Please use this identifier to cite or link to this item:
http://hdl.handle.net/11375/26217
Title: | A Comparison of Whole Genome Sequencing of SARS-CoV-2 Using Amplicon-Based Sequencing, Random Hexamers, and Bait Capture |
Authors: | Nasir JA Kozak RA Aftanas P Raphenya AR Smith KM Maguire F Maan H Alruwaili M Banerjee A Mbareche H Alcock BP Knox NC Mossman K Wang B Hiscox JA McArthur AG Mubareka S |
Keywords: | SARS-CoV-2;amplicon sequencing;bait capture;genome sequencing;Base Sequence;Betacoronavirus;COVID-19;COVID-19 Testing;Clinical Laboratory Techniques;Coronavirus Infections;DNA, Complementary;Genome, Viral;Humans;Molecular Epidemiology;Multiplex Polymerase Chain Reaction;Pandemics;Pneumonia, Viral;RNA, Viral;SARS-CoV-2;Whole Genome Sequencing |
Publication Date: | 15-Aug-2020 |
Publisher: | MDPI AG |
Citation: | Nasir, J.A.; Kozak, R.A.; Aftanas, P.; Raphenya, A.R.; Smith, K.M.; Maguire, F.; Maan, H.; Alruwaili, M.; Banerjee, A.; Mbareche, H.; Alcock, B.P.; Knox, N.C.; Mossman, K.; Wang, B.; Hiscox, J.A.; McArthur, A.G.; Mubareka, S. A Comparison of Whole Genome Sequencing of SARS-CoV-2 Using Amplicon-Based Sequencing, Random Hexamers, and Bait Capture. Viruses 2020, 12, 895. https://doi.org/10.3390/v12080895 |
Abstract: | Genome sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is increasingly important to monitor the transmission and adaptive evolution of the virus. The accessibility of high-throughput methods and polymerase chain reaction (PCR) has facilitated a growing ecosystem of protocols. Two differing protocols are tiling multiplex PCR and bait capture enrichment. Each method has advantages and disadvantages but a direct comparison with different viral RNA concentrations has not been performed to assess the performance of these approaches. Here we compare Liverpool amplification, ARTIC amplification, and bait capture using clinical diagnostics samples. All libraries were sequenced using an Illumina MiniSeq with data analyzed using a standardized bioinformatics workflow (SARS-CoV-2 Illumina GeNome Assembly Line; SIGNAL). One sample showed poor SARS-CoV-2 genome coverage and consensus, reflective of low viral RNA concentration. In contrast, the second sample had a higher viral RNA concentration, which yielded good genome coverage and consensus. ARTIC amplification showed the highest depth of coverage results for both samples, suggesting this protocol is effective for low concentrations. Liverpool amplification provided a more even read coverage of the SARS-CoV-2 genome, but at a lower depth of coverage. Bait capture enrichment of SARS-CoV-2 cDNA provided results on par with amplification. While only two clinical samples were examined in this comparative analysis, both the Liverpool and ARTIC amplification methods showed differing efficacy for high and low concentration samples. In addition, amplification-free bait capture enriched sequencing of cDNA is a viable method for generating a SARS-CoV-2 genome sequence and for identification of amplification artifacts. |
URI: | http://hdl.handle.net/11375/26217 https://publichealth.jmir.org/2020/2/e18668/ |
metadata.dc.identifier.doi: | 10.3390/v12080895 |
ISSN: | 1999-4915 1999-4915 10.3390/v12080895 |
Appears in Collections: | Faculty Publications (via McMaster Experts) |
Files in This Item:
File | Description | Size | Format | |
---|---|---|---|---|
A Comparison of Whole Genome Sequencing of SARS-CoV-2 Using Amplicon-Based Sequencing, Random Hexamers, and Bait Capture.pdf | Published version | 1.13 MB | Adobe PDF | View/Open |
This item is licensed under a Creative Commons License