencing (NGS) of genomic data has established its fundamental value in public health surveillance, research and development, and precision medicine. In Africa, severe shortages of competent experts in genomics and bioinformatics, few opportunities for research, and inadequate genomic infrastructure have had a knock-on effect on the use of NGS technologies for research and public health practice. Several reasons-ranging from poor funding, inadequate infrastructure for training and practice, to brain drain-might partly account for the scarcity of genomics and bioinformatics expertise in the region. In recognition of these shortcomings and the importance of NGS genomic data, which was amplified during the COVID-19 pandemic in mid-2021, the Africa Centres for Disease Control and Prevention (Africa CDC) through the Africa Pathogen Genomics Initiative began building and expanding Africa's workforce in pathogen surveillance. By the end of 2022, the Africa CDC in collaboration with its partners and centres of excellence had trained 413 personnel, mostly from public health institutions, in 53 (96%) of 55 African Union Member States. Although this training has increased genomics, bioinformatics, and genomic epidemiology literacy, and genomic-informed pathogen surveillance, there is still a need for a strategic and sustainable public health workforce development in Africa.
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Affiliation(s)
- Harris Onywera
- Africa Centres for Disease Control and Prevention, African Union, Addis Ababa, Ethiopia
| | - Pascale Ondoa
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia; Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam, Netherlands
| | - Faith Nfii
- Africa Centres for Disease Control and Prevention, African Union, Addis Ababa, Ethiopia
| | - Ahmed Ogwell
- Africa Centres for Disease Control and Prevention, African Union, Addis Ababa, Ethiopia
| | - Yenew Kebede
- Africa Centres for Disease Control and Prevention, African Union, Addis Ababa, Ethiopia
| | - Alan Christoffels
- Africa Centres for Disease Control and Prevention, African Union, Addis Ababa, Ethiopia; South African National Bioinformatics Institute, South African Medical Research Council, Bioinformatics Unit, University of the Western Cape, Cape Town, South Africa
| | - Sofonias K Tessema
- Africa Centres for Disease Control and Prevention, African Union, Addis Ababa, Ethiopia.
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2
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Nafea AM, Wang Y, Wang D, Salama AM, Aziz MA, Xu S, Tong Y. Application of next-generation sequencing to identify different pathogens. Front Microbiol 2024; 14:1329330. [PMID: 38348304 PMCID: PMC10859930 DOI: 10.3389/fmicb.2023.1329330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 12/18/2023] [Indexed: 02/15/2024] Open
Abstract
Early and precise detection and identification of various pathogens are essential for epidemiological monitoring, disease management, and reducing the prevalence of clinical infectious diseases. Traditional pathogen detection techniques, which include mass spectrometry, biochemical tests, molecular testing, and culture-based methods, are limited in application and are time-consuming. Next generation sequencing (NGS) has emerged as an essential technology for identifying pathogens. NGS is a cutting-edge sequencing method with high throughput that can create massive volumes of sequences with a broad application prospects in the field of pathogen identification and diagnosis. In this review, we introduce NGS technology in detail, summarizes the application of NGS in that identification of different pathogens, including bacteria, fungi, and viruses, and analyze the challenges and outlook for using NGS to identify clinical pathogens. Thus, this work provides a theoretical basis for NGS studies and provides evidence to support the application of NGS in distinguishing various clinical pathogens.
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Affiliation(s)
- Aljuboori M. Nafea
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
- College of Medicine, Department of Microbiology, Ibn Sina University of Medical and Pharmaceutical Science, Baghdad, Iraq
| | - Yuer Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Duanyang Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Ahmed M. Salama
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, China
- Medical Laboratory at Sharkia Health Directorate, Ministry of Health, Sharkia, Egypt
| | - Manal A. Aziz
- College of Medicine, Department of Microbiology, Ibn Sina University of Medical and Pharmaceutical Science, Baghdad, Iraq
| | - Shan Xu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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3
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Techera C, Tomás G, Grecco S, Williman J, Hernández M, Olivera V, Banda A, Vagnozzi A, Panzera Y, Marandino A, Pérez R. A rapid and affordable amplicon-based method for next-generation genome sequencing of the infectious bursal disease virus. J Virol Methods 2023; 322:114807. [PMID: 37683937 DOI: 10.1016/j.jviromet.2023.114807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/10/2023]
Abstract
The infectious bursal disease virus (IBDV) causes a severe immunosuppressive disorder in young chickens. IBDV evolution resulted in the emergence of strains with divergent genetic, antigenic, and pathogenic characteristics. Genetic classification is typically performed by sequencing the coding region of the most immunogenic region of the viral protein 2 (VP2). Sequencing both double-stranded RNA genome segments is essential to achieve a more comprehensive IBDV classification that can detect recombinants and reassortments. Here, we report the development and standardization of a tiled PCR amplicon protocol for the direct and cost-effective genome sequencing of global IBDV strains using next-generation technology. Primers for tiled PCR were designed with adapters to bypass expensive and time-consuming library preparation steps. Sequencing was performed on Illumina MiniSeq equipment, and fourteen complete genomes of field strains were assembled using reference sequences. The PCR-enrichment step was used to obtain genomes from low-titer biological samples that were difficult to amplify using traditional sequencing. Phylogenetic analyses of the obtained genomes confirmed previous strain classification. By combining the enrichment methodology with massive sequencing, it is possible to obtain IBDV genomic sequences in a fast and affordable manner. This procedure can be a valuable tool to better understand virus epidemiology.
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Affiliation(s)
- Claudia Techera
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Gonzalo Tomás
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Sofía Grecco
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Joaquín Williman
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Martín Hernández
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Valeria Olivera
- Instituto de Virología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, 1712 Buenos Aires, Argentina
| | - Alejandro Banda
- Poultry Research and Diagnostic Laboratory, College of Veterinary Medicine, Mississippi State University, Pearl, MS, United States
| | - Ariel Vagnozzi
- Instituto de Virología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, 1712 Buenos Aires, Argentina
| | - Yanina Panzera
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Ana Marandino
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
| | - Ruben Pérez
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
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Abouelkhair MA, Roozitalab A, Elsakhawy OK. Molecular characterization of a reptarenavirus detected in a Colombian Red-Tailed Boa (Boa constrictor imperator). Virol J 2023; 20:265. [PMID: 37968659 PMCID: PMC10652540 DOI: 10.1186/s12985-023-02237-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/07/2023] [Indexed: 11/17/2023] Open
Abstract
The global decline in biodiversity is a matter of great concern for members of the class Reptilia. Reptarenaviruses infect snakes, and have been linked to various clinical conditions, such as Boid Inclusion Body Disease (BIBD) in snakes belonging to the families Boidae and Pythonidae. However, there is a scarcity of information regarding reptarenaviruses found in snakes in both the United States and globally. This study aimed to contribute to the understanding of reptarenavirus diversity by molecularly characterizing a reptarenavirus detected in a Colombian Red-Tailed Boa (Boa constrictor imperator). Using a metagenomics approach, we successfully identified, and de novo assembled the whole genomic sequences of a reptarenavirus in a Colombian Red-Tailed Boa manifesting clinically relevant symptoms consistent with BIBD. The analysis showed that the Colombian Red-Tailed Boa in this study carried the University of Giessen virus (UGV-1) S or S6 (UGV/S6) segment and L genotype 7. The prevalence of the UGV/S6 genotype, in line with prior research findings, implies that this genotype may possess specific advantageous characteristics or adaptations that give it a competitive edge over other genotypes in the host population. This research underscores the importance of monitoring and characterizing viral pathogens in captive and wild snake populations. Knowledge of such viruses is crucial for the development of effective diagnostic methods, potential intervention strategies, and the conservation of vulnerable reptilian species. Additionally, our study provides valuable insights for future studies focusing on the evolutionary history, molecular epidemiology, and biological properties of reptarenaviruses in boas and other snake species.
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Affiliation(s)
- Mohamed A Abouelkhair
- Department of Biomedical and Diagnostic Sciences, University of Tennessee, Knoxville, TN, USA.
| | - Ashkan Roozitalab
- Department of Biomedical and Diagnostic Sciences, University of Tennessee, Knoxville, TN, USA
| | - Ola K Elsakhawy
- Department of Biomedical and Diagnostic Sciences, University of Tennessee, Knoxville, TN, USA
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Lema NK, Gemeda MT, Woldesemayat AA. Recent Advances in Metagenomic Approaches, Applications, and Challenge. Curr Microbiol 2023; 80:347. [PMID: 37733134 DOI: 10.1007/s00284-023-03451-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 08/20/2023] [Indexed: 09/22/2023]
Abstract
Advances in metagenomics analysis with the advent of next-generation sequencing have extended our knowledge of microbial communities as compared to conventional techniques providing advanced approach to identify novel and uncultivable microorganisms based on their genetic information derived from a particular environment. Shotgun metagenomics involves investigating the DNA of the entire community without the requirement of PCR amplification. It provides access to study all genes present in the sample. On the other hand, amplicon sequencing targets taxonomically important marker genes, the analysis of which is restricted to previously known DNA sequences. While sequence-based metagenomics is used to analyze DNA sequences directly from the environment without the requirement of library construction and with limited identification of novel genes and products that can be complemented by functional genomics, function-based metagenomics requires fragmentation and cloning of extracted metagenome DNA in a suitable host with subsequent functional screening and sequencing clone for detection of a novel gene. Although advances were made in metagenomics, different challenges arise. This review provides insight into advances in the metagenomic approaches combined with next-generation sequencing, their recent applications highlighting the emerging ones, such as in astrobiology, forensic sciences, and SARS-CoV-2 infection diagnosis, and the challenges associated. This review further discusses the different types of metagenomics and outlines advancements in bioinformatics tools and their significance in the analysis of metagenomic datasets.
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Affiliation(s)
- Niguse K Lema
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
- Biotechnology and Bioprocess Center of Excellence, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
- Department of Biotechnology, Arba Minch University, Arba Minch, Ethiopia
| | - Mesfin T Gemeda
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
- Biotechnology and Bioprocess Center of Excellence, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
| | - Adugna A Woldesemayat
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia.
- Biotechnology and Bioprocess Center of Excellence, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia.
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Panneerselvam P, Senapati A, Chidambaranathan P, Prabhukarthikeyan SR, Mitra D, Pandi Govindharaj GP, Nayak AK, Anandan A. Long-term impact of pulses crop rotation on soil fungal diversity in aerobic and wetland rice cultivation. Fungal Biol 2023; 127:1053-1066. [PMID: 37344007 DOI: 10.1016/j.funbio.2023.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 03/17/2023] [Accepted: 04/17/2023] [Indexed: 06/23/2023]
Abstract
Pulse crop rotation in rice cultivation is a widely accepted agronomic practice. Depending upon the water regime, rice cultivation has been classified into wetland and aerobic practices. However, no studies have been conducted so far to understand the impact of pulse crop rotation and rice mono-cropping on fungal diversity, particularly in aerobic soil. A targeted metagenomic study was conducted to compare the effects of crop rotations (rice-rice and rice-pulse) on fungal diversity in wetland and aerobic rice soils. Out of 445 OTUs, 41.80% was unknown and 58.20% were assigned to six phyla, namely Ascomycota (56.57%), Basidiomycota (1.32%), Zygomycota (0.22%), Chytridiomycota (0.04%), Glomeromycota (0.03%), and Blastocladiomycota (0.02%). Functional trait analysis found wetland rice-pulse rotation increased symbiotrophs (36.7%) and saprotrophs (62.1%) population, whereas higher pathotrophs were found in aerobic rice-rice (62.8%) and rice-pulse (61.4%) cropping system. Certain soil nutrients played a major role in shaping the fungal community; Ca had significant (p < 0.05) positive impact on saprotroph, symbiotroph and endophytes, whereas Cu had significant (p < 0.05) negative impact on pathotrophs. This study showed that rice-pulse crop rotation could enhance the saprophytic and symbiotic fungal diversity in wetland and reduce the population of pathogens in aerobic rice cultivation.
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Affiliation(s)
- Periyasamy Panneerselvam
- Crop Production Division, ICAR - National Rice Research Institute, Cuttack, Odisha, 753006, India.
| | - Ansuman Senapati
- Crop Production Division, ICAR - National Rice Research Institute, Cuttack, Odisha, 753006, India
| | | | - S R Prabhukarthikeyan
- Crop Protection Division, ICAR - National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Debasis Mitra
- Crop Production Division, ICAR - National Rice Research Institute, Cuttack, Odisha, 753006, India
| | | | - Amaresh Kumar Nayak
- Crop Production Division, ICAR - National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Annamalai Anandan
- Crop Improvement Division, ICAR - National Rice Research Institute, Cuttack, Odisha, 753006, India; ICAR-Indian Institute of Seed Science, Regional Station, Bangalore, 560065, India.
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Altindiş M, Kahraman Kilbaş EP. Managing Viral Emerging Infectious Diseases via Current and Future Molecular Diagnostics. Diagnostics (Basel) 2023; 13:diagnostics13081421. [PMID: 37189522 DOI: 10.3390/diagnostics13081421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/10/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Emerging viral infectious diseases have been a constant threat to global public health in recent times. In managing these diseases, molecular diagnostics has played a critical role. Molecular diagnostics involves the use of various technologies to detect the genetic material of various pathogens, including viruses, in clinical samples. One of the most commonly used molecular diagnostics technologies for detecting viruses is polymerase chain reaction (PCR). PCR amplifies specific regions of the viral genetic material in a sample, making it easier to detect and identify viruses. PCR is particularly useful for detecting viruses that are present in low concentrations in clinical samples, such as blood or saliva. Another technology that is becoming increasingly popular for viral diagnostics is next-generation sequencing (NGS). NGS can sequence the entire genome of a virus present in a clinical sample, providing a wealth of information about the virus, including its genetic makeup, virulence factors, and potential to cause an outbreak. NGS can also help identify mutations and discover new pathogens that could affect the efficacy of antiviral drugs and vaccines. In addition to PCR and NGS, there are other molecular diagnostics technologies that are being developed to manage emerging viral infectious diseases. One of these is CRISPR-Cas, a genome editing technology that can be used to detect and cut specific regions of viral genetic material. CRISPR-Cas can be used to develop highly specific and sensitive viral diagnostic tests, as well as to develop new antiviral therapies. In conclusion, molecular diagnostics tools are critical for managing emerging viral infectious diseases. PCR and NGS are currently the most commonly used technologies for viral diagnostics, but new technologies such as CRISPR-Cas are emerging. These technologies can help identify viral outbreaks early, track the spread of viruses, and develop effective antiviral therapies and vaccines.
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Affiliation(s)
- Mustafa Altindiş
- Medical Microbiology Department, Faculty of Medicine, Sakarya University, Sakarya 54050, Türkiye
| | - Elmas Pınar Kahraman Kilbaş
- Medical Laboratory Techniques, Vocational School of Health Services, Fenerbahce University, Istanbul 34758, Türkiye
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Yousef M, Ozdemir F, Jaber A, Allmer J, Bakir-Gungor B. PriPath: identifying dysregulated pathways from differential gene expression via grouping, scoring, and modeling with an embedded feature selection approach. BMC Bioinformatics 2023; 24:60. [PMID: 36823571 PMCID: PMC9947447 DOI: 10.1186/s12859-023-05187-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 02/14/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND Cell homeostasis relies on the concerted actions of genes, and dysregulated genes can lead to diseases. In living organisms, genes or their products do not act alone but within networks. Subsets of these networks can be viewed as modules that provide specific functionality to an organism. The Kyoto encyclopedia of genes and genomes (KEGG) systematically analyzes gene functions, proteins, and molecules and combines them into pathways. Measurements of gene expression (e.g., RNA-seq data) can be mapped to KEGG pathways to determine which modules are affected or dysregulated in the disease. However, genes acting in multiple pathways and other inherent issues complicate such analyses. Many current approaches may only employ gene expression data and need to pay more attention to some of the existing knowledge stored in KEGG pathways for detecting dysregulated pathways. New methods that consider more precompiled information are required for a more holistic association between gene expression and diseases. RESULTS PriPath is a novel approach that transfers the generic process of grouping and scoring, followed by modeling to analyze gene expression with KEGG pathways. In PriPath, KEGG pathways are utilized as the grouping function as part of a machine learning algorithm for selecting the most significant KEGG pathways. A machine learning model is trained to differentiate between diseases and controls using those groups. We have tested PriPath on 13 gene expression datasets of various cancers and other diseases. Our proposed approach successfully assigned biologically and clinically relevant KEGG terms to the samples based on the differentially expressed genes. We have comparatively evaluated the performance of PriPath against other tools, which are similar in their merit. For each dataset, we manually confirmed the top results of PriPath in the literature and found that most predictions can be supported by previous experimental research. CONCLUSIONS PriPath can thus aid in determining dysregulated pathways, which applies to medical diagnostics. In the future, we aim to advance this approach so that it can perform patient stratification based on gene expression and identify druggable targets. Thereby, we cover two aspects of precision medicine.
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Affiliation(s)
- Malik Yousef
- Department of Information Systems, Zefat Academic College, 13206, Zefat, Israel. .,Galilee Digital Health Research Center (GDH), Zefat Academic College, Zefat, Israel.
| | - Fatma Ozdemir
- grid.440414.10000 0004 0558 2628Department of Computer Engineering, Faculty of Engineering, Abdullah Gul University, Kayseri, Turkey ,grid.5570.70000 0004 0490 981XUniversity Institute of Digital Communication Systems, Ruhr-University, Bochum, Germany
| | - Amhar Jaber
- grid.440414.10000 0004 0558 2628Department of Computer Engineering, Faculty of Engineering, Abdullah Gul University, Kayseri, Turkey
| | - Jens Allmer
- grid.454318.f0000 0004 0431 5034Medical Informatics and Bioinformatics, Institute for Measurement Engineering and Sensor Technology, Hochschule Ruhr West, University of Applied Sciences, Mülheim an der Ruhr, Germany
| | - Burcu Bakir-Gungor
- grid.440414.10000 0004 0558 2628Department of Computer Engineering, Faculty of Engineering, Abdullah Gul University, Kayseri, Turkey
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La Polla R, Goumaidi A, Daniau M, Legras-Lachuer C, De Saint-Vis B. NGS method by library enrichment for rapid pestivirus purity testing in biologics. Vaccine 2023; 41:855-861. [PMID: 36564275 DOI: 10.1016/j.vaccine.2022.12.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 09/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
NGS sequencing was evaluated to understand its added value for animal health vaccine candidates. We have previously established the proof of concept for its application in purity testing on several Master Seeds. Here we evaluate the NGS method after enrichment to detect pestiviruses. To achieve this, we conducted a spiking study using 6 viruses, consisting of 3 pestiviruses and 3 other RNA-viruses at different concentrations into cell suspension. A deep Illumina random sequencing of all nucleic acids (DNA and RNA) was performed. The bioinformatics analysis including both assembly into contigs and annotation were processed using viral public databases for the spiked viruses' identification. Here we present the results of spiking experiments for the simultaneous spike of 6 viruses at 100-10 and 1 TCID50/ml. Using Illumina sequencing, the 3 pestiviruses were all detected at the highest concentration, and even at the lowest one such as 1 TCID50/ml for CSFV. Regarding the other viruses, they were not detected at all. Overall, the study showed consistent results for specific detection of pestiviruses with an increase of sensitivity after enrichment. The sensitivity of NGS evaluated by virus spiking experiments of cells demonstrated that NGS method is a valuable and sensitive tool for specific agent detection required in purity testing during vaccine development. This NGS method should be considered as an alternative tool of current purity testing for the prospective testing of biological products.
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Affiliation(s)
- Rémi La Polla
- Boehringer Ingelheim Animal Health, Site Lyon porte des Alpes, 813 cours du 3eme Millénaire, 69800 Saint Priest, France; Laboratoire d'Écologie Microbienne - UMR 5557, Université Claude Bernard Lyon 1, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
| | - Abdelghafar Goumaidi
- Viroscan3D, Faculté de Médecine et de Pharmacie, 8 avenue Rockefeller, 69373 Lyon, France
| | - Maïlys Daniau
- Viroscan3D, Faculté de Médecine et de Pharmacie, 8 avenue Rockefeller, 69373 Lyon, France
| | - Catherine Legras-Lachuer
- Laboratoire d'Écologie Microbienne - UMR 5557, Université Claude Bernard Lyon 1, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
| | - Blandine De Saint-Vis
- Boehringer Ingelheim Animal Health, Site Lyon porte des Alpes, 813 cours du 3eme Millénaire, 69800 Saint Priest, France
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Lee HJ, Cho IS, Jeong RD. Nanopore Metagenomics Sequencing for Rapid Diagnosis and Characterization of Lily Viruses. Plant Pathol J 2022; 38:503-512. [PMID: 36221922 PMCID: PMC9561158 DOI: 10.5423/ppj.oa.06.2022.0084] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/28/2022] [Accepted: 08/12/2022] [Indexed: 05/21/2023]
Abstract
Lilies (Lilium spp.) are one of the most important ornamental flower crops grown in Korea. Most viral diseases in lilies are transmitted by infected bulbs, which cause serious economic losses due to reduced yields. Various diagnostic techniques and high-throughput sequencing methods have been used to detect lily viruses. According to Oxford Nanopore Technologies (ONT), MinION is a compact and portable sequencing device. In this study, three plant viruses, lily mottle, lily symptomless, and plantago asiatica mosaic virus, were detected in lily samples using the ONT platform. As a result of genome assembly of reads obtained through ONT, 100% coverage and 90.3-93.4% identity were obtained. Thus, we show that the ONT platform is a promising tool for the diagnosis and characterization of viruses that infect crops.
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Affiliation(s)
- Hyo-Jeong Lee
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 61185,
Korea
| | - In-Sook Cho
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365,
Korea
| | - Rae-Dong Jeong
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 61185,
Korea
- Corresponding author. Phone) +82-62-530-2075, FAX) +82-62-530-2069, E-mail)
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Kwok KTT, de Rooij MMT, Messink AB, Wouters IM, Smit LAM, Cotten M, Heederik DJJ, Koopmans MPG, Phan MVT. Establishing farm dust as a useful viral metagenomic surveillance matrix. Sci Rep 2022; 12:16308. [PMID: 36175536 PMCID: PMC9521564 DOI: 10.1038/s41598-022-20701-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 09/16/2022] [Indexed: 11/26/2022] Open
Abstract
Farm animals may harbor viral pathogens, some with zoonotic potential which can possibly cause severe clinical outcomes in animals and humans. Documenting the viral content of dust may provide information on the potential sources and movement of viruses. Here, we describe a dust sequencing strategy that provides detailed viral sequence characterization from farm dust samples and use this method to document the virus communities from chicken farm dust samples and paired feces collected from the same broiler farms in the Netherlands. From the sequencing data, Parvoviridae and Picornaviridae were the most frequently found virus families, detected in 85-100% of all fecal and dust samples with a large genomic diversity identified from the Picornaviridae. Sequences from the Caliciviridae and Astroviridae familes were also obtained. This study provides a unique characterization of virus communities in farmed chickens and paired farm dust samples and our sequencing methodology enabled the recovery of viral genome sequences from farm dust, providing important tracking details for virus movement between livestock animals and their farm environment. This study serves as a proof of concept supporting dust sampling to be used in viral metagenomic surveillance.
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Affiliation(s)
- Kirsty T T Kwok
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.
| | - Myrna M T de Rooij
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Aniek B Messink
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Inge M Wouters
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Lidwien A M Smit
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Matthew Cotten
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Dick J J Heederik
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - My V T Phan
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
- London School of Hygiene and Tropical Medicine, London, UK.
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12
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Bhar A. The application of next generation sequencing technology in medical diagnostics: a perspective. Proc Indian Natl Sci Acad 2022. [PMCID: PMC9395867 DOI: 10.1007/s43538-022-00098-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rapid isolation, characterization, and identification are prerequisites of any successful medical intervention to infectious disease treatment. This is a real challenge to the scientific as well as a medical community to find out a proper and robust method of pathogen detection. Classical cultural, as well as biochemical test-based identification, has its own limitations to their time-consuming and ineffectiveness for closely related pathovars. Molecular diagnostics became a popular alternative to classical techniques for the past couple of decades but it required some prior information to detect the pathogen successfully. Recently, with the advent of next-generation sequencing (NGS) technology identification, and characterization of almost all the pathogenic bacteria become possible without any information a priori. Metagenomic next generation sequencing is another specialized type of NGS that is profoundly utilized in medical biotechnology and diagnostics now a days. Therefore, the present review is focused on a brief introduction to NGS technology, its application in medical microbiology, and possible future aspects for the development of medical sciences.
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Affiliation(s)
- Anirban Bhar
- Post Graduate Department of Botany, Ramakrishna Mission Vivekananda Centenary College, Rahara, Kolkata 700118 India
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13
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Galli C, Ebranati E, Pellegrinelli L, Airoldi M, Veo C, Della Ventura C, Seiti A, Binda S, Galli M, Zehender G, Pariani E. From Clinical Specimen to Whole Genome Sequencing of A(H3N2) Influenza Viruses: A Fast and Reliable High-Throughput Protocol. Vaccines (Basel) 2022; 10. [PMID: 36016246 DOI: 10.3390/vaccines10081359] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/11/2022] [Accepted: 08/11/2022] [Indexed: 11/29/2022] Open
Abstract
(1) Background: Over the last few years, there has been growing interest in the whole genome sequencing (WGS) of rapidly mutating pathogens, such as influenza viruses (IVs), which has led us to carry out in-depth studies on viral evolution in both research and diagnostic settings. We aimed at describing and determining the validity of a WGS protocol that can obtain the complete genome sequence of A(H3N2) IVs directly from clinical specimens. (2) Methods: RNA was extracted from 80 A(H3N2)-positive respiratory specimens. A one-step RT-PCR assay, based on the use of a single set of specific primers, was used to retro-transcribe and amplify the entire IV type A genome in a single reaction, thus avoiding additional enrichment approaches and host genome removal treatments. Purified DNA was quantified; genomic libraries were prepared and sequenced by using Illumina MiSeq platform. The obtained reads were evaluated for sequence quality and read-pair length. (3) Results: All of the study specimens were successfully amplified, and the purified DNA concentration proved to be suitable for NGS (at least 0.2 ng/µL). An acceptable coverage depth for all eight genes of influenza A(H3N2) virus was obtained for 90% (72/80) of the clinical samples with viral loads >105 genome copies/mL. The mean depth of sequencing ranged from 105 to 200 reads per position, with the majority of the mean depth values being above 103 reads per position. The total turnaround time per set of 20 samples was four working days, including sequence analysis. (4) Conclusions: This fast and reliable high-throughput sequencing protocol should be used for influenza surveillance and outbreak investigation.
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da Silva e Silva LH, da Silva FS, Medeiros DBDA, Cruz ACR, da Silva SP, Aragão ADO, Dias DD, Sena do Nascimento BL, Júnior JWR, Vieira DBR, Monteiro HADO, Neto JPN. Description of the mitogenome and phylogeny of Aedes spp. (Diptera: Culicidae) from the Amazon region. Acta Trop 2022; 232:106500. [PMID: 35584780 DOI: 10.1016/j.actatropica.2022.106500] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/29/2022] [Accepted: 05/01/2022] [Indexed: 11/01/2022]
Abstract
The genus Aedes (Diptera: Culicidae) includes species of great epidemiological relevance, particularly involved in transmission cycles of leading arboviruses in the Brazilian Amazon region, such as the Zika virus (ZIKV), Dengue virus (DENV), Yellow fever virus (YFV), and Chikungunya virus (CHIKV). We report here the first putatively complete sequencing of the mitochondrial genomes of Brazilian populations of the species Aedes albopictus, Aedes scapularis and Aedes serratus. The sequences obtained showed an average length of 14,947 bp, comprising 37 functional subunits, typical in animal mitochondria (13 PCGs, 22 tRNA, and 2 rRNA). The phylogeny reconstructed by Maximum likelihood method, based on the concatenated sequences of all 13 PCGs produced at least two non-directly related groupings, composed of representatives of the subgenus Ochlerotatus and Stegomyia of the genus Aedes. The data and information produced here may be useful for future taxonomic and evolutionary studies of the genus Aedes, as well as the Culicidae family.
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Gupta AK, Kumar M. Benchmarking and Assessment of Eight De Novo Genome Assemblers on Viral Next-Generation Sequencing Data, Including the SARS-CoV-2. OMICS 2022; 26:372-381. [PMID: 35759429 DOI: 10.1089/omi.2022.0042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Viral genomics has become crucial in clinical diagnostics and ecology, not to mention to stem the COVID-19 pandemic. Whole-genome sequencing (WGS) is pivotal in gaining an improved understanding of viral evolution, genomic epidemiology, infectious outbreaks, pathobiology, clinical management, and vaccine development. Genome assembly is one of the crucial steps in WGS data analyses. A series of different assemblers has been developed with the advent of high-throughput next-generation sequencing (NGS). Various studies have reported the evaluation of these assembly tools on distinct datasets; however, these lack data from viral origin. In this study, we performed a comparative evaluation and benchmarking of eight de novo assemblers: SOAPdenovo, Velvet, assembly by short sequences (ABySS), iterative De Bruijn graph assembler (IDBA), SPAdes, Edena, iterative virus assembler, and VICUNA on the viral NGS data from distinct Illumina (GAIIx, Hiseq, Miseq, and Nextseq) platforms. WGS data of diverse viruses, that is, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), dengue virus 3, human immunodeficiency virus 1, hepatitis B virus, human herpesvirus 8, human papillomavirus 16, rhinovirus A, and West Nile virus, were utilized to assess these assemblers. Performance metrics such as genome fraction recovery, assembly lengths, NG50, N50, contig length, contig numbers, mismatches, and misassemblies were analyzed. Overall, three assemblers, that is, SPAdes, IDBA, and ABySS, performed consistently well, including for genome assembly of SARS-CoV-2. These assembly methods should be considered and recommended for future studies of viruses. The study also suggests that implementing two or more assembly approaches should be considered in viral NGS studies, especially in clinical settings. Taken together, the benchmarking of eight de novo genome assemblers reported in this study can inform future public health and ecology research concerning the viruses, the COVID-19 pandemic, and viral outbreaks.
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Affiliation(s)
- Amit Kumar Gupta
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Manoj Kumar
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Abstract
Currently, both pathogenic and commensal viruses are continuously being discovered and acknowledged as ubiquitous components of microbial communities. The advancements of systems microbiological approaches have changed the face of virome research. Here, we focus on viral metagenomic approach to study virus community and their interactions with other microbial members as well as their hosts. This review also summarizes challenges, limitations, and benefits of the current virome approaches. Potentially, the studies of virome can be further applied in various biological and clinical fields.
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Affiliation(s)
- Suwalak Chitcharoen
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand,Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pavaret Sivapornnukul
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Sunchai Payungporn.
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Babaei A, Pouremamali A, Rafiee N, Sohrabi H, Mokhtarzadeh A, de la Guardia M. Genosensors as an alternative diagnostic sensing approaches for specific detection of various certain viruses: a review of common techniques and outcomes. Trends Analyt Chem 2022; 155:116686. [PMID: 35611316 PMCID: PMC9119280 DOI: 10.1016/j.trac.2022.116686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 05/08/2022] [Accepted: 05/15/2022] [Indexed: 12/19/2022]
Abstract
Viral infections are responsible for the deaths of millions of people throughout the world. Since outbreak of highly contagious and mutant viruses such as contemporary sars-cov-2 pandemic, has challenged the conventional diagnostic methods, the entity of a thoroughly sensitive, specific, rapid and inexpensive detecting technique with minimum level of false-positivity or -negativity, is desperately needed more than any time in the past decades. Biosensors as minimized devices could detect viruses in simple formats. So far, various nucleic acid, immune- and protein-based biosensors were designed and tested for recognizing the genome, antigen, or protein level of viruses, respectively; however, nucleic acid-based sensing techniques, which is the foundation of constructing genosensors, are preferred not only because of their ultra-sensitivity and applicability in the early stages of infections but also for their ability to differentiate various strains of the same virus. To date, the review articles related to genosensors are just confined to particular pathogenic diseases; In this regard, the present review covers comprehensive information of the research progress of the electrochemical, optical, and surface plasmon resonance (SPR) genosensors that applied for human viruses' diseases detection and also provides a well description of viruses' clinical importance, the conventional diagnosis approaches of viruses and their disadvantages. This review would address the limitations in the current developments as well as the future challenges involved in the successful construction of sensing approaches with the functionalized nanomaterials and also allow exploring into core-research works regarding this area.
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Affiliation(s)
- Abouzar Babaei
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Amir Pouremamali
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Nastaran Rafiee
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hessamaddin Sohrabi
- Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Miguel de la Guardia
- Department of Analytical Chemistry, University of Valencia, Dr. Moliner 50, 46100, Burjassot, Valencia, Spain
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18
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Kim N, Lee H, Kim S, Jeong R. Identification of Viruses Infecting Oats in Korea by Metatranscriptomics. Plants 2022; 11:256. [PMID: 35161235 PMCID: PMC8839655 DOI: 10.3390/plants11030256] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 11/24/2022]
Abstract
Controlling infectious plant viruses presents a constant challenge in agriculture. As a source of valuable nutrients for human health, the cultivation of oats (Avena sativa L.) has recently been increased in Korea. To date, however, few studies have been undertaken to identify the viruses infecting oats in this country. In this study, we carried out RNA-sequencing followed by bioinformatics analyses to understand the virosphere in six different geographical locations in Korea where oats are cultivated. We identified three different virus species, namely, barley yellow dwarf virus (BYDV) (BYDV-PAV and BYDV-PAS), cereal yellow dwarf virus (CYDV) (CYDV-RPS and CYDV-RPV), and rice black-streaked dwarf virus (RBSDV). Based on the number of virus-associated reads and contigs, BYDV-PAV was a dominant virus infecting winter oats in Korea. Interestingly, RBSDV was identified in only a single region, and this is the first report of this virus infecting oats in Korea. Single nucleotide polymorphisms analyses indicated that most BYDV, CYDV, and RBSDV isolates show considerable genetic variations. Phylogenetic analyses indicated that BYDVs and CYDVs were largely grouped in isolates from Asia and USA, whereas RBSDV was genetically similar to isolates from China. Overall, the findings of this study provide a preliminary characterization of the types of plant viruses infecting oats in six geographical regions of Korea.
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Marques-Pereira C, Pires M, Moreira IS. Discovery of Virus-Host interactions using bioinformatic tools. Methods Cell Biol 2022; 169:169-198. [DOI: 10.1016/bs.mcb.2022.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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20
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do Nascimento BLS, da Silva FS, Nunes-Neto JP, de Almeida Medeiros DB, Cruz ACR, da Silva SP, da Silva e Silva LH, de Oliveira Monteiro HA, Dias DD, Vieira DBR, Rosa JW, Brandão RCF, Chiang JO, Martins LC, da Costa Vasconcelos PF. First Description of the Mitogenome and Phylogeny of Culicinae Species from the Amazon Region. Genes (Basel) 2021; 12:genes12121983. [PMID: 34946932 PMCID: PMC8701802 DOI: 10.3390/genes12121983] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 11/26/2021] [Accepted: 12/01/2021] [Indexed: 01/25/2023] Open
Abstract
The Culicidae family is distributed worldwide and comprises about 3587 species subdivided into the subfamilies Anophelinae and Culicinae. This is the first description of complete mitochondrial DNA sequences from Aedes fluviatilis, Aedeomyia squamipennis, Coquillettidia nigricans, Psorophora albipes, and Psorophora ferox. The mitogenomes showed an average length of 15,046 pb and 78.02% AT content, comprising 37 functional subunits (13 protein coding genes, 22 tRNAs, and two rRNAs). The most common start codons were ATT/ATG, and TAA was the stop codon for all PCGs. The tRNAs had the typical leaf clover structure, except tRNASer1. Phylogeny was inferred by analyzing the 13 PCGs concatenated nucleotide sequences of 48 mitogenomes. Maximum likelihood and Bayesian inference analysis placed Ps. albipes and Ps. ferox in the Janthinosoma group, like the accepted classification of Psorophora genus. Ae. fluviatilis was placed in the Aedini tribe, but was revealed to be more related to the Haemagogus genus, a result that may have been hampered by the poor sampling of Aedes sequences. Cq. nigricans clustered with Cq. chrysonotum, both related to Mansonia. Ae. squamipennis was placed as the most external lineage of the Culicinae subfamily. The yielded topology supports the concept of monophyly of all groups and ratifies the current taxonomic classification.
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Affiliation(s)
- Bruna Laís Sena do Nascimento
- Department of Arbovirology and Hemorrhagic Fevers, Ananindeua, Evandro Chagas Institute—IEC/SVS/MS, Belém 67030-000, Brazil; (B.L.S.d.N.); (F.S.d.S.); (D.B.d.A.M.); (A.C.R.C.); (S.P.d.S.); (H.A.d.O.M.); (D.B.R.V.); (J.W.R.J.); (R.C.F.B.); (J.O.C.); (L.C.M.)
- Biological and Health Sciences Center, Parasitary Biology in the Amazon Posgraduation Program, State of Pará University, Belém 66095-662, Brazil; (L.H.d.S.e.S.); (D.D.D.); (P.F.d.C.V.)
| | - Fábio Silva da Silva
- Department of Arbovirology and Hemorrhagic Fevers, Ananindeua, Evandro Chagas Institute—IEC/SVS/MS, Belém 67030-000, Brazil; (B.L.S.d.N.); (F.S.d.S.); (D.B.d.A.M.); (A.C.R.C.); (S.P.d.S.); (H.A.d.O.M.); (D.B.R.V.); (J.W.R.J.); (R.C.F.B.); (J.O.C.); (L.C.M.)
- Biological and Health Sciences Center, Parasitary Biology in the Amazon Posgraduation Program, State of Pará University, Belém 66095-662, Brazil; (L.H.d.S.e.S.); (D.D.D.); (P.F.d.C.V.)
| | - Joaquim Pinto Nunes-Neto
- Department of Arbovirology and Hemorrhagic Fevers, Ananindeua, Evandro Chagas Institute—IEC/SVS/MS, Belém 67030-000, Brazil; (B.L.S.d.N.); (F.S.d.S.); (D.B.d.A.M.); (A.C.R.C.); (S.P.d.S.); (H.A.d.O.M.); (D.B.R.V.); (J.W.R.J.); (R.C.F.B.); (J.O.C.); (L.C.M.)
- Biological and Health Sciences Center, Parasitary Biology in the Amazon Posgraduation Program, State of Pará University, Belém 66095-662, Brazil; (L.H.d.S.e.S.); (D.D.D.); (P.F.d.C.V.)
- Correspondence:
| | - Daniele Barbosa de Almeida Medeiros
- Department of Arbovirology and Hemorrhagic Fevers, Ananindeua, Evandro Chagas Institute—IEC/SVS/MS, Belém 67030-000, Brazil; (B.L.S.d.N.); (F.S.d.S.); (D.B.d.A.M.); (A.C.R.C.); (S.P.d.S.); (H.A.d.O.M.); (D.B.R.V.); (J.W.R.J.); (R.C.F.B.); (J.O.C.); (L.C.M.)
| | - Ana Cecília Ribeiro Cruz
- Department of Arbovirology and Hemorrhagic Fevers, Ananindeua, Evandro Chagas Institute—IEC/SVS/MS, Belém 67030-000, Brazil; (B.L.S.d.N.); (F.S.d.S.); (D.B.d.A.M.); (A.C.R.C.); (S.P.d.S.); (H.A.d.O.M.); (D.B.R.V.); (J.W.R.J.); (R.C.F.B.); (J.O.C.); (L.C.M.)
| | - Sandro Patroca da Silva
- Department of Arbovirology and Hemorrhagic Fevers, Ananindeua, Evandro Chagas Institute—IEC/SVS/MS, Belém 67030-000, Brazil; (B.L.S.d.N.); (F.S.d.S.); (D.B.d.A.M.); (A.C.R.C.); (S.P.d.S.); (H.A.d.O.M.); (D.B.R.V.); (J.W.R.J.); (R.C.F.B.); (J.O.C.); (L.C.M.)
| | - Lucas Henrique da Silva e Silva
- Biological and Health Sciences Center, Parasitary Biology in the Amazon Posgraduation Program, State of Pará University, Belém 66095-662, Brazil; (L.H.d.S.e.S.); (D.D.D.); (P.F.d.C.V.)
| | - Hamilton Antônio de Oliveira Monteiro
- Department of Arbovirology and Hemorrhagic Fevers, Ananindeua, Evandro Chagas Institute—IEC/SVS/MS, Belém 67030-000, Brazil; (B.L.S.d.N.); (F.S.d.S.); (D.B.d.A.M.); (A.C.R.C.); (S.P.d.S.); (H.A.d.O.M.); (D.B.R.V.); (J.W.R.J.); (R.C.F.B.); (J.O.C.); (L.C.M.)
| | - Daniel Damous Dias
- Biological and Health Sciences Center, Parasitary Biology in the Amazon Posgraduation Program, State of Pará University, Belém 66095-662, Brazil; (L.H.d.S.e.S.); (D.D.D.); (P.F.d.C.V.)
| | - Durval Bertram Rodrigues Vieira
- Department of Arbovirology and Hemorrhagic Fevers, Ananindeua, Evandro Chagas Institute—IEC/SVS/MS, Belém 67030-000, Brazil; (B.L.S.d.N.); (F.S.d.S.); (D.B.d.A.M.); (A.C.R.C.); (S.P.d.S.); (H.A.d.O.M.); (D.B.R.V.); (J.W.R.J.); (R.C.F.B.); (J.O.C.); (L.C.M.)
| | - José Wilson Rosa
- Department of Arbovirology and Hemorrhagic Fevers, Ananindeua, Evandro Chagas Institute—IEC/SVS/MS, Belém 67030-000, Brazil; (B.L.S.d.N.); (F.S.d.S.); (D.B.d.A.M.); (A.C.R.C.); (S.P.d.S.); (H.A.d.O.M.); (D.B.R.V.); (J.W.R.J.); (R.C.F.B.); (J.O.C.); (L.C.M.)
| | - Roberto Carlos Feitosa Brandão
- Department of Arbovirology and Hemorrhagic Fevers, Ananindeua, Evandro Chagas Institute—IEC/SVS/MS, Belém 67030-000, Brazil; (B.L.S.d.N.); (F.S.d.S.); (D.B.d.A.M.); (A.C.R.C.); (S.P.d.S.); (H.A.d.O.M.); (D.B.R.V.); (J.W.R.J.); (R.C.F.B.); (J.O.C.); (L.C.M.)
| | - Jannifer Oliveira Chiang
- Department of Arbovirology and Hemorrhagic Fevers, Ananindeua, Evandro Chagas Institute—IEC/SVS/MS, Belém 67030-000, Brazil; (B.L.S.d.N.); (F.S.d.S.); (D.B.d.A.M.); (A.C.R.C.); (S.P.d.S.); (H.A.d.O.M.); (D.B.R.V.); (J.W.R.J.); (R.C.F.B.); (J.O.C.); (L.C.M.)
| | - Livia Carício Martins
- Department of Arbovirology and Hemorrhagic Fevers, Ananindeua, Evandro Chagas Institute—IEC/SVS/MS, Belém 67030-000, Brazil; (B.L.S.d.N.); (F.S.d.S.); (D.B.d.A.M.); (A.C.R.C.); (S.P.d.S.); (H.A.d.O.M.); (D.B.R.V.); (J.W.R.J.); (R.C.F.B.); (J.O.C.); (L.C.M.)
| | - Pedro Fernando da Costa Vasconcelos
- Biological and Health Sciences Center, Parasitary Biology in the Amazon Posgraduation Program, State of Pará University, Belém 66095-662, Brazil; (L.H.d.S.e.S.); (D.D.D.); (P.F.d.C.V.)
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Daniyarov A, Molkenov A, Rakhimova S, Akhmetova A, Yerezhepov D, Chingissova L, Bismilda V, Toksanbayeva B, Rakisheva A, Akilzhanova A, Kozhamkulov U, Kairov U. Genomic Analysis of Multidrug-Resistant Mycobacterium tuberculosis Strains From Patients in Kazakhstan. Front Genet 2021; 12:683515. [PMID: 34858467 PMCID: PMC8630622 DOI: 10.3389/fgene.2021.683515] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 10/15/2021] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) is an infectious disease that remains an essential public health problem in many countries. Despite decreasing numbers of new cases worldwide, the incidence of antibiotic-resistant forms (multidrug resistant and extensively drug-resistant) of TB is increasing. Next-generation sequencing technologies provide a high-throughput approach to identify known and novel potential genetic variants that are associated with drug resistance in Mycobacterium tuberculosis (Mtb). There are limited reports and data related to whole-genome characteristics of drug-resistant Mtb strains circulating in Kazakhstan. Here, we report whole-genome sequencing and analysis results of eight multidrug-resistant strains collected from TB patients in Kazakhstan. Genotyping and validation of all strains by MIRU-VNTR and spoligotyping methodologies revealed that these strains belong to the Beijing family. The spectrum of specific and potentially novel genomic variants (single-nucleotide polymorphisms, insertions, and deletions) related to drug resistance was identified and annotated. ResFinder, CARD, and CASTB antibiotic resistance databases were used for the characterization of genetic variants in genes associated with drug resistance. Our results provide reference data and genomic profiles of multidrug-resistant isolates for further comparative studies and investigations of genetic patterns in drug-resistant Mtb strains.
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Affiliation(s)
- Asset Daniyarov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Askhat Molkenov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Saule Rakhimova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ainur Akhmetova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Dauren Yerezhepov
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Lyailya Chingissova
- National Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty, Kazakhstan
| | - Venera Bismilda
- National Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty, Kazakhstan
| | - Bekzat Toksanbayeva
- National Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty, Kazakhstan
| | - Anar Rakisheva
- Department of Phthisiopulmonology, School of General Medicine, Asfendiyarov Kazakh National Medical University, Almaty, Kazakhstan
| | - Ainur Akilzhanova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ulan Kozhamkulov
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ulykbek Kairov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
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22
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Ma C, Wu H, Chen G, Liang C, Wu L, Xiao Y. The potential of metagenomic next-generation sequencing in diagnosis of spinal infection: a retrospective study. Eur Spine J 2021. [PMID: 34677679 DOI: 10.1007/s00586-021-07026-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/02/2021] [Accepted: 10/11/2021] [Indexed: 12/19/2022]
Abstract
PURPOSE Metagenomic next-generation sequencing (mNGS) is a new approach to identify the infecting organism in infectious diseases. Our aim was to evaluate the accuracy of mNGS in determining the etiology of spinal infection. METHODS In this retrospective study, patients who had a suspected spinal infection and underwent mNGS for diagnosis in our hospital were eligible for inclusion. Samples for mNGS, culture, and histopathological tests were collected surgically or with a CT-guided needle biopsy. Sensitivity and specificity were calculated for mNGS and culture test, using histopathological results as reference. RESULTS A total of 31 mNGS tests in 30 cases were included. Twenty-six cases were classified as infected, and four cases were considered aseptic. mNGS achieved a specificity of 75.0% [95% confidence interval (CI), 21.9% to 98.7%], sensitivity was 70.3% (95% CI, 49.7% to 85.5%). mNGS was more sensitive than culture at 14.8% (95% CI, 4.9% to 34.6%, P < 0.0001). However, the specificities of mNGS and culture were statistically similar. CONCLUSION We described here the power of mNGS in the etiological diagnosing of spinal infection. Our study opens the possibility for more extensive use of mNGS techniques in the identification of pathogens in patients with suspected spinal infection.
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Lee SH, Kim K, Kim J, No JS, Park K, Budhathoki S, Lee SH, Lee J, Cho SH, Cho S, Lee GY, Hwang J, Kim HC, Klein TA, Uhm CS, Kim WK, Song JW. Discovery and Genetic Characterization of Novel Paramyxoviruses Related to the Genus Henipavirus in Crocidura Species in the Republic of Korea. Viruses 2021; 13:2020. [PMID: 34696450 DOI: 10.3390/v13102020] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/04/2021] [Accepted: 10/04/2021] [Indexed: 12/21/2022] Open
Abstract
Paramyxoviruses, negative-sense single-stranded RNA viruses, pose a critical threat to human public health. Currently, 78 species, 17 genera, and 4 subfamilies of paramyxoviruses are harbored by multiple natural reservoirs, including rodents, bats, birds, reptiles, and fish. Henipaviruses are critical zoonotic pathogens that cause severe acute respiratory distress and neurological diseases in humans. Using reverse transcription-polymerase chain reaction, 115 Crocidura species individuals were examined for the prevalence of paramyxovirus infections. Paramyxovirus RNA was observed in 26 (22.6%) shrews collected at five trapping sites, Republic of Korea. Herein, we report two genetically distinct novel paramyxoviruses (genus: Henipavirus): Gamak virus (GAKV) and Daeryong virus (DARV) isolated from C. lasiura and C. shantungensis, respectively. Two GAKVs and one DARV were nearly completely sequenced using next-generation sequencing. GAKV and DARV contain six genes (3′-N-P-M-F-G-L-5′) with genome sizes of 18,460 nucleotides and 19,471 nucleotides, respectively. The phylogenetic inference demonstrated that GAKV and DARV form independent genetic lineages of Henipavirus in Crocidura species. GAKV-infected human lung epithelial cells elicited the induction of type I/III interferons, interferon-stimulated genes, and proinflammatory cytokines. In conclusion, this study contributes further understandings of the molecular prevalence, genetic characteristics and diversity, and zoonotic potential of novel paramyxoviruses in shrews.
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Kim S, Lee S, Park HT, Song JY, Kim T. Genomic Consideration in Chemotherapy-Induced Ovarian Damage and Fertility Preservation. Genes (Basel) 2021; 12:1525. [PMID: 34680919 PMCID: PMC8535252 DOI: 10.3390/genes12101525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/25/2021] [Accepted: 09/25/2021] [Indexed: 11/25/2022] Open
Abstract
Chemotherapy-induced ovarian damage and fertility preservation in young patients with cancer are emerging disciplines. The mechanism of treatment-related gonadal damage provides important information for targeting prevention methods. The genomic aspects of ovarian damage after chemotherapy are not fully understood. Several studies have demonstrated that gene alterations related to follicular apoptosis or accelerated follicle activation are related to ovarian insufficiency and susceptibility to ovarian damage following chemotherapy. This may accelerate follicular apoptosis and follicle reservoir utilization and damage the ovarian stroma via multiple molecular reactions after chemotherapy. This review highlights the importance of genomic considerations in chemotherapy-induced ovarian damage and multidisciplinary oncofertility strategies for providing high-quality care to young female cancer patients.
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Affiliation(s)
- Seongmin Kim
- Gynecologic Cancer Center, CHA Ilsan Medical Center, CHA University College of Medicine, 1205 Jungang-ro, Ilsandong-gu, Goyang-si 10414, Korea;
| | - Sanghoon Lee
- Department of Obstetrics and Gynecology, Korea University College of Medicine, 73 Inchon-ro, Seongbuk-gu, Seoul 02841, Korea; (H.-T.P.); (J.-Y.S.); (T.K.)
| | - Hyun-Tae Park
- Department of Obstetrics and Gynecology, Korea University College of Medicine, 73 Inchon-ro, Seongbuk-gu, Seoul 02841, Korea; (H.-T.P.); (J.-Y.S.); (T.K.)
| | - Jae-Yun Song
- Department of Obstetrics and Gynecology, Korea University College of Medicine, 73 Inchon-ro, Seongbuk-gu, Seoul 02841, Korea; (H.-T.P.); (J.-Y.S.); (T.K.)
| | - Tak Kim
- Department of Obstetrics and Gynecology, Korea University College of Medicine, 73 Inchon-ro, Seongbuk-gu, Seoul 02841, Korea; (H.-T.P.); (J.-Y.S.); (T.K.)
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25
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Zhao E, Wang D, Li N, Huang S, Zhao Z, Hu S, He X, Wen G. Clinical study on the diagnosis of porcine streptococcal meningitis with negative blood and cerebrospinal fluid culture by next-generation sequencing. Eur J Med Res 2021; 26:85. [PMID: 34344456 PMCID: PMC8330088 DOI: 10.1186/s40001-021-00554-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/15/2021] [Indexed: 11/21/2022] Open
Abstract
Background Streptococcus suis (Ss) is a Gram-positive and anaerobic zoonotic pathogen that is susceptible to all populations and can cause meningitis, septicemia, endocarditis and arthritis in humans. Methods In this study, patients with meningitis who were admitted to our hospital with negative blood and cerebrospinal fluid culture were divided into a next-generation sequencing group and a control group. In the next-generation sequencing group, we used the next-generation sequencing method to detect pathogenic bacteria in the patients’ cerebrospinal fluid. In the control group, we used blood and cerebrospinal fluid bacterial culture method to detect pathogenic bacteria in the patients' cerebrospinal fluid. The detection rates of pathogenic bacteria in the cerebrospinal fluid of the two groups were compared and analyzed. Results A total of 18 patients were included in this study, including 8 patients in the next-generation sequencing group and 10 patients in the control group. The mean age (P = 0.613) and mean disease duration (P = 0.294) were similar in both groups. Patients in the next-generation sequencing group had a leukocyte count of 13.13 ± 4.79 × 109, a neutrophil percentage of 83.39 ± 10.36%, and a C-reactive protein level of 134.95 ± 107.69 mg/L. Patients in the control group had a temperature of 38.32 ± 1.07, a leukocyte count of 8.00 ± 2.99 × 109, and a neutrophil percentage of 74.61 ± 8.89%, and C-reactive protein level was 4.75 ± 6.8 mg/L. The statistical results showed that the leukocytes (P = 0.013) and C-reactive protein levels (P = 0.001) were significantly higher in the patients of the next-generation sequencing group than in the control group. No statistically significant differences were seen in body temperature and neutrophil percentage between the two groups (P > 0.05). The incidence of intracranial pressure and meningeal irritation signs were similar in the two groups (P > 0.05). The detection rate of Streptococcus suis in the cerebrospinal fluid of patients in the next-generation sequencing group was 100%, and the detection rate of Streptococcus suis in the cerebrospinal fluid of the control group was 0%. Conclusion The detection rate of Streptococcus suis infection in cerebrospinal fluid by next-generation sequencing was significantly higher than that by blood and cerebrospinal fluid bacterial culture. Therefore, the diagnosis of porcine streptococcal meningitis by next-generation sequencing method is worthy of clinical promotion and application.
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Affiliation(s)
- Eryi Zhao
- Department of Neurology, Hainan General Hospital, Hainan Affilicated Hospital of Hainan Medical University, Haikou, 570311, Hainan, China
| | - Daimei Wang
- Department of Pharmacy, Hainan General Hospital, Hainan Affilicated Hospital of Hainan Medical University, Haikou, 570311, Hainan, China
| | - Na Li
- Department of Pharmacy, Qianjiang Central Hospital of Chongqing, No. 63 of Road 9, Chengxi Street, Qianjiang District, Chongqing, 409099, China.
| | - Shixiong Huang
- Department of Neurology, Hainan General Hospital, Hainan Affilicated Hospital of Hainan Medical University, Haikou, 570311, Hainan, China
| | - Zhongyan Zhao
- Department of Neurology, Hainan General Hospital, Hainan Affilicated Hospital of Hainan Medical University, Haikou, 570311, Hainan, China
| | - Shijun Hu
- Department of Neurology, Hainan General Hospital, Hainan Affilicated Hospital of Hainan Medical University, Haikou, 570311, Hainan, China
| | - Xiangying He
- Department of Neurology, Hainan General Hospital, Hainan Affilicated Hospital of Hainan Medical University, Haikou, 570311, Hainan, China
| | - Guoqiang Wen
- Department of Neurology, Hainan General Hospital, Hainan Affilicated Hospital of Hainan Medical University, Haikou, 570311, Hainan, China
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Abstract
Coronavirus disease 2019 (COVID-19) is an on-going pandemic disease infecting millions of people across the globe. Recent reports of reduction in antibody levels and the re-emergence of the disease in recovered patients necessitated the understanding of the pandemic at the core level. The cases of multiple organ failures emphasized the consideration of different organ systems while managing the disease. The present study employed RNA sequencing data to determine the disease associated differentially regulated genes and their related protein interactions in several organ systems. It signified the importance of early diagnosis and treatment of the disease. A map of protein interactions of multiple organ systems was built and uncovered CAV1 and CTNNB1 as the top degree nodes. A core interactions sub-network was analyzed to identify different modules of functional significance. AR, CTNNB1, CAV1, and PIK3R1 proteins were unfolded as bridging nodes interconnecting different modules for the information flow across several pathways. The present study also highlighted some of the druggable targets to analyze in drug re-purposing strategies against the COVID-19 pandemic. Therefore, the protein interactions map and the modular interactions of the differentially regulated genes in the multiple organ systems would incline the scientists and researchers to investigate in novel therapeutics for the COVID-19 pandemic expeditiously.
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Affiliation(s)
- Dhammapal Bharne
- Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad 500046, India
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27
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Lee SH, No JS, Kim K, Budhathoki S, Park K, Lee GY, Cho S, Kim BH, Cho S, Kim J, Lee J, Cho SH, Kim HC, Klein TA, Uhm CS, Kim WK, Song JW. Novel Paju Apodemus paramyxovirus 1 and 2, harbored by Apodemus agrarius in the Republic of Korea. Virology 2021; 562:40-49. [PMID: 34256243 DOI: 10.1016/j.virol.2021.06.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 01/19/2023]
Abstract
Paramyxoviruses harbored by multiple natural reservoirs pose a potential threat to public health. Jeilongvirus has been proposed as a novel paramyxovirus genus found in rodents, bats, and cats. Paramyxovirus RNA was detected in 108/824 (13.1%) Apodemus agrarius captured at 14 trapping sites in the Republic of Korea. We first present two genetically distinct novel paramyxoviruses, Paju Apodemus paramyxovirus 1 (PAPV-1) and 2 (PAPV-2). The disparity between PAPV-1 (19,716 nucleotides) and -2 (17,475 nucleotides) revealed the presence of the SH gene and length of the G gene in the genome organization. The phylogeny of PAPV-1 and -2 belonged to distinct genetic lineages of Jeilongvirus, respectively, even though these viruses were originated from A. agrarius. PAPV-1 infected human epithelial and endothelial cells, facilitating the induction of type I/III interferons, interferon-stimulated genes, and pro-inflammatory cytokines. Therefore, this study provides insights into the molecular epidemiology, genetic diversity, and virus-host interactions of novel rodent-borne paramyxoviruses.
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Affiliation(s)
- Seung-Ho Lee
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jin Sun No
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kijin Kim
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Shailesh Budhathoki
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Kyungmin Park
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea; BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Geum-Young Lee
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seungchan Cho
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
| | | | | | - Jongwoo Kim
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jingyeong Lee
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seung Hye Cho
- Department of Biomedical Science, College of Natural Sciences, Hallym University, Chuncheon, Republic of Korea
| | - Heung-Chul Kim
- Force Health Protection and Preventive Medicine, Medical Department Activity-Korea/65th, Medical Brigade, Unit 15281, APO AP, 96271-5281, USA
| | - Terry A Klein
- Force Health Protection and Preventive Medicine, Medical Department Activity-Korea/65th, Medical Brigade, Unit 15281, APO AP, 96271-5281, USA
| | - Chang-Sub Uhm
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Won-Keun Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea; Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea.
| | - Jin-Won Song
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea; BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea.
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28
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Sun B, Yeh J. Onco-fertility and personalized testing for potential for loss of ovarian reserve in patients undergoing chemotherapy: proposed next steps for development of genetic testing to predict changes in ovarian reserve. Fertil Res Pract 2021; 7:13. [PMID: 34193292 PMCID: PMC8244159 DOI: 10.1186/s40738-021-00105-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/19/2021] [Indexed: 12/29/2022]
Abstract
Women of reproductive age undergoing chemotherapy face the risk of irreversible ovarian insufficiency. Current methods of ovarian reserve testing do not accurately predict future reproductive potential for patients undergoing chemotherapy. Genetic markers that more accurately predict the reproductive potential of each patient undergoing chemotherapy would be critical tools that would be useful for evidence-based fertility preservation counselling. To assess the possible approaches to take to develop personalized genetic testing for these patients, we review current literature regarding mechanisms of ovarian damage due to chemotherapy and genetic variants associated with both the damage mechanisms and primary ovarian insufficiency. The medical literature point to a number of genetic variants associated with mechanisms of ovarian damage and primary ovarian insufficiency. Those variants that appear at a higher frequency, with known pathways, may be considered as potential genetic markers for predictive ovarian reserve testing. We propose developing personalized testing of the potential for loss of ovarian function for patients with cancer, prior to chemotherapy treatment. There are advantages of using genetic markers complementary to the current ovarian reserve markers of AMH, antral follicle count and day 3 FSH as predictors of preservation of fertility after chemotherapy. Genetic markers will help identify upstream pathways leading to high risk of ovarian failure not detected by present clinical markers. Their predictive value is mechanism-based and will encourage research towards understanding the multiple pathways contributing to ovarian failure after chemotherapy.
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Affiliation(s)
- Bei Sun
- Sackler School of Medicine, New York State/American Program of Tel Aviv University, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
| | - John Yeh
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics & Gynecology, University of Massachusetts Medical School, UMass Memorial Medical Center, 119 Belmont Street, Worcester, MA, 01605, USA.
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29
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Abstract
Approximately 15% of human cancers are estimated to be attributed to viruses. Virus sequences can be integrated into the host genome, leading to genomic instability and carcinogenesis. Here, a new deep convolutional neural network (CNN) model is developed with attention architecture, namely DeepVISP, for accurately predicting oncogenic virus integration sites (VISs) in the human genome. Using the curated benchmark integration data of three viruses, hepatitis B virus (HBV), human herpesvirus (HPV), and Epstein-Barr virus (EBV), DeepVISP achieves high accuracy and robust performance for all three viruses through automatically learning informative features and essential genomic positions only from the DNA sequences. In comparison, DeepVISP outperforms conventional machine learning methods by 8.43-34.33% measured by area under curve (AUC) value enhancement in three viruses. Moreover, DeepVISP can decode cis-regulatory factors that are potentially involved in virus integration and tumorigenesis, such as HOXB7, IKZF1, and LHX6. These findings are supported by multiple lines of evidence in literature. The clustering analysis of the informative motifs reveales that the representative k-mers in clusters could help guide virus recognition of the host genes. A user-friendly web server is developed for predicting putative oncogenic VISs in the human genome using DeepVISP.
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Affiliation(s)
- Haodong Xu
- Center for Precision HealthSchool of Biomedical InformaticsThe University of Texas Health Science Center at Houston (UTHealth)HoustonTX77030USA
| | - Peilin Jia
- Center for Precision HealthSchool of Biomedical InformaticsThe University of Texas Health Science Center at Houston (UTHealth)HoustonTX77030USA
| | - Zhongming Zhao
- Center for Precision HealthSchool of Biomedical InformaticsThe University of Texas Health Science Center at Houston (UTHealth)HoustonTX77030USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical SciencesHoustonTX77030USA
- Department of Biomedical InformaticsVanderbilt University Medical CenterNashvilleTN37203USA
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30
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Goettsch W, Beerenwinkel N, Deng L, Dölken L, Dutilh BE, Erhard F, Kaderali L, von Kleist M, Marquet R, Matthijnssens J, McCallin S, McMahon D, Rattei T, Van Rij RP, Robertson DL, Schwemmle M, Stern-Ginossar N, Marz M. ITN-VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics. Viruses 2021; 13:v13050766. [PMID: 33925452 PMCID: PMC8145447 DOI: 10.3390/v13050766] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/15/2021] [Accepted: 04/22/2021] [Indexed: 11/16/2022] Open
Abstract
Many recent studies highlight the fundamental importance of viruses. Besides their important role as human and animal pathogens, their beneficial, commensal or harmful functions are poorly understood. By developing and applying tailored bioinformatical tools in important virological models, the Marie Skłodowska-Curie Initiative International Training Network VIROINF will provide a better understanding of viruses and the interaction with their hosts. This will open the door to validate methods of improving viral growth, morphogenesis and development, as well as to control strategies against unwanted microorganisms. The key feature of VIROINF is its interdisciplinary nature, which brings together virologists and bioinformaticians to achieve common goals.
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Affiliation(s)
- Winfried Goettsch
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University, 07743 Jena, Germany;
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland;
| | - Li Deng
- Institute of Virology, Helmholtz Centre Munich and Technical University Munich, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany;
| | - Lars Dölken
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, 97078 Würzburg, Germany; (L.D.); (F.E.)
| | - Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Hugo R. Kruytgebouw, Padualaan 8, 3584 CH Utrecht, The Netherlands;
| | - Florian Erhard
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, 97078 Würzburg, Germany; (L.D.); (F.E.)
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany;
| | - Max von Kleist
- MF1 Bioinformatics, Robert Koch-Institute, 13353 Berlin, Germany;
| | - Roland Marquet
- CNRS, Architecture et Réactivité de l’ARN, Université de Strasbourg, UPR 9002 Strasbourg, France;
| | - Jelle Matthijnssens
- Department of Microbiology and Immunology, Katholieke Universiteit Leuven, Herestraat 49 Box 1040, 3000 Leuven, Belgium;
| | - Shawna McCallin
- Department of Neuro-Urology, Balgrist University Hospital, University of Zürich, Forchstrasse 340, 8008 Zürich, Switzerland;
| | - Dino McMahon
- Institute of Biology, Freie Universität Berlin, Schwendenerstr. 1, 14195 Berlin, Germany;
| | - Thomas Rattei
- Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria;
| | - Ronald P. Van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands;
| | - David L. Robertson
- MRC, University of Glasgow Centre for Virus Research (CVR), 464 Bearsden Road, Glasgow G61 1QH, UK;
| | - Martin Schwemmle
- Institute of Virology, Medical Center—University of Freiburg, Hermann-Herder-Strasse 11, 79104 Freiburg, Germany;
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel;
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University, 07743 Jena, Germany;
- FLI Leibniz Institute for Age Research, 07745 Jena, Germany
- Correspondence: ; Tel.: +49-3641-9-46480
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31
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Cassedy A, Parle-McDermott A, O’Kennedy R. Virus Detection: A Review of the Current and Emerging Molecular and Immunological Methods. Front Mol Biosci 2021; 8:637559. [PMID: 33959631 PMCID: PMC8093571 DOI: 10.3389/fmolb.2021.637559] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/01/2021] [Indexed: 12/14/2022] Open
Abstract
Viruses are ubiquitous in the environment. While many impart no deleterious effects on their hosts, several are major pathogens. This risk of pathogenicity, alongside the fact that many viruses can rapidly mutate highlights the need for suitable, rapid diagnostic measures. This review provides a critical analysis of widely used methods and examines their advantages and limitations. Currently, nucleic-acid detection and immunoassay methods are among the most popular means for quickly identifying viral infection directly from source. Nucleic acid-based detection generally offers high sensitivity, but can be time-consuming, costly, and require trained staff. The use of isothermal-based amplification systems for detection could aid in the reduction of results turnaround and equipment-associated costs, making them appealing for point-of-use applications, or when high volume/fast turnaround testing is required. Alternatively, immunoassays offer robustness and reduced costs. Furthermore, some immunoassay formats, such as those using lateral-flow technology, can generate results very rapidly. However, immunoassays typically cannot achieve comparable sensitivity to nucleic acid-based detection methods. Alongside these methods, the application of next-generation sequencing can provide highly specific results. In addition, the ability to sequence large numbers of viral genomes would provide researchers with enhanced information and assist in tracing infections.
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Affiliation(s)
- A. Cassedy
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | | | - R. O’Kennedy
- School of Biotechnology, Dublin City University, Dublin, Ireland
- Hamad Bin Khalifa University, Doha, Qatar
- Qatar Foundation, Doha, Qatar
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Sharma MMM, Ramekar RV, Park NI, Choi IY, Choi SK, Park KC. Editor's introduction to this issue (G&I 19:1, 2021). Genomics Inform 2021; 19:e45. [PMID: 35172475 PMCID: PMC8752983 DOI: 10.5808/gi.21055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 09/29/2021] [Indexed: 11/20/2022] Open
Abstract
Brassica napus is the third most important oilseed crop in the world; however, in Korea, it is greatly affected by cold stress, limiting seed growth and production. Plants have developed specific stress responses that are generally divided into three categories: cold-stress signaling, transcriptional/post-transcriptional regulation, and stress-response mechanisms. Large numbers of functional and regulatory proteins are involved in these processes when triggered by cold stress. Here, our objective was to investigate the different genetic factors involved in the cold-stress responses of B. napus. Consequently, we treated the Korean B. napus cultivar Naehan at the 4-week stage in cold chambers under different conditions, and RNA and cDNA were obtained. An in silico analysis included 80 cold-responsive genes downloaded from the National Center for Biotechnology Information (NCBI) database. Expression levels were assessed by reverse transcription polymerase chain reaction, and 14 cold-triggered genes were identified under cold-stress conditions. The most significant genes encoded zinc-finger proteins (33.7%), followed by MYB transcription factors (7.5%). In the future, we will select genes appropriate for improving the cold tolerance of B. napus.
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Affiliation(s)
| | - Rahul Vasudeo Ramekar
- Department of Agriculture and Life Industries, Kangwon National University, Chuncheon 24341, Korea
| | - Nam-Il Park
- Department of Plant Science, Gangneung-Wonju National University, Gangneung 25457, Korea
| | - Ik-Young Choi
- Department of Agriculture and Life Industries, Kangwon National University, Chuncheon 24341, Korea
| | - Seon-Kang Choi
- Department of Agriculture and Life Industries, Kangwon National University, Chuncheon 24341, Korea
| | - Kyong-Cheul Park
- Department of Agriculture and Life Industries, Kangwon National University, Chuncheon 24341, Korea
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Affiliation(s)
- Taesung Park
- Department of Statistics, Seoul National University, Seoul 08826, Korea
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Borland EM, Kading RC. Modernizing the Toolkit for Arthropod Bloodmeal Identification. Insects 2021; 12:37. [PMID: 33418885 DOI: 10.3390/insects12010037] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 11/24/2022]
Abstract
Simple Summary The ability to identify the source of vertebrate blood in mosquitoes, ticks, and other blood-feeding arthropod vectors greatly enhances our knowledge of how vector-borne pathogens are spread. The source of the bloodmeal is identified by analyzing the remnants of blood remaining in the arthropod at the time of capture, though this is often fraught with challenges. This review provides a roadmap and guide for those considering modern techniques for arthropod bloodmeal identification with a focus on progress made in the field over the past decade. We highlight genome regions that can be used to identify the vertebrate source of arthropod bloodmeals as well as technological advances made in other fields that have introduced innovative new ways to identify vertebrate meal source based on unique properties of the DNA sequence, protein signatures, or residual molecules present in the blood. Additionally, engineering progress in miniaturization has led to a number of field-deployable technologies that bring the laboratory directly to the arthropods at the site of collection. Although many of these advancements have helped to address the technical challenges of the past, the challenge of successfully analyzing degraded DNA in bloodmeals remains to be solved. Abstract Understanding vertebrate–vector interactions is vitally important for understanding the transmission dynamics of arthropod-vectored pathogens and depends on the ability to accurately identify the vertebrate source of blood-engorged arthropods in field collections using molecular methods. A decade ago, molecular techniques being applied to arthropod blood meal identification were thoroughly reviewed, but there have been significant advancements in the techniques and technologies available since that time. This review highlights the available diagnostic markers in mitochondrial and nuclear DNA and discusses their benefits and shortcomings for use in molecular identification assays. Advances in real-time PCR, high resolution melting analysis, digital PCR, next generation sequencing, microsphere assays, mass spectrometry, and stable isotope analysis each offer novel approaches and advantages to bloodmeal analysis that have gained traction in the field. New, field-forward technologies and platforms have also come into use that offer promising solutions for point-of-care and remote field deployment for rapid bloodmeal source identification. Some of the lessons learned over the last decade, particularly in the fields of DNA barcoding and sequence analysis, are discussed. Though many advancements have been made, technical challenges remain concerning the prevention of sample degradation both by the arthropod before the sample has been obtained and during storage. This review provides a roadmap and guide for those considering modern techniques for arthropod bloodmeal identification and reviews how advances in molecular technology over the past decade have been applied in this unique biomedical context.
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Prasad A, Bhargava H, Gupta A, Shukla N, Rajagopal S, Gupta S, Sharma A, Valadi J, Nigam V, Suravajhala P. Next Generation Sequencing. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Anis E, Ilha MRS, Engiles JB, Wilkes RP. Evaluation of targeted next-generation sequencing for detection of equine pathogens in clinical samples. J Vet Diagn Invest 2020; 33:227-234. [PMID: 33305693 DOI: 10.1177/1040638720978381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Equine infectious disease outbreaks may have profound economic impact, resulting in losses of millions of dollars of revenue as a result of horse loss, quarantine, and cancelled events. Early and accurate diagnosis is essential to limit the spread of infectious diseases. However, laboratory detection of infectious agents, especially the simultaneous detection of multiple agents, can be challenging to the clinician and diagnostic laboratory. Next-generation sequencing (NGS), which allows millions of DNA templates to be sequenced simultaneously in a single reaction, is an ideal technology for comprehensive testing. We conducted a proof-of-concept study of targeted NGS to detect 62 common equine bacterial, viral, and parasitic pathogens in clinical samples. We designed 264 primers and constructed a bioinformatics tool for the detection of targeted pathogens. The designed primers were able to specifically detect the intended pathogens. Results of testing 27 clinical samples with our targeted NGS assay compared with results of routine tests (assessed as a group) yielded positive percent agreement of 81% and negative percent agreement of 83%, overall agreement of 81%, and kappa of 0.56 (moderate agreement). This moderate agreement was likely the result of low sensitivity of some primers. However, our NGS assay successfully detected multiple pathogens in the clinical samples, including some pathogens missed by routine techniques.
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Affiliation(s)
- Eman Anis
- Department of Pathobiology, New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA.,Department of Virology, Faculty of Veterinary Medicine, University of Sadat, El Beheira Governorate, Sadat City, Egypt
| | - Marcia R S Ilha
- Tifton Veterinary Diagnostic and Investigational Laboratory, College of Veterinary Medicine, University of Georgia, Tifton, GA
| | - Julie B Engiles
- Department of Pathobiology, New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA
| | - Rebecca P Wilkes
- Tifton Veterinary Diagnostic and Investigational Laboratory, College of Veterinary Medicine, University of Georgia, Tifton, GA.,Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN
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Jansen SA, Nijhuis W, Leavis HL, Riezebos-Brilman A, Lindemans CA, Schuurman R. Broad Virus Detection and Variant Discovery in Fecal Samples of Hematopoietic Transplant Recipients Using Targeted Sequence Capture Metagenomics. Front Microbiol 2020; 11:560179. [PMID: 33281758 PMCID: PMC7705093 DOI: 10.3389/fmicb.2020.560179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022] Open
Abstract
Pediatric allogeneic hematopoietic stem cell transplantation (HSCT) patients often suffer from gastro-intestinal (GI) disease caused by viruses, Graft-versus-Host Disease (GVHD) or a combination of the two. Currently, the GI eukaryotic virome of HSCT recipients remains relatively understudied, which complicates the understanding of its role in GVHD pathogenicity. As decisions regarding immunosuppressive therapy in the treatment of virus infection or GVHD, respectively, can be completely contradicting, it is crucial to better understand the prevalence and relevance of viruses in the GI tract in the HSCT setting. A real time PCR panel for a set of specific viruses widely used to diagnose the most common causes of GI viral gastroenteritis is possibly insufficient to grasp the full extent of viruses present. Therefore, we applied the targeted sequence capture method ViroCap to residual fecal samples of 11 pediatric allogeneic HSCT recipients with GI symptoms and a suspicion of GVHD, to enrich for nucleic acids of viruses that are known to infect vertebrate hosts. After enrichment, NGS was applied to broadly detect viral sequences. Using ViroCap, we were able to detect viruses such as norovirus and adenovirus (ADV), that had been previously detected using clinical diagnostic PCR on the same sample. In addition, multiple, some of which clinically relevant viruses were detected, including ADV, human rhinovirus (HRV) and BK polyomavirus (BKV). Interestingly, in samples in which specific PCR testing for regular viral GI pathogens did not result in a diagnosis, the ViroCap pipeline led to the detection of viral sequences of human herpesvirus (HHV)-7, BKV, HRV, KI polyomavirus and astrovirus. The latter was an only recently described variant and showed extensive sequence mismatches with the applied real time PCR primers and would therefore not have been detected if tested. Our results indicate that target enrichment of viral nucleic acids through ViroCap leads to sensitive and broad possibly clinically relevant virus detection, including the detection of newer variants in clinical HSCT recipient samples. As such, ViroCap could be a useful detection tool clinically, but also in studying the associations between viral presence and GVHD.
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Affiliation(s)
- Suze A Jansen
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, Netherlands.,Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Wouter Nijhuis
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Helen L Leavis
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | | | - Caroline A Lindemans
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, Netherlands.,Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Rob Schuurman
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
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da Silva FS, Cruz ACR, de Almeida Medeiros DB, da Silva SP, Nunes MRT, Martins LC, Chiang JO, da Silva Lemos P, Cunha GM, de Araujo RF, de Oliveira Monteiro HA, Nunes Neto JP. Mitochondrial genome sequencing and phylogeny of Haemagogus albomaculatus, Haemagogus leucocelaenus, Haemagogus spegazzinii, and Haemagogus tropicalis (Diptera: Culicidae). Sci Rep 2020; 10:16948. [PMID: 33046768 DOI: 10.1038/s41598-020-73790-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/14/2020] [Indexed: 12/22/2022] Open
Abstract
The genus Haemagogus (Diptera: Culicidae) comprises species of great epidemiological relevance, involved in transmission cycles of the Yellow fever virus and other arboviruses in South America. So far, only Haemagogus janthinomys has complete mitochondrial sequences available. Given the unavailability of information related to aspects of the evolutionary biology and molecular taxonomy of this genus, we report here, the first sequencing of the mitogenomes of Haemagogus albomaculatus, Haemagogus leucocelaenus, Haemagogus spegazzinii, and Haemagogus tropicalis. The mitogenomes showed an average length of 15,038 bp, average AT content of 79.3%, positive AT-skews, negative GC-skews, and comprised 37 functional subunits (13 PCGs, 22 tRNA, and 02 rRNA). The PCGs showed ATN as start codon, TAA as stop codon, and signs of purifying selection. The tRNAs had the typical leaf clover structure, except tRNASer1. Phylogenetic analyzes of Bayesian inference and Maximum Likelihood, based on concatenated sequences from all 13 PCGs, produced identical topologies and strongly supported the monophyletic relationship between the Haemagogus and Conopostegus subgenera, and corroborated with the known taxonomic classification of the evaluated taxa, based on external morphological aspects. The information produced on the mitogenomes of the Haemagogus species evaluated here may be useful in carrying out future taxonomic and evolutionary studies of the genus.
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Hasan MR, Sundararaju S, Tang P, Tsui KM, Lopez AP, Janahi M, Tan R, Tilley P. A metagenomics-based diagnostic approach for central nervous system infections in hospital acute care setting. Sci Rep 2020; 10:11194. [PMID: 32641704 PMCID: PMC7343800 DOI: 10.1038/s41598-020-68159-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 06/16/2020] [Indexed: 01/22/2023] Open
Abstract
The etiology of central nervous system (CNS) infections such as meningitis and encephalitis remains unknown in a large proportion of cases partly because the diversity of pathogens that may cause CNS infections greatly outnumber available test methods. We developed a metagenomic next generation sequencing (mNGS)-based approach for broad-range detection of pathogens associated with CNS infections suitable for application in the acute care hospital setting. The analytical sensitivity of mNGS performed on an Illumina MiSeq was assessed using simulated cerebrospinal fluid (CSF) specimens (n = 9). mNGS data were then used as a training dataset to optimize a bioinformatics workflow based on the IDseq pipeline. For clinical validation, residual CSF specimens (n = 74) from patients with suspected CNS infections previously tested by culture and/or PCR, were analyzed by mNGS. In simulated specimens, the NGS reads aligned to pathogen genomes in IDseq were correlated to qPCR CT values for the respective pathogens (R = 0.96; p < 0.0001), and the results were highly specific for the spiked pathogens. In clinical samples, the diagnostic accuracy, sensitivity and specificity of the mNGS with reference to conventional methods were 100%, 95% and 96%, respectively. The clinical application of mNGS holds promise to benefit patients with CNS infections of unknown etiology.
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Affiliation(s)
- Mohammad Rubayet Hasan
- Department of Pathology, Sidra Medicine, Level 2M, Office H2M-24093, PO BOX 26999, Doha, Qatar. .,Weill Cornell Medical College in Qatar, Doha, Qatar. .,Sidra Medicine, Doha, Qatar.
| | | | - Patrick Tang
- Weill Cornell Medical College in Qatar, Doha, Qatar.,Sidra Medicine, Doha, Qatar
| | - Kin-Ming Tsui
- Weill Cornell Medical College in Qatar, Doha, Qatar.,Sidra Medicine, Doha, Qatar
| | - Andres Perez Lopez
- Weill Cornell Medical College in Qatar, Doha, Qatar.,Sidra Medicine, Doha, Qatar
| | - Mohammad Janahi
- Weill Cornell Medical College in Qatar, Doha, Qatar.,Sidra Medicine, Doha, Qatar
| | - Rusung Tan
- Weill Cornell Medical College in Qatar, Doha, Qatar.,Sidra Medicine, Doha, Qatar
| | - Peter Tilley
- British Columbia Children's Hospital, Vancouver, BC, Canada.,University of British Columbia, Vancouver, BC, Canada
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Lu IN, Muller CP, He FQ. Applying next-generation sequencing to unravel the mutational landscape in viral quasispecies. Virus Res 2020; 283:197963. [PMID: 32278821 PMCID: PMC7144618 DOI: 10.1016/j.virusres.2020.197963] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/03/2020] [Accepted: 04/04/2020] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) has revolutionized the scale and depth of biomedical sciences. Because of its unique ability for the detection of sub-clonal variants within genetically diverse populations, NGS has been successfully applied to analyze and quantify the exceptionally-high diversity within viral quasispecies, and many low-frequency drug- or vaccine-resistant mutations of therapeutic importance have been discovered. Although many works have intensively discussed the latest NGS approaches and applications in general, none of them has focused on applying NGS in viral quasispecies studies, mostly due to the limited ability of current NGS technologies to accurately detect and quantify rare viral variants. Here, we summarize several error-correction strategies that have been developed to enhance the detection accuracy of minority variants. We also discuss critical considerations for preparing a sequencing library from viral RNAs and for analyzing NGS data to unravel the mutational landscape.
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Affiliation(s)
- I-Na Lu
- DKFZ-Division Translational Neurooncology at the WTZ, DKTK partner site, University Hospital Essen, D-45147 Essen, Germany; Department of Infectious Diseases, Aarhus University Hospital, DK-8200 Aarhus N, Denmark.
| | - Claude P Muller
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-Sur-Alzette, Luxembourg; Laboratoire National de Santé, L-3583 Dudelange, Luxembourg
| | - Feng Q He
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-Sur-Alzette, Luxembourg; Institute of Medical Microbiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany.
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Hess J, Kohl T, Kotrová M, Rönsch K, Paprotka T, Mohr V, Hutzenlaub T, Brüggemann M, Zengerle R, Niemann S, Paust N. Library preparation for next generation sequencing: A review of automation strategies. Biotechnol Adv 2020; 41:107537. [DOI: 10.1016/j.biotechadv.2020.107537] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/27/2020] [Accepted: 03/16/2020] [Indexed: 01/08/2023]
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Smith M, Zuckerman M, Kandanearatchi A, Thompson R, Davenport M. Using next-generation sequencing of microRNAs to identify host and/or pathogen nucleic acid signatures in samples from children with biliary atresia - a pilot study. Access Microbiol 2020; 2:acmi000127. [PMID: 32974591 PMCID: PMC7497833 DOI: 10.1099/acmi.0.000127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 02/24/2020] [Indexed: 12/11/2022] Open
Abstract
Biliary atresia (BA) is a progressive disease affecting infants resulting in inflammatory obliteration and fibrosis of the extra- and intra-hepatic biliary tree. BA may be grouped into type 1 isolated; type 2 syndromic, where other congenital malformations may be present; type 3 cystic BA, where there is cyst formation within an otherwise obliterated biliary tree; and cytomegalovirus-associated BA. The cause of BA is unclear, with immune dysregulation, inflammation and infection, particularly with cytomegalovirus (CMV), all implicated. In this study a total of 50/67 samples were tested for CMV DNA using quantitative real-time PCR. Ten liver tissue and 8 bile samples from 10 patients representing the range of BA types were also analysed by next-generation sequencing. CMV DNA was found in 8/50 (16 %) patients and a total of 265 differentially expressed microRNAs were identified. No statistically significant differences between the various types of BA were found. However, differences were identified in the expression patterns of 110 microRNAs in bile and liver tissue samples (P<0.05). A small number of bacterial and viral sequences were found, although their relevance to BA remains to be determined. No direct evidence of viral causes of BA were found, although clear evidence of microRNAs associated with hepatocyte and cholangiocyte differentiation together with fibrosis and inflammation were identified. These include miR-30 and the miR-23 cluster (liver and bile duct development) and miR-29, miR-483, miR-181, miR-199 and miR-200 (inflammation and fibrosis).
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Affiliation(s)
- Melvyn Smith
- Viapath Analytics, South London Specialist Virology Centre, Denmark Hill, London
| | - Mark Zuckerman
- Viapath Analytics, South London Specialist Virology Centre, Denmark Hill, London
| | | | - Richard Thompson
- Institute of Liver Studies and Paediatric Liver Services, Denmark Hill, London
| | - Mark Davenport
- Department of Paediatric Surgery, King's College Hospital NHS Foundation Trust, Denmark Hill, London SE5 9RS
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Abstract
Background Varicella is normally a self-limited childhood disease caused by varicella-zoster virus infection. However, it sometimes causes severe diseases, especially in immunocompromised individuals. We report a case of severe varicella in a young woman. Case presentation A 19-year-old woman presented to the emergency department with abdominal pain and a rash after taking methylprednisolone for 2 weeks for systemic lupus erythematosis. The laboratory data showed leukocytosis, thrombocytopenia, an elevated level of the liver transaminases and disseminated intravascular coagulation. Computed tomography of the abdomen revealed multiple air-fluid levels in the intestines. Hemorrhagic varicella was considered and antiviral therapy as well as immunoglobin were applied. Her condition deteriorated and she eventually died due to multi-organ failure and refractory shock. Next-generation sequencing performed on fluid from an unroofed vesicle confirmed the diagnosis of varicella. Conclusion In its severe form, VZV infection can be fatal, especially in immunocompromised patients. Hemorrhagic varicella can be misdiagnosed by clinicians because of unfamiliar with the disease, although it is associated with a high mortality rate. In patients with suspected hemorrhagic varicella infection, antiviral therapies along with supportive treatment need to be initiated as soon as possible in order to minimize the case fatality rate.
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Affiliation(s)
- Wei Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Qiao-Ling Ruan
- Department of Infectious Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Fang Yan
- Department of Dermatology, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Yue-Kai Hu
- Department of Infectious Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China.
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Ahmed A, Dietrich I, LaBeaud AD, Lindsay SW, Musa A, Weaver SC. Risks and Challenges of Arboviral Diseases in Sudan: The Urgent Need for Actions. Viruses 2020; 12:E81. [PMID: 31936607 PMCID: PMC7019415 DOI: 10.3390/v12010081] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/07/2020] [Accepted: 01/07/2020] [Indexed: 12/16/2022] Open
Abstract
The risk of emergence and/or re-emergence of arthropod-borne viral (arboviral) infections is rapidly growing worldwide, particularly in Africa. The burden of arboviral infections and diseases is not well scrutinized because of the inefficient surveillance systems in endemic countries. Furthermore, the health systems are fully occupied by the burden of other co-existing febrile illnesses, especially malaria. In this review we summarize the epidemiology and risk factors associated with the major human arboviral diseases and highlight the gap in knowledge, research, and control in Sudan. Published data in English up to March 2019 were reviewed and are discussed to identify the risks and challenges for the control of arboviruses in the country. In addition, the lack of suitable diagnostic tools such as viral genome sequencing, and the urgent need for establishing a genomic database of the circulating viruses and potential sources of entry are discussed. Moreover, the research and healthcare gaps and global health threats are analyzed, and suggestions for developing strategic health policy for the prevention and control of arboviruses with focus on building the local diagnostic and research capacity and establishing an early warning surveillance system for the early detection and containment of arboviral epidemics are offered.
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Affiliation(s)
- Ayman Ahmed
- Institute of Endemic Diseases, University of Khartoum, Khartoum 11111, Sudan
- Institute for Human Infections and Immunity, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77755, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX 77755, USA
| | | | | | - Steve W. Lindsay
- Department of Biosciences, Durham University, Durham DH1 3LE, UK
| | - Ahmed Musa
- Institute of Endemic Diseases, University of Khartoum, Khartoum 11111, Sudan
| | - Scott C. Weaver
- Institute for Human Infections and Immunity, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77755, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX 77755, USA
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Kaszab E, Doszpoly A, Lanave G, Verma A, Bányai K, Malik YS, Marton S. Metagenomics revealing new virus species in farm and pet animals and aquaculture. Genomics and Biotechnological Advances in Veterinary, Poultry, and Fisheries 2020. [PMCID: PMC7149329 DOI: 10.1016/b978-0-12-816352-8.00002-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Viral metagenomics is slowly taking over the traditional and widely used molecular techniques for the investigation of pathogenic viruses responsible for illness and inflicting great economic burden on the farm animal industry. Owing to the continued improvements in sequencing technologies and the dramatic reduction of per base costs of sequencing the use of next generation sequencing have been key factors in this progress. Discoveries linked to viral metagenomics are expected to be beneficial to the field of veterinary medicine starting from the development of better diagnostic assays to the design of new subunit vaccines with minimal investments. With these achievements the research has taken a giant leap even toward the better healthcare of animals and, as a result, the animal sector could be growing at an unprecedented pace.
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Archakov AI, Aseev AL, Bykov VA, Grigoriev AI, Govorun VM, Ilgisonis EV, Ivanov YD, Ivanov VT, Kiseleva OI, Kopylov AT, Lisitsa AV, Mazurenko SN, Makarov AA, Naryzhny SN, Pleshakova TO, Ponomarenko EA, Poverennaya EV, Pyatnitskii MA, Sagdeev RZ, Skryabin KG, Zgoda VG. Challenges of the Human Proteome Project: 10-Year Experience of the Russian Consortium. J Proteome Res 2019; 18:4206-4214. [PMID: 31599598 DOI: 10.1021/acs.jproteome.9b00358] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This manuscript collects all the efforts of the Russian Consortium, bottlenecks revealed in the course of the C-HPP realization, and ways of their overcoming. One of the main bottlenecks in the C-HPP is the insufficient sensitivity of proteomic technologies, hampering the detection of low- and ultralow-copy number proteins forming the "dark part" of the human proteome. In the frame of MP-Challenge, to increase proteome coverage we suggest an experimental workflow based on a combination of shotgun technology and selected reaction monitoring with two-dimensional alkaline fractionation. Further, to detect proteins that cannot be identified by such technologies, nanotechnologies such as combined atomic force microscopy with molecular fishing and/or nanowire detection may be useful. These technologies provide a powerful tool for single molecule analysis, by analogy with nanopore sequencing during genome analysis. To systematically analyze the functional features of some proteins (CP50 Challenge), we created a mathematical model that predicts the number of proteins differing in amino acid sequence: proteoforms. According to our data, we should expect about 100 000 different proteoforms in the liver tissue and a little more in the HepG2 cell line. The variety of proteins forming the whole human proteome significantly exceeds these results due to post-translational modifications (PTMs). As PTMs determine the functional specificity of the protein, we propose using a combination of gene-centric transcriptome-proteomic analysis with preliminary fractionation by two-dimensional electrophoresis to identify chemically modified proteoforms. Despite the complexity of the proposed solutions, such integrative approaches could be fruitful for MP50 and CP50 Challenges in the framework of the C-HPP.
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Affiliation(s)
| | | | | | | | - Vadim M Govorun
- Federal Research and Clinical Center of Physical-Chemical Medicine , Moscow 119435 , Russia
| | | | - Yuri D Ivanov
- Institute of Biomedical Chemistry , Moscow 119435 , Russia
| | - Vadim T Ivanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow 117997 , Russia
| | | | | | | | - Sergey N Mazurenko
- Joint Institute for Nuclear Research , Dubna, Moscow region 141980 , Russia
| | | | | | | | | | | | | | - Renad Z Sagdeev
- International Tomography Center , Novosibirsk 630090 , Russia
| | - Konstantin G Skryabin
- The Federal Research Centre "Fundamentals of Biotechnology" , Moscow 119071 , Russia
| | - Victor G Zgoda
- Institute of Biomedical Chemistry , Moscow 119435 , Russia
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Wang S, Chen Y, Wang D, Wu Y, Zhao D, Zhang J, Xie H, Gong Y, Sun R, Nie X, Jiang H, Zhang J, Li W, Liu G, Li X, Huang K, Huang Y, Li Y, Guan H, Pan S, Hu Y. The Feasibility of Metagenomic Next-Generation Sequencing to Identify Pathogens Causing Tuberculous Meningitis in Cerebrospinal Fluid. Front Microbiol 2019; 10:1993. [PMID: 31551954 PMCID: PMC6733977 DOI: 10.3389/fmicb.2019.01993] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 08/14/2019] [Indexed: 01/22/2023] Open
Abstract
Purpose The application of metagenomic next-generation sequencing (mNGS) in the diagnosis of tuberculous meningitis (TBM) remains poorly characterized. Here, we retrospectively analyzed data from patients with TBM who had taken both mNGS and conventional tests including culture of Mycobacterium tuberculosis (MTB), polymerase chain reaction (PCR) and acid-fast bacillus (AFB) stain, and the sensitivity and specificity of these methods were compared. Methods We retrospectively recruited TBM patients admitted to the hospital between December 2015 and October 2018. The first collection of cerebrospinal fluid (CSF) samples underwent both mNGS and conventional tests. In addition, patients with bacterial/cryptococcal meningitis or viral meningoencephalitis were mNGS positive controls, and a patient with auto-immune encephalitis was an mNGS negative control. Results Twenty three TBM patients were classified as 12 definite and 11 clinical diagnoses, which were based on clinical manifestations, pathogen evidence, CSF parameters, brain imaging, and treatment response. The mNGS method identified sequences of Mycobacterium tuberculosis complex (MBTC) from 18 samples (18/23, 78.26%). In patients with definite TBM, the sensitivity of mNGS, AFB, PCR, and culture to detect MTB in the first CSF samples were 66.67, 33.33, 25, and 8.33%, respectively. The specificity of each method was 100%. Among the four negative mNGS cases (4/23, 17.39%), three turned out positive by repeated AFB stain. The agreement of mNGS with the total of conventional methods was 44.44% (8/18). Combination of mNGS and conventional methods increased the detection rate to 95.65%. One patient was diagnosed as complex of TBM and cryptococcal meningitis, in which AFB stain and cryptococcal antigen enzyme immunoassay were positive and the DNA of Cryptococcus neoformans was detected by mNGS. Conclusion Our study indicates that mNGS is an alternative method to detect the presence of mycobacterial DNA in CSF samples from patients with TBM and deserves to be applied as a front-line CSF test.
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Affiliation(s)
- Shengnan Wang
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yingli Chen
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Dongmei Wang
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yongming Wu
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Deqiang Zhao
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jianzhao Zhang
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Huifang Xie
- Department of Neurology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yanping Gong
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Ruixue Sun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Xifang Nie
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Haishan Jiang
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jian Zhang
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Wei Li
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Guanghui Liu
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xuan Li
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Kaibin Huang
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yingwei Huang
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yongjun Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Hongzhi Guan
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Suyue Pan
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yafang Hu
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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48
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Zhang Y, Hong K, Zou Y, Bu H. Rapid detection of human herpes virus by next-generation sequencing in a patient with encephalitis. Virol J 2019; 16:104. [PMID: 31419985 PMCID: PMC6697991 DOI: 10.1186/s12985-019-1205-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/18/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The inflammatory or non-inflammatory changes caused by the virus entering the nervous system and related tissues are central nervous system virus infections. Viral infection is a common infectious disease of the central nervous system, of which herpes simplex virus encephalitis is the most common. However, conventional laboratory techniques to detect an infectious agent are difficult to achieve etiological diagnosis. CASE PRESENTATION Here we present a patient with severe and progressive encephalitis, requiring diagnosis of the specific pathogen to guide clinical treatments. CONCLUSIONS Application of next-generation sequencing provided a quick and definite diagnosis of the etiology of encephalitis and enabled our patient to be treated appropriately.
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Affiliation(s)
- Yu Zhang
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang City, Hebei Province, China
| | - Kun Hong
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang City, Hebei Province, China
| | - Yueli Zou
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang City, Hebei Province, China
| | - Hui Bu
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang City, Hebei Province, China.
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Carrasco P, Inostroza C, Didier M, Godoy M, Holt CL, Tabak J, Loftus A. Optimizing DNA recovery and forensic typing of degraded blood and dental remains using a specialized extraction method, comprehensive qPCR sample characterization, and massively parallel sequencing. Int J Legal Med 2019; 134:79-91. [PMID: 31414202 PMCID: PMC6949324 DOI: 10.1007/s00414-019-02124-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/10/2019] [Indexed: 12/30/2022]
Abstract
Human dental remains encountered in criminal casework evidence, missing person cases, or mass disaster tragedies provide a valuable sample source for DNA typing when suitable soft tissue is unavailable. Using traditional methods, teeth samples can be challenging to process, resulting in low-quantity and/or quality nuclear DNA and insufficient profiles for comparisons. This study examines the performance of a three-part nuclear DNA analysis workflow for teeth samples based on (1) improved dental tissue recovery using the Dental Forensic Kit (DFKMR) (Universidad de los Andes) and DNA extraction with QuickExtract™ FFPE DNA Extraction Kit (Lucigen®), (2) quantification with InnoQuant® HY (InnoGenomics Technologies) for sensitive assessment of total human and male DNA quantity/quality, and (3) massively parallel sequencing for simultaneous genotyping of 231 short tandem repeat (STR) and single-nucleotide polymorphism (SNP) markers with the ForenSeq® DNA Signature Prep Kit (Verogen, Inc.). Initial evaluation of artificially degraded blood samples (n = 10) achieved highly sensitive and informative quantification results with InnoQuant® HY, enabling successful first pass genotyping with the MiSeq FGx® System. Twenty-three STR alleles (out of 85) and 70 identity informative SNP loci (out of 94) were recovered from two pg total long target DNA input (0.86 ng total short target input) and an InnoQuant degradation index (DI) of 460 (severely degraded). The three-part workflow was subsequently applied to teeth samples (dental pulp, root cement tissues; n = 13) with postmortem intervals (PMI) of the teeth ranging from 8 days to approximately 6 months. Informative SNP and STR DNA profiles were obtained, to include 78 STR alleles and 85 identity informative SNP loci typed (of 94 total SNP targets) in a 1 month, four-day PMI root cement sample with one pg total long target DNA input and a DI of 76. These data indicate successful performance of the proposed workflow from degraded DNA from teeth samples.
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Affiliation(s)
- Patricio Carrasco
- Universidad de los Andes, Mons. Álvaro del Portillo 12.455, Las Condes, Santiago Chile
| | - Carolina Inostroza
- Universidad de los Andes, Mons. Álvaro del Portillo 12.455, Las Condes, Santiago Chile
| | - Meghan Didier
- Verogen, Inc., 11111 Flintkote Avenue, San Diego, CA 92121 USA
| | - Marianela Godoy
- Universidad de los Andes, Mons. Álvaro del Portillo 12.455, Las Condes, Santiago Chile
| | - Cydne L. Holt
- Verogen, Inc., 11111 Flintkote Avenue, San Diego, CA 92121 USA
| | - Jonathan Tabak
- Verogen, Inc., 11111 Flintkote Avenue, San Diego, CA 92121 USA
| | - Andrew Loftus
- InnoGenomics Technologies, LLC, 1441 Canal Street, New Orleans, LA 70112 USA
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50
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Abstract
PURPOSE OF REVIEW This article reviews the spectrum of neurologic disease associated with human herpesvirus infections. RECENT FINDINGS As more patients are becoming therapeutically immunosuppressed, human herpesvirus infections are increasingly common. Historically, infections with human herpesviruses were described as temporal lobe encephalitis caused by herpes simplex virus type 1 or type 2. More recently, however, additional pathogens, such as varicella-zoster virus, Epstein-Barr virus, cytomegalovirus, and human herpesvirus 6 have been identified to cause serious neurologic infections. As literature emerges, clinical presentations of herpesvirus infections have taken on many new forms, becoming heterogeneous and involving nearly every location along the neuraxis. Advanced diagnostic methods are now available for each specific pathogen in the herpesvirus family. As data emerge on viral resistance to conventional therapies, newer antiviral medications must be considered. SUMMARY Infections from the herpesvirus family can have devastating neurologic outcomes without prompt and appropriate treatment. Clinical recognition of symptoms and appropriate advanced testing are necessary to correctly identify the infectious etiology. Knowledge of secondary neurologic complications of disease is equally important to prevent additional morbidity and mortality. This article discusses infections of the central and peripheral nervous systems caused by herpes simplex virus type 1 and type 2, varicella-zoster virus, Epstein-Barr virus, cytomegalovirus, and human herpesvirus 6. The pathophysiology, epidemiology, clinical presentations of disease, diagnostic investigations, imaging characteristics, and treatment for each infectious etiology are discussed in detail.
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