scholarly journals Coinfections of Zika and Chikungunya Viruses in Bahia, Brazil, Identified by Metagenomic Next-Generation Sequencing

2016 ◽  
Vol 54 (9) ◽  
pp. 2348-2353 ◽  
Author(s):  
Silvia I. Sardi ◽  
Sneha Somasekar ◽  
Samia N. Naccache ◽  
Antonio C. Bandeira ◽  
Laura B. Tauro ◽  
...  
Keyword(s):  
Differential Diagnosis ◽  
Next Generation Sequencing ◽  
Chikungunya Virus ◽  
Clinical Presentation ◽  
Febrile Illness ◽  
Acute Febrile Illness ◽  
Next Generation ◽  
Zikv Infection ◽  
Viral Pathogens ◽  
Generation Sequencing

Metagenomic next-generation sequencing (mNGS) of samples from 15 patients with documented Zika virus (ZIKV) infection in Bahia, Brazil, from April 2015 to January 2016 identified coinfections with chikungunya virus (CHIKV) in 2 of 15 ZIKV-positive cases by PCR (13.3%). While generally nonspecific, the clinical presentation corresponding to these two CHIKV/ZIKV coinfections reflected infection by the virus present at a higher titer. Aside from CHIKV and ZIKV, coinfections of other viral pathogens were not detected. The mNGS approach is promising for differential diagnosis of acute febrile illness and identification of coinfections, although targeted arbovirus screening may be sufficient in the current ZIKV outbreak setting.

scholarly journals Next Generation Sequencing Reveals Regulation of Distinct Aedes microRNAs during Chikungunya Virus Development

2014 ◽  
Vol 8 (1) ◽  
pp. e2616 ◽  
Author(s):  
Jatin Shrinet ◽  
Shanu Jain ◽  
Jaspreet Jain ◽  
Raj K. Bhatnagar ◽  
Sujatha Sunil
Keyword(s):  
Next Generation Sequencing ◽  
Chikungunya Virus ◽  
Next Generation ◽  
Generation Sequencing

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 Metagenomic next-generation sequencing of samples from pediatric febrile illness in Tororo, Uganda

PLoS ONE ◽  
2019 ◽  
Vol 14 (6) ◽  
pp. e0218318 ◽  
Author(s):  
Akshaya Ramesh ◽  
Sara Nakielny ◽  
Jennifer Hsu ◽  
Mary Kyohere ◽  
Oswald Byaruhanga ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Febrile Illness ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Etiology of fever in Ugandan children: identification of microbial pathogens using metagenomic next-generation sequencing and IDseq, a platform for unbiased metagenomic analysis

2018 ◽  
Author(s):  
Akshaya Ramesh ◽  
Sara Nakielny ◽  
Jennifer Hsu ◽  
Mary Kyohere ◽  
Oswald Byaruhanga ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Pilot Study ◽  
Infectious Diseases ◽  
Parvovirus B19 ◽  
Human Herpesvirus ◽  
Febrile Illness ◽  
Microbial Pathogens ◽  
Next Generation ◽  
Syncytial Virus ◽  
Generation Sequencing

AbstractBackgroundFebrile illness is a major burden in African children, and non-malarial causes of fever are uncertain. We built and employed IDseq, a cloud-based, open access, bioinformatics platform and service to identify microbes from metagenomic next-generation sequencing of tissue samples. In this pilot study, we evaluated blood, nasopharyngeal, and stool specimens from 94 children (aged 2-54 months) with febrile illness admitted to Tororo District Hospital, Uganda.ResultsThe most common pathogens identified were Plasmodium falciparum (51.1% of samples) and parvovirus B19 (4.4%) from blood; human rhinoviruses A and C (40%), respiratory syncytial virus (10%), and human herpesvirus 5 (10%) from nasopharyngeal swabs; and rotavirus A (50% of those with diarrhea) from stool. Among other potential pathogens, we identified one novel orthobunyavirus, tentatively named Nyangole virus, from the blood of a child diagnosed with malaria and pneumonia, and Bwamba orthobunyavirus in the nasopharynx of a child with rash and sepsis. We also identified two novel human rhinovirus C species.ConclusionsThis exploratory pilot study demonstrates the utility of mNGS and the IDseq platform for defining the molecular landscape of febrile infectious diseases in resource limited areas. These methods, supported by a robust data analysis and sharing platform, offer a new tool for the surveillance, diagnosis, and ultimately treatment and prevention of infectious diseases.

Combined biochemical and targeted-next generation sequencing panel for differential diagnosis of inherited myopathies

2020 ◽  
Vol 129 (2) ◽  
pp. S85
Author(s):  
David C. Kasper ◽  
Thomas P. Mechtler ◽  
Petra Oliva ◽  
Markus Schwarz ◽  
Thomas Wiesinger ◽  
...  
Keyword(s):  
Differential Diagnosis ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
Targeted Next Generation Sequencing ◽  
Generation Sequencing

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.

Intraarticular Inflammatory Myofibroblastic Tumor of the Left Knee With ALK-CARS Fusion Detected With Archer Fusionplex Sarcoma NGS Panel: Case Report and Literature Review

2020 ◽  
pp. 106689692093777
Author(s):  
Janet Pineda-Díaz ◽  
Irit Solar ◽  
Dov Hershkovitz ◽  
Ido Drukman ◽  
Osnat Sher
Keyword(s):  
Differential Diagnosis ◽  
Next Generation Sequencing ◽  
Inflammatory Myofibroblastic Tumor ◽  
Left Knee ◽  
Added Value ◽  
Nodular Fasciitis ◽  
Next Generation ◽  
Biological Potential ◽  
Orthopedic Oncology ◽  
Generation Sequencing

Inflammatory myofibroblastic tumor (IMT) is a lesion of intermediate biological potential with local recurrences and rare metastases found in multiple anatomical locations. We present a case of a pure intraarticular IMT of the knee, a location that has not been previously documented, with genetic confirmation of ALK-CARS fusion detected with next-generation sequencing. A 20-year-old healthy male was admitted to the orthopedic oncology department due to several months of pain and restriction in movement of his left knee. On magnetic resonance imaging, multiple intraarticular nodular lesions were seen. The patient underwent 2 synovectomies within the course of 1 year. The initial biopsy was interpreted as nodular fasciitis. The second biopsy revealed exuberant tissue displaying compact fascicles of spindle cells intermixed with myxoid areas in a background of inflammatory cells, highly suggestive for IMT. Due to the unusual intraarticular location, equivocal ALK immunostaining and the differential diagnosis with nodular fasciitis, we performed targeted next-generation sequencing using Archer FusionPlex Sarcoma panel, which can identify multiple fusions in a single assay. An ALK-CARS fusion was found, supporting the diagnosis of IMT. This report emphasizes the added value of broad molecular analysis in cases with unusual clinical presentation, equivocal immunohistochemistry, and a wide differential diagnosis.

scholarly journals Clinical and genetic spectrum of monogenic liver diseases in children diagnosed using next generation sequencing: a single centre experience from Kerala

2021 ◽  
Author(s):  
Prasanth Kunjan Nadar Sobhan ◽  
Bindu Sarojam ◽  
Sankar Vaikom Hariharan
Keyword(s):  
Liver Disease ◽  
Next Generation Sequencing ◽  
Liver Diseases ◽  
Clinical Presentation ◽  
Genetic Disorder ◽  
Tertiary Care ◽  
Chronic Liver ◽  
Next Generation ◽  
Infantile Cholestasis ◽  
Generation Sequencing

Background: Children presenting with chronic liver disease have a high likelihood of an underlying genetic disorder. There is a delay in establishing a diagnosis of monogenic liver diseases if relied on typical clinical phenotypes and conventional laboratory investigations or imaging studies alone. Early diagnosis improves patient outcome through timely and adequate therapy.Methods: This study retrospectively analyzed the clinical and genetic spectra of monogenic liver disease in children diagnosed using next-generation sequencing (NGS) in a tertiary care teaching hospital in Kerala. Patients were classified into five groups according to their clinical presentation: neonatal/infantile cholestasis, hepatomegaly/ hepatosplenomegaly, progressive cholestasis (beyond infancy), acute liver failure and decompensated chronic liver disease.Results: There were 31 children enrolled, 14 (45.16%) males and 17 (54.84%) females. The median age at genetic diagnosis was 25.74 months. NGS identified 20 distinct genes related to varying clinical presentation. Six genes were identified in Group A, nine genes were identified in Group B, three genes were identified in Group C and two genes each in Group D and E. JAG1, ABCB4 and PYL1 (13 % each) were the top three genes related to monogenic liver disease in this study.Conclusions: Patients with hepatomegaly or hepatosplenomegaly constituted the major clinical presentation of genetic disorders followed by neonatal/infantile cholestasis in our study. Genetic cholestatic disorders and glycogen storage disorders were the most common monogenic liver diseases. NGS has an important role in the diagnosis of monogenic liver disease in children and can facilitate early medical treatment and predict the prognosis.  

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