Viral Pathogens in Clinical Samples by Use of a Metagenomic Approach

2015 ◽  
pp. 719-723
Author(s):  
Jian Yang
Keyword(s):  
Clinical Samples ◽  
Viral Pathogens ◽  
Metagenomic Approach

scholarly journals Unbiased Parallel Detection of Viral Pathogens in Clinical Samples by Use of a Metagenomic Approach

2011 ◽  
Vol 49 (10) ◽  
pp. 3463-3469 ◽  
Author(s):  
J. Yang ◽  
F. Yang ◽  
L. Ren ◽  
Z. Xiong ◽  
Z. Wu ◽  
...  
Keyword(s):  
Clinical Samples ◽  
Viral Pathogens ◽  
Parallel Detection ◽  
Metagenomic Approach

scholarly journals Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples

2021 ◽  
Author(s):  
Jutte J.C. de Vries ◽  
Julianne R. Brown ◽  
Nicole Fischer ◽  
Igor A. Sidorov ◽  
Sofia Morfopoulou ◽  
...  
Keyword(s):  
De Novo ◽  
Respiratory Infections ◽  
Limit Of Detection ◽  
Bioinformatic Analysis ◽  
Clinical Samples ◽  
Mixed Infections ◽  
Metagenomic Sequencing ◽  
User Friendliness ◽  
Viral Pathogens ◽  
Clinical Diagnostic

Metagenomic sequencing is increasingly being used in clinical settings for difficult to diagnose cases. The performance of viral metagenomic protocols relies to a large extent on the bioinformatic analysis. In this study, the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS) initiated a benchmark of metagenomic pipelines currently used in clinical virological laboratories. Methods Metagenomic datasets from 13 clinical samples from patients with encephalitis or viral respiratory infections characterized by PCR were selected. The datasets were analysed with 13 different pipelines currently used in virological diagnostic laboratories of participating ENNGS members. The pipelines and classification tools were: Centrifuge, DAMIAN, DIAMOND, DNASTAR, FEVIR, Genome Detective, Jovian, MetaMIC, MetaMix, One Codex, RIEMS, VirMet, and Taxonomer. Performance, characteristics, clinical use, and user-friendliness of these pipelines were analysed. Results Overall, viral pathogens with high loads were detected by all the evaluated metagenomic pipelines. In contrast, lower abundance pathogens and mixed infections were only detected by 3/13 pipelines, namely DNASTAR, FEVIR, and MetaMix. Overall sensitivity ranged from 80% (10/13) to 100% (13/13 datasets). Overall positive predictive value ranged from 71-100%. The majority of the pipelines classified sequences based on nucleotide similarity (8/13), only a minority used amino acid similarity, and 6 of the 13 pipelines assembled sequences de novo. No clear differences in performance were detected that correlated with these classification approaches. Read counts of target viruses varied between the pipelines over a range of 2-3 log, indicating differences in limit of detection. Conclusion A wide variety of viral metagenomic pipelines is currently used in the participating clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implicating the need for standardization and validation of metagenomic analysis for clinical diagnostic use. Future studies should address the selective effects due to the choice of different reference viral databases.

Simultaneous detection of multiple pathogens by multiplex PCR coupled with DNA biochip hybridization

2017 ◽  
Vol 52 (2) ◽  
pp. 186-195 ◽  
Author(s):  
Hsiang-Yun Tung ◽  
Wei-Chen Chen ◽  
Bor-Rung Ou ◽  
Jan-Ying Yeh ◽  
Yeong-Hsiang Cheng ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Simultaneous Detection ◽  
Clinical Samples ◽  
Single Infection ◽  
Pcr Analysis ◽  
Enzyme Linked Immunosorbent Assay ◽  
Viral Pathogens ◽  
Single Target ◽  
Primer Sets ◽  
Multiple Pathogens

Traditional serological enzyme-linked immunosorbent assay (ELISA) is routinely used to monitor pathogens during quarantine in most animal facilities to prevent possible infection. However, the ELISA platform is a single-target assay, and screening all targeted pathogens is time-consuming and laborious. In this study, to increase sensitivity and to reduce diagnosis time for high-throughput processes, multiplex PCR and DNA biochip techniques were combined to develop a multi-pathogen diagnostic method for use instead of routine ELISA. Eight primer sets were designed for multiplex PCR to detect genes from seven targeted bacterial and viral pathogens. DNA–DNA hybridization was conducted on a biochip following the multiple PCR analysis. Using this method, a total of 24 clinical samples were tested, and the result showed that not only single infection but also co-infection by multi-pathogens can be detected. In conclusion, multiplex PCR coupled with a DNA biochip is an efficient method for detecting multi-pathogens in a reaction. This platform is a useful tool for quarantine services and disease prevention in animal facilities.

scholarly journals Fast Evaluation of Viral Emerging Risks (FEVER): A computational tool for biosurveillance, diagnostics, and mutation typing of emerging viral pathogens

2021 ◽  
Author(s):  
Zachary R Stromberg ◽  
James Theiler ◽  
Brian T Foley ◽  
Adán Myers y Gutiérrez ◽  
Attelia Hollander ◽  
...  
Keyword(s):  
Clinical Samples ◽  
Computational Tool ◽  
Emerging Viruses ◽  
Public Health Importance ◽  
Outbreak Strain ◽  
Viral Pathogens ◽  
Fast Evaluation ◽  
Single Nucleotide ◽  
Viral Pathogen ◽  
Human Immunity

Viral pathogen can rapidly evolve, adapt to novel hosts and evade human immunity. The early detection of emerging viral pathogens through biosurveillance coupled with rapid and accurate diagnostics are required to mitigate global pandemics. However, RNA viruses can mutate rapidly, hampering biosurveillance and diagnostic efforts. Here, we present a novel computational approach called FEVER (Fast Evaluation of Viral Emerging Risks) to design assays that simultaneously accomplish: 1) broad-coverage biosurveillance of an entire class of viruses, 2) accurate diagnosis of an outbreak strain, and 3) mutation typing to detect variants of public health importance. We demonstrate the application of FEVER to generate assays to simultaneously 1) detect sarbecoviruses for biosurveillance; 2) diagnose infections specifically caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); and 3) perform rapid mutation typing of the D614G SARS-CoV-2 spike variant associated with increased pathogen transmissibility. These FEVER assays had a high in silico recall (predicted positive) up to 99.7% of 525,708 SARS-CoV-2 sequences analyzed and displayed sensitivities and specificities as high as 92.4% and 100% respectively when validated in 100 clinical samples. The D614G SARS-CoV-2 spike mutation PCR test was able to identify the single nucleotide identity at position 23,403 in the viral genome of 96.6% SARS-CoV-2 positive samples without the need for sequencing. This study demonstrates the utility of FEVER to design assays for biosurveillance, diagnostics, and mutation typing to rapidly detect, track, and mitigate future outbreaks and pandemics caused by emerging viruses.

Detection and molecular characterisation of feline viruses from swab samples

2021 ◽  
Author(s):  
Hasan Abayli ◽  
Kezban Can-Sahna ◽  
Remziye Ozbek ◽  
Oznur Aslan ◽  
Sukru Tonbak ◽  
...  
Keyword(s):  
Feline Immunodeficiency Virus ◽  
Foamy Virus ◽  
Clinical Samples ◽  
Viral Pathogens ◽  
Leukaemia Virus ◽  
Feline Panleukopenia Virus ◽  
Two Samples ◽  
Immunodeficiency Virus ◽  
Feline Leukaemia Virus ◽  
Subtype A

AbstractFeline calicivirus (FCV), feline alphaherpesvirus 1 (FHV-1) and feline panleukopenia virus (FPLV) as well as retroviral agents such as feline leukaemia virus (FeLV) and feline immunodeficiency virus (FIV) are important viral pathogens of cats. The aim of this study was to detect and characterise FHV-1, FPLV, FeLV, FIV and feline foamy virus (FFV) in oropharyngeal, nasal and conjunctival swabs from 93 cats that had been screened for FCV previously. We wanted to determine the possible risk factors for infection with these viruses. The prevalence was found to be 12.9% for FHV-1 and 9.7% for FPLV. FIV was detected only in two samples and FeLV in one sample, whereas the presence of FFV was not demonstrated in any of the clinical samples. The statistical analysis of the results showed that breed, age, health status, and lifestyle are important predisposing factors to FHV-1 (P < 0.05). For FPLV, only clinically unhealthy animals were found to be at risk (P < 0.001). Sequence analysis revealed that the two FIV-positive samples in this study contained different (A and B) subtypes of the virus. This is the first report on the occurrence of subtype A FIV in Turkey.

scholarly journals Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

2015 ◽  
Vol 7 (1) ◽  
Author(s):  
Alexander L. Greninger ◽  
Samia N. Naccache ◽  
Scot Federman ◽  
Guixia Yu ◽  
Placide Mbala ◽  
...  
Keyword(s):  
Real Time ◽  
Clinical Samples ◽  
Sequencing Analysis ◽  
Nanopore Sequencing ◽  
Viral Pathogens

scholarly journals Improvement of field-deployable metagenomic virus detection by a simple pretreatment method.

2022 ◽  
Author(s):  
Anna S Fomsgaard ◽  
Morten Rasmussen ◽  
Katja Spiess ◽  
Anders Fomsgaard ◽  
Graham J Belsham ◽  
...  
Keyword(s):  
Rna Viruses ◽  
Virus Detection ◽  
Clinical Samples ◽  
Viral Pathogens ◽  
Pretreatment Method ◽  
Genetic Components ◽  
Laboratory Facilities ◽  
Simple Protocol ◽  
Animal Reservoirs ◽  
Generation Sequencing

As both the current COVID-19 pandemic and earlier pandemics have shown, animals are the source for some of the deadliest viral pathogens, which can spread to humans. Therefore, early detection at the point of incidence is crucial to both prevent and understand the threats posed to human health from pathogens in animal reservoirs. Often, the exact genetic nature of these zoonotic pathogens is unknown and advanced laboratory facilities do not exist in most field settings and therefore the development of methods for unbiased metagenomic and point of incidence detection is crucial in order to identify novel viral pathogens in animals with zoonotic and pandemic potential. Here we addressed some of these issues by developing a metagenomic Nanopore next-generation sequencing (mNGS) method for nucleic acids extracted from clinical samples from patients with SARS-CoV-2. To reduce the non-RNA viral genetic components in the samples, we used DNase pretreatment in a syringe followed by filtration and found that these pretreatments increased the number of SARS-CoV2 reads by > 500-fold compared with no pretreatment. The simple protocol, described here, allows for fast (within 6 hours) metagenomic detection of RNA viruses in biological samples exemplified by SARS-CoV-2 detection in clinical throat swabs. This method could also be applied in field settings for point of incidence detection of virus pathogens, thus eliminating the need for transport of infectious samples, cold storage and a specialized laboratory.

scholarly journals Bioinformatics in Disease Research: Brief Introduction

2020 ◽  
Author(s):  
Ratna Prabha ◽  
Rajni Kumari ◽  
D.P. Singh ◽  
Anil Rai ◽  
Sanjay Kumar
Keyword(s):  
Antimicrobial Resistance ◽  
Infectious Diseases ◽  
Clinical Samples ◽  
Pathogen Identification ◽  
Viral Pathogens ◽  
Disease Research ◽  
Bioinformatics Tools ◽  
Disease Biology ◽  
Tools And Techniques

Bioinformatics is a newly emerging discipline playing important role in all biological disciplines including disease research. Bioinformatics tools and techniques are continuously applied in research of infectious diseases. Bioinformatics is assisting in Pathogen identification and typing, identification of pathogenicity and virulence along with detecting and combating antimicrobial resistance. With the use of bioinformatics, many different bacterial and viral pathogens are detected from clinical samples. In this article, we are giving a brief overview about the use and importance of bioinformatics in research of disease biology.

scholarly journals Metagenomic detection and characterisation of multiple viruses in apparently healthy Australian Neophema birds

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Subir Sarker
Keyword(s):  
Evolutionary Relationship ◽  
Human Adenovirus ◽  
Critically Endangered ◽  
Viral Pathogens ◽  
The Past ◽  
Virus Research ◽  
Virus Communities ◽  
Relationship Of ◽  
Metagenomic Approach ◽  
Apparently Healthy

AbstractEmerging viral pathogens are a significant concern, with potential consequences for human, animal and environmental health. Over the past several decades, many novel viruses have been found in animals, including birds, and often pose a significant threat to vulnerable species. However, despite enormous interest in virus research, little is known about virus communities (viromes) in Australian Neophema birds. Therefore, this study was designed to characterise the viromes of Neophema birds and track the evolutionary relationships of recently emerging psittacine siadenovirus F (PsSiAdV-F) circulating in the critically endangered, orange-bellied parrot (OBP, Neophema chrysogaster), using a viral metagenomic approach. This study identified 16 viruses belonging to the families Adenoviridae, Circoviridae, Endornaviridae, Picobirnaviridae and Picornaviridae. In addition, this study demonstrated a potential evolutionary relationship of a PsSiAdV-F sequenced previously from the critically endangered OBP. Strikingly, five adenoviral contigs identified in this study show the highest identities with human adenovirus 2 and human mastadenovirus C. This highlights an important and unexpected aspects of the avian virome and warrants further studies dedicated to this subject. Finally, the findings of this study emphasise the importance of testing birds used for trade or in experimental settings for potential pathogens to prevent the spread of infections.

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