Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients.

MBio
Heba H MostafaPatricia J Simner

Abstract

Metagenomic next-generation sequencing (mNGS) offers an agnostic approach for emerging pathogen detection directly from clinical specimens. In contrast to targeted methods, mNGS also provides valuable information on the composition of the microbiome and might uncover coinfections that may associate with disease progression and impact prognosis. To evaluate the use of mNGS for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and/or other infecting pathogens, we applied direct Oxford Nanopore long-read third-generation metatranscriptomic and metagenomic sequencing. Nasopharyngeal (NP) swab specimens from 50 patients under investigation for CoV disease 2019 (COVID-19) were sequenced, and the data were analyzed by the CosmosID bioinformatics platform. Further, we characterized coinfections and the microbiome associated with a four-point severity index. SARS-CoV-2 was identified in 77.5% (31/40) of samples positive by RT-PCR, correlating with lower cycle threshold (Ct) values and fewer days from symptom onset. At the time of sampling, possible bacterial or viral coinfections were detected in 12.5% of SARS-CoV-2-positive specimens. A decrease in microbial diversity was observed among COVID-19-confirmed patients ...Continue Reading

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Citations

Jan 12, 2021·Journal of Proteome Research·Shalini AggarwalSanjeeva Srivastava
Feb 16, 2021·Oxford Open Immunology·Claire F PearsonEmily E Thornton
Feb 9, 2021·Chemical Engineering Journal·Shariq SulemanTejraj M Aminabhavi
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Feb 14, 2021·Journal of Clinical Microbiology·Melissa Richard-GreenblattLaurel Glaser
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Sep 3, 2021·Nature Immunology·Nikaïa SmithJames P Di Santo

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Methods Mentioned

BETA
bronchoalveolar lavage
reverse transcription-PCR
PCR
nucleic acid extraction

Software Mentioned

Minimap
Minimap2
R
CosmosID
MinKNOW
CosmosID Metagenomics
R package vegan
SAMtools
R package ggplot2
R package ggsignif

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