Alrezaihi, Abdulrahman, Penrice-Randal, Rebekah 
ORCID: 0000-0002-0653-2097, Dong, Xiaofeng, Prince, Tessa ORCID: 0000-0002-8796-2629, Randle, Nadine ORCID: 0000-0002-3775-9585, Semple, Malcolm G ORCID: 0000-0001-9700-0418, Openshaw, Peter JM, MacGill, Tracy, Myers, Todd, Orr, Robert et al (show 7 more authors)
(2023)
Enrichment of SARS-CoV-2 sequence from nasopharyngeal swabs whilst identifying the nasal microbiome.
Journal of Clinical Virology, 171.
p. 105620.
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1-s2.0-S1386653223002433-main.pdf - Author Accepted Manuscript Available under License Creative Commons Attribution. Download (2MB) | Preview |
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.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | ISARIC4C Investigators, Nasopharynx, Humans, Genome, Viral, Microbiota, COVID-19, SARS-CoV-2 |
| Divisions: | Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 17 Jan 2024 09:38 |
| Last Modified: | 02 Apr 2024 09:31 |
| DOI: | 10.1016/j.jcv.2023.105620 |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3177658 |
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