| Title: |
Enrichment of SARS-CoV-2 sequence from nasopharyngeal swabs whilst identifying the nasal microbiome. |
| Authors: |
Alrezaihi, A; Penrice-Randal, R; Dong, X; Prince, T; Randle, N; Semple, MG; Openshaw, PJM; MacGill, T; Myers, T; Orr, R; Zakotnik, S; Suljič, A; Avšič-Županc, T; Petrovec, M; Korva, M; AlJabr, W; Hiscox, JA; ISARIC4C Investigators |
| Contributors: |
Imperial College Healthcare NHS Trust- BRC Funding; UKRI MRC COVID-19 Rapid Response Call |
| Source: |
105620. |
| Publication Year: |
2023 |
| Collection: |
Imperial College London: Spiral |
| Subject Terms: |
Clinical sample; Humans coronaviruses; Microbiome; Nanopore; SARS-CoV-2; Sequencing; ISARIC4C Investigators; 0605 Microbiology; 1103 Clinical Sciences; 1108 Medical Microbiology; Virology |
| Subject Geographic: |
Netherlands |
| Description: |
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. |
| Document Type: |
article in journal/newspaper |
| Language: |
English |
| Relation: |
J Clin Virol; http://hdl.handle.net/10044/1/109906; PA5564; MC_PC19025 |
| DOI: |
10.1016/j.jcv.2023.105620 |
| Availability: |
http://hdl.handle.net/10044/1/109906; https://doi.org/10.1016/j.jcv.2023.105620 |
| Rights: |
© 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/ ; https://creativecommons.org/licenses/by-nc-nd/4.0/ |
| Accession Number: |
edsbas.1D4299FB |
| Database: |
BASE |