Alrezaihi, Abdulrahman, Penrice-Randal, Rebekah, Dong, Xiaofeng, Prince, Tessa, Randle, Nadine, 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 and Life Sciences Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 31 Aug 2023 07:40 |
| Last Modified: | 01 Dec 2023 11:32 |
| DOI: | 10.2139/ssrn.4484216 |
| Open Access URL: | https://dx.doi.org/10.2139/ssrn.4484216 |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3172444 |
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