Nanopore metagenomic sequencing for detection and characterization of SARS-CoV-2 in clinical samples

Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic

(2021) Yatish Turakhia et al.   NATURE GENETICS

Next-generation sequencing for cytomegalovirus antiviral resistance genotyping in a clinical virology laboratory

(2021) Samuel D. Chorlton et al.   ANTIVIRAL RESEARCH

Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

(2020) Victor M Corman et al.   Eurosurveillance

First genomic characterization of a Belgian Enterovirus C104 using sequence-independent Nanopore sequencing

(2020) Elke Wollants et al.   INFECTION GENETICS AND EVOLUTION

Reduction of Human DNA Contamination in Clinical Cerebrospinal Fluid Specimens Improves the Sensitivity of Metagenomic Next-Generation Sequencing

(2020) Xin-Chao Ji et al.   JOURNAL OF MOLECULAR NEUROSCIENCE

A new coronavirus associated with human respiratory disease in China

(2020) Fan Wu et al.   NATURE

Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance

(2020) Xianding Deng et al.   Nature Microbiology

Co-infections in people with COVID-19: a systematic review and meta-analysis

(2020) Louise Lansbury et al.   JOURNAL OF INFECTION

Molecular immune pathogenesis and diagnosis of COVID-19

(2020) Xiaowei Li et al.   Journal of Pharmaceutical Analysis

Bacterial co-infection and secondary infection in patients with COVID-19: a living rapid review and meta-analysis

(2020) Bradley J. Langford et al.   CLINICAL MICROBIOLOGY AND INFECTION

ResFinder 4.0 for predictions of phenotypes from genotypes

(2020) Valeria Bortolaia et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Suboptimal Biological Sampling as a Probable Cause of False-Negative COVID-19 Diagnostic Test Results

(2020) Natalie N Kinloch et al.   JOURNAL OF INFECTIOUS DISEASES

Prevalence of Co-infection at the Time of Hospital Admission in COVID-19 Patients, A Multicenter Study

(2020) Sara M Karaba et al.   Open Forum Infectious Diseases

Clinical metagenomics

(2019) Charles Y. Chiu et al.   NATURE REVIEWS GENETICS

Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection

(2019) Themoula Charalampous et al.   NATURE BIOTECHNOLOGY

From the Pipeline to the Bedside: Advances and Challenges in Clinical Metagenomics

(2019) Augusto Dulanto Chiang et al.   JOURNAL OF INFECTIOUS DISEASES

SHERLOCK: nucleic acid detection with CRISPR nucleases

(2019) Max J. Kellner et al.   Nature Protocols

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

Highlighting Clinical Metagenomics for Enhanced Diagnostic Decision-making: A Step Towards Wider Implementation

(2018) Jessica D. Forbes et al.   Computational and Structural Biotechnology Journal

Assessment of metagenomic Nanopore and Illumina sequencing for recovering whole genome sequences of chikungunya and dengue viruses directly from clinical samples

(2018) Liana E. Kafetzopoulou et al.   Eurosurveillance

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

(2017) Joshua Quick et al.   Nature Protocols

Use of Sequence-Independent, Single-Primer-Amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses

(2017) Klaudia Chrzastek et al.   VIROLOGY

Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing

(2016) K. Schmidt et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Alexander L. Greninger et al.   Genome Medicine