Alrezaihi, Abdulrahman, Penrice-Randal, Rebekah 
ORCID: 0000-0002-0653-2097, Dong, Xiaofeng, Prince, Tessa, Randle, Nadine ORCID: 0000-0002-3775-9585, Semple, Malcolm ORCID: 0000-0001-9700-0418, Openshaw, Peter, Investigators, ISARIC4C, Zakotnik, Samo, Suljič, Alen et al (show 5 more authors)
(2023)
Enrichment of Sars-Cov-2 and Seasonal Coronavirus Sequence from Nasopharyngeal Swabs Whilst Maintaining the Background Context of the Microbiome
SSRN.
Abstract
Simultaneously characterising coronavirus genomic information and the underlying microbiome from a single clinical sample would help characterise resulting disease. Metagenomic approaches can be used to sequence SARS-CoV-2 (and other coronavirus infections) and identify mRNAs associated with active transcription in the microbiome. However, given the large sequence background, metagenomic 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, Oxford nanopore technologies were applied to assess different methods of enrichment using SISPA (a random sequencing approach) as basis for detection of SARS-CoV-2 and lineage calling as well as providing detailed information on the underlying microbiome. By adding a specific primer to the appropriate coronavirus leader sequence combined with SISPA, specific variants of SARS-CoV-2 and seasonal coronaviruses could be identified, together with potential novel viral transcripts and complex information on the surrounding microbiome.
| Item Type: | Article |
|---|---|
| Additional Information: | Source info: JCV-D-23-00371 |
| Uncontrolled Keywords: | clinical sample, humans coronaviruses, microbiome, nanopore, SARS-CoV-2, Sequencing |
| Divisions: | Faculty of Health & Life Sciences Faculty of Health & Life Sciences > Inst. Infection, Vet & Ecological Sciences |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 31 Aug 2023 07:40 |
| Last Modified: | 06 Dec 2024 18:26 |
| DOI: | 10.2139/ssrn.4484216 |
| Open Access URL: | https://dx.doi.org/10.2139/ssrn.4484216 |
| Related Websites: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3172444 |
| Disclaimer: | The University of Liverpool is not responsible for content contained on other websites from links within repository metadata. Please contact us if you notice anything that appears incorrect or inappropriate. |
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