Enrichment of SARS-CoV-2 sequence from nasopharyngeal swabs whilst identifying the nasal microbiome
File(s)
Author(s)
Type
Journal Article
Abstract
Simultaneously characterising the genomic information of coronaviruses and the underlying nasal microbiome from a single clinical sample would help characterise infection and disease. Metatranscriptomic approaches can be used to sequence SARS-CoV-2 (and other coronaviruses) and identify mRNAs associated with active transcription in the nasal microbiome. However, given the large sequence background, unenriched metatranscriptomic approaches often do not sequence SARS-CoV-2 to sufficient read and coverage depth to obtain a consensus genome, especially with moderate and low viral loads from clinical samples. In this study, various enrichment methods were assessed to detect SARS-CoV-2, identify lineages and define the nasal microbiome. The methods were underpinned by Oxford Nanopore long-read sequencing and variations of sequence independent single primer amplification (SISPA). The utility of the method(s) was also validated on samples from patients infected seasonal coronaviruses. The feasibility of profiling the nasal microbiome using these enrichment methods was explored. The findings shed light on the performance of different enrichment strategies and their applicability in characterising the composition of the nasal microbiome.
Date Issued
2023-11-25
Date Acceptance
2023-11-18
Citation
Journal of Clinical Virology, 2023, 171
ISSN
1386-6532
Publisher
Elsevier
Start Page
105620
Journal / Book Title
Journal of Clinical Virology
Volume
171
Copyright Statement
© 2023 Published by Elsevier B.V. All rights reserved. This manuscript version is made available under the CC-BY-NC-ND 4.0 license https://creativecommons.org/licenses/by-nc-nd/4.0/
Sponsor
Imperial College Healthcare NHS Trust- BRC Funding
UKRI MRC COVID-19 Rapid Response Call
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/38237303
PII: S1386-6532(23)00243-3
Grant Number
PA5564
MC_PC19025
Subjects
Clinical sample
Humans coronaviruses
Microbiome
Nanopore
SARS-CoV-2
Sequencing
Publication Status
Published
Coverage Spatial
Netherlands
Article Number
105620
Date Publish Online
2023-11-25