scholarly journals Application of Next Generation Sequencing for Diagnostic Testing of Tree Fruit Viruses and Viroids

Plant Disease ◽  
2017 ◽  
Vol 101 (8) ◽  
pp. 1489-1499 ◽  
Author(s):  
M. Rott ◽  
Y. Xiang ◽  
I. Boyes ◽  
M. Belton ◽  
H. Saeed ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Diagnostic Testing ◽  
Virus Detection ◽  
Plant Viruses ◽  
Next Generation ◽  
Viral Pathogens ◽  
Plant Virus Detection ◽  
Biological Indexing ◽  
Tree Fruit ◽  
Generation Sequencing

Conventional detection of viruses and virus-like diseases of plants is accomplished using a combination of molecular, serological, and biological indexing. These are the primary tools used by plant virologists to monitor and ensure trees are free of known viral pathogens. The biological indexing assay, or bioassay, is considered to be the “gold standard” as it is the only method of the three that can detect new, uncharacterized, or poorly characterized viral disease agents. Unfortunately, this method is also the most labor intensive and can take up to three years to complete. Next generation sequencing (NGS) is a technology with rapidly expanding possibilities including potential applications for the detection of plant viruses. In this study, comparisons are made between tree fruit testing by conventional and NGS methods, to demonstrate the efficacy of NGS. A comparison of 178 infected trees, many infected with several viral pathogens, demonstrated that conventional and NGS were equally capable of detecting known viruses and viroids. Comparable results were obtained for 170 of 178 of the specimens. Of the remaining eight specimens, some discrepancies were observed between viruses detected by the two methods, representing less than 5% of the specimens. NGS was further demonstrated to be equal or superior for the detection of new or poorly characterized viruses when compared with a conventional bioassay. These results validated both the effectiveness of conventional virus testing methods and the use of NGS as an additional or alternative method for plant virus detection.

scholarly journals Report of the second international conference on next generation sequencing for adventitious virus detection in biologics for humans and animals

Biologicals ◽  
2020 ◽  
Vol 67 ◽  
pp. 94-111
Author(s):  
Arifa S. Khan ◽  
Johannes Blümel ◽  
Dieter Deforce ◽  
Marion F. Gruber ◽  
Carmen Jungbäck ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Virus Detection ◽  
Next Generation ◽  
International Conference ◽  
Generation Sequencing ◽  
Second International

scholarly journals Unveiling Viruses Associated with Gastroenteritis Using a Metagenomics Approach

Viruses ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 1432
Author(s):  
Xavier Fernandez-Cassi ◽  
Sandra Martínez-Puchol ◽  
Marcelle Silva-Sales ◽  
Thais Cornejo ◽  
Rosa Bartolome ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Acute Gastroenteritis ◽  
Clinical Analysis ◽  
Viral Metagenomics ◽  
Next Generation ◽  
Sequencing Data ◽  
Viral Pathogens ◽  
Viral Pathogen ◽  
Infectious Gastroenteritis ◽  
Generation Sequencing

Acute infectious gastroenteritis is an important illness worldwide, especially on children, with viruses accounting for approximately 70% of the acute cases. A high number of these cases have an unknown etiological agent and the rise of next generation sequencing technologies has opened new opportunities for viral pathogen detection and discovery. Viral metagenomics in routine clinical settings has the potential to identify unexpected or novel variants of viral pathogens that cause gastroenteritis. In this study, 124 samples from acute gastroenteritis patients from 2012–2014 previously tested negative for common gastroenteritis pathogens were pooled by age and analyzed by next generation sequencing (NGS) to elucidate unidentified viral infections. The most abundant sequences detected potentially associated to acute gastroenteritis were from Astroviridae and Caliciviridae families, with the detection of norovirus GIV and sapoviruses. Lower number of contigs associated to rotaviruses were detected. As expected, other viruses that may be associated to gastroenteritis but also produce persistent infections in the gut were identified including several Picornaviridae members (EV, parechoviruses, cardioviruses) and adenoviruses. According to the sequencing data, astroviruses, sapoviruses and NoV GIV should be added to the list of viral pathogens screened in routine clinical analysis.

scholarly journals Assessment of the incorporation of CNV surveillance into gene panel next-generation sequencing testing for inherited retinal diseases

2017 ◽  
Vol 55 (2) ◽  
pp. 114-121 ◽  
Author(s):  
Jamie M Ellingford ◽  
Bradley Horn ◽  
Christopher Campbell ◽  
Gavin Arno ◽  
Stephanie Barton ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Diagnostic Yield ◽  
Diagnostic Testing ◽  
Read Depth ◽  
Gene Panel ◽  
Genomic Variation ◽  
Next Generation ◽  
Diagnostic Laboratory ◽  
Inherited Retinal Dystrophies ◽  
Generation Sequencing

BackgroundDiagnostic use of gene panel next-generation sequencing (NGS) techniques is commonplace for individuals with inherited retinal dystrophies (IRDs), a highly genetically heterogeneous group of disorders. However, these techniques have often failed to capture the complete spectrum of genomic variation causing IRD, including CNVs. This study assessed the applicability of introducing CNV surveillance into first-tier diagnostic gene panel NGS services for IRD.MethodsThree read-depth algorithms were applied to gene panel NGS data sets for 550 referred individuals, and informatics strategies used for quality assurance and CNV filtering. CNV events were confirmed and reported to referring clinicians through an accredited diagnostic laboratory.ResultsWe confirmed the presence of 33 deletions and 11 duplications, determining these findings to contribute to the confirmed or provisional molecular diagnosis of IRD for 25 individuals. We show that at least 7% of individuals referred for diagnostic testing for IRD have a CNV within genes relevant to their clinical diagnosis, and determined a positive predictive value of 79% for the employed CNV filtering techniques.ConclusionIncorporation of CNV analysis increases diagnostic yield of gene panel NGS diagnostic tests for IRD, increases clarity in diagnostic reporting and expands the spectrum of known disease-causing mutations.

scholarly journals Comparison of Next-Generation Sequencing Versus Biological Indexing for the Optimal Detection of Viral Pathogens in Grapevine

2015 ◽  
Vol 105 (6) ◽  
pp. 758-763 ◽  
Author(s):  
Maher Al Rwahnih ◽  
Steve Daubert ◽  
Deborah Golino ◽  
Christina Islas ◽  
Adib Rowhani
Keyword(s):  
Next Generation Sequencing ◽  
Host Plants ◽  
Next Generation ◽  
Virus Infections ◽  
Laboratory Procedure ◽  
Viral Pathogens ◽  
Dna And Rna ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Propagation Material

A bioassay is routinely used to determine the viral phytosanitary status of commercial grapevine propagation material in many countries around the world. That test is based on the symptoms developed in the field by specific indicator host plants that are graft-inoculated from the vines being tested. We compared the bioassay against next-generation sequencing (NGS) analysis of grapevine material. NGS is a laboratory procedure that catalogs the genomic sequences of the viruses and other pathogens extracted as DNA and RNA from infected vines. NGS analysis was found to be superior to the standard bioassay in detection of viruses of agronomic significance, including virus infections at low titers. NGS was also found to be superior to the bioassay in its comprehensiveness, the speed of its analysis, and for the discovery of novel, uncharacterized viruses.

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