High throughput sequencing for the detection and characterization of RNA viruses

AH Fitzpatrick, A Rupnik, H O'Shea, F Crispie… - Frontiers in …, 2021 - frontiersin.org
This review aims to assess and recommend approaches for targeted and agnostic High
Throughput Sequencing of RNA viruses in a variety of sample matrices. HTS also referred to …

Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome

N Sandybayev, V Beloussov, V Strochkov… - Microorganisms, 2022 - mdpi.com
The COVID-19 pandemic and heightened perception of the risk of emerging viral infections
have boosted the efforts to better understand the virome or complete repertoire of viruses in …

Insights into the microbiome of breast implants and periprosthetic tissue in breast implant-associated anaplastic large cell lymphoma

JN Walker, BM Hanson, CL Pinkner, SR Simar… - Scientific reports, 2019 - nature.com
Though rare, breast implant-associated anaplastic large cell lymphoma (BIA-ALCL), a
CD30+ T-cell lymphoma associated with textured breast implants, has adversely impacted …

Recentrifuge: Robust comparative analysis and contamination removal for metagenomics

JM Martí - PLoS computational biology, 2019 - journals.plos.org
Metagenomic sequencing is becoming widespread in biomedical and environmental
research, and the pace is increasing even more thanks to nanopore sequencing. With a …

Quality control implementation for universal characterization of DNA and RNA viruses in clinical respiratory samples using single metagenomic next-generation …

A Bal, M Pichon, C Picard, JS Casalegno… - BMC infectious …, 2018 - Springer
Background In recent years, metagenomic Next-Generation Sequencing (mNGS) has
increasingly been used for an accurate assumption-free virological diagnosis. However, the …

Clinical metagenomics for infectious corneal ulcers: Rags to riches?

L Ung, PJM Bispo, T Doan, RN Van Gelder… - The ocular …, 2020 - Elsevier
The emergence of clinical metagenomics as an unbiased, hypothesis-free approach to
diagnostic testing is set to fundamentally alter the way infectious diseases are detected …

Batch effects in a multiyear sequencing study: False biological trends due to changes in read lengths

DM Leigh, HEL Lischer, C Grossen… - Molecular Ecology …, 2018 - Wiley Online Library
High‐throughput sequencing is a powerful tool, but suffers biases and errors that must be
accounted for to prevent false biological conclusions. Such errors include batch effects; …

Comparison of nucleic acid extraction methods for a viral metagenomics analysis of respiratory viruses

M Sabatier, A Bal, G Destras, H Regue, G Quéromès… - Microorganisms, 2020 - mdpi.com
Viral metagenomics next-generation sequencing (mNGS) is increasingly being used to
characterize the human virome. The impact of viral nucleic extraction on virome profiling has …

A Case of Successful Treatment of Recurrent Urinary Tract Infection by Extended-Spectrum β-Lactamase Producing Klebsiella pneumoniae Using Oral Lyophilized …

N Bier, B Hanson, ZD Jiang, HL DuPont… - Microbial Drug …, 2023 - liebertpub.com
Recurrent urinary tract infections (UTIs) are a challenging clinical entity that can be
frustrating for patient and physician alike. Repeated rounds of antibiotics can select for …

[HTML][HTML] Blood virome research in myalgic encephalomyelitis/chronic fatigue syndrome: challenges and opportunities

D Obraitis, D Li - Current Opinion in Virology, 2024 - Elsevier
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating disease with
a complex clinical presentation and an unknown etiology. Various viral infections have been …