Clinical metagenomics

CY Chiu, SA Miller - Nature Reviews Genetics, 2019 - nature.com
Clinical metagenomic next-generation sequencing (mNGS), the comprehensive analysis of
microbial and host genetic material (DNA and RNA) in samples from patients, is rapidly …

[HTML][HTML] Next generation and other sequencing technologies in diagnostic microbiology and infectious diseases

EE Hilt, P Ferrieri - Genes, 2022 - mdpi.com
Next-generation sequencing (NGS) technologies have become increasingly available for
use in the clinical microbiology diagnostic environment. There are three main applications of …

Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California

X Deng, W Gu, S Federman, L Du Plessis, OG Pybus… - Science, 2020 - science.org
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2) has spread globally, with> 365,000 cases in …

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

X Deng, A Achari, S Federman, G Yu… - Nature …, 2020 - nature.com
Metagenomic next-generation sequencing (mNGS), the shotgun sequencing of RNA and
DNA from clinical samples, has proved useful for broad-spectrum pathogen detection and …

[HTML][HTML] Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries

M Asplund, KR Kjartansdóttir, S Mollerup… - Clinical Microbiology …, 2019 - Elsevier
Objectives Sample preparation for high-throughput sequencing (HTS) includes treatment
with various laboratory components, potentially carrying viral nucleic acids, the extent of …

A dynamic neural network model for predicting risk of Zika in real time

M Akhtar, MUG Kraemer, LM Gardner - BMC medicine, 2019 - Springer
Abstract Background In 2015, the Zika virus spread from Brazil throughout the Americas,
posing an unprecedented challenge to the public health community. During the epidemic …

Increased interregional virus exchange and nucleotide diversity outline the expansion of chikungunya virus in Brazil

J Xavier, LCJ Alcantara, V Fonseca, M Lima… - Nature …, 2023 - nature.com
The emergence and reemergence of mosquito-borne diseases in Brazil such as yellow
fever, zika, chikungunya, and dengue have had serious impacts on public health. Concerns …

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 …