Evaluation of EPISEQ SARS-CoV-2 and a Fully Integrated Application to Identify SARS-CoV-2 Variants from Several Next-Generation Sequencing Approaches
Abstract
:1. Introduction
2. Materials and Methods
2.1. Patients and Samples
2.2. Sequencing
2.3. Sequencing Data Export and Analysis
2.4. Data Analysis
3. Results
3.1. EPISEQ® SARS-CoV-2 Application
3.2. Validation of EPISEQ SARS-CoV-2
3.2.1. SARS-CoV-2 Genome Coverage
3.2.2. SARS-CoV-2 Variant Call
3.2.3. SARS-CoV-2 Whole-Genome Consensus Sequence
3.2.4. SARS-CoV-2 Spike Protein Mutations
3.3. Comparative Performance of Sequencing Platforms and Kits Using EPISEQ SARS-CoV-2
3.3.1. SARS-CoV-2 Genome Coverage
3.3.2. SARS-CoV-2 Variant Call
3.3.3. SARS-CoV-2 Amino Acid and Nucleotide Mutations
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Sequencer | Primer Pool | Kits |
---|---|---|
MiSeq (Illumina) | ARTIC v3 | NEBNext® ARTIC SARS-CoV-2 Library Prep Kit (Illumina) (NEB, E7650) |
ARTIC v4 | NEBNext® ARTIC SARS-CoV-2 Library Prep Kit (Illumina) (NEB, E7650); ARTIC V4 NCOV-2019 Panel (IDT, 10008554) | |
ARTIC v4.1 | NEBNext® ARTIC SARS-CoV-2 FS Library Prep Kit (Illumina) (NEB, E7658); ARTIC V4.1 NCOV-2019 Panel (IDT, 10011442) | |
VSS v1 | NEBNext® ARTIC SARS-CoV-2 FS Library Prep Kit (Illumina) (NEB, E7658) | |
VSS v2 | NEBNext® ARTIC SARS-CoV-2 FS Library Prep Kit (Illumina) (NEB, E7658) | |
GridION Mk1 (Oxford Nanopore Technologies) | ARTIC v3 | NEBNext® ARTIC SARS-CoV-2 Companion Kit (ONT) (NEB, E7660) |
ARTIC v4 | NEBNext® ARTIC SARS-CoV-2 Companion Kit (ONT) (NEB, E7660); ARTIC V4 NCOV-2019 Panel (IDT, 10008554) | |
ARTIC v4.1 | NEBNext® ARTIC SARS-CoV-2 Companion Kit (ONT) (NEB, E7660); ARTIC V4.1 NCOV-2019 Panel (IDT, 10011442) | |
VSS v1 | NEBNext® ARTIC SARS-CoV-2 Companion Kit (ONT) (NEB, E7660) | |
VSS v2 | NEBNext® ARTIC SARS-CoV-2 Companion Kit (ONT) (NEB, E7660) |
Nextstrain Clade | Pango Lineage | |||
---|---|---|---|---|
Sequencing Kit | n/N 1 | % [95% CI] | n/N 1 | % [95% CI] |
ARTIC v3 | 527/527 2 | 100.0% [99.3–100.0] | 525/527 | 99.6% [98.6–99.9] |
ARTIC v4 | 316/316 3 | 100.0% [98.8–100.0] | 315/316 | 99.7% [98.3–99.9] |
ARTIC v4.1 | 517/519 4 | 99.6% [98.6–99.9] | 512/519 | 98.7% [97.2–99.5] |
Total | 1360/1362 | 99.9% [99.5–100.0] | 1352/1362 | 99.3% [98.7–99.7] |
Sequencing Kit | 0 SNP n/N 1 (%) | 1 SNP n/N 1 (%) | 2 SNPs n/N 1 (%) | >2 SNPs n/N 1 (%) |
---|---|---|---|---|
ARTIC v3 | 524/527 (99.4%) | 3/527 (0.6%) | 0/527 (0.0%) | 0/527 (0.0%) |
ARTIC v4 | 253/316 (80.1%) | 55/316 (17.4%) | 8/316 (2.5%) | 0/316 (0.0%) |
ARTIC v4.1 | 363/519 (69.9%) | 137/519 (26.4%) | 15/519 (2.9%) | 4/519 (0.8%) |
Total | 1140/1362 (83.7%) | 195/1362 (14.3%) | 23/1362 (1.7%) | 4/1362 (0.3%) |
Sequencing Kit | Spike Mutations, n/N 1 (%) |
---|---|
ARTIC v3 | 527/527 (100.0%) |
ARTIC v4 | 315/316 (99.7%) |
ARTIC v4.1 | 510/519 (98.3%) |
Total | 1352/1362 (99.3%) |
SARS-CoV-2 Samples | Nextstrain Clade | Pango Lineage |
---|---|---|
Pre-omicron variants 1 | 21/21 (100.0%) | 21/21 (100.0%) |
Omicron variants 2 | 19/19 (100.0%) | 19/19 (100.0%) |
Total | 40/40 (100.0%) | 40/40 (100.0%) |
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Mugnier, N.; Griffon, A.; Simon, B.; Rambaud, M.; Regue, H.; Bal, A.; Destras, G.; Tournoud, M.; Jaillard, M.; Betraoui, A.; et al. Evaluation of EPISEQ SARS-CoV-2 and a Fully Integrated Application to Identify SARS-CoV-2 Variants from Several Next-Generation Sequencing Approaches. Viruses 2022, 14, 1674. https://doi.org/10.3390/v14081674
Mugnier N, Griffon A, Simon B, Rambaud M, Regue H, Bal A, Destras G, Tournoud M, Jaillard M, Betraoui A, et al. Evaluation of EPISEQ SARS-CoV-2 and a Fully Integrated Application to Identify SARS-CoV-2 Variants from Several Next-Generation Sequencing Approaches. Viruses. 2022; 14(8):1674. https://doi.org/10.3390/v14081674
Chicago/Turabian StyleMugnier, Nathalie, Aurélien Griffon, Bruno Simon, Maxence Rambaud, Hadrien Regue, Antonin Bal, Gregory Destras, Maud Tournoud, Magali Jaillard, Abel Betraoui, and et al. 2022. "Evaluation of EPISEQ SARS-CoV-2 and a Fully Integrated Application to Identify SARS-CoV-2 Variants from Several Next-Generation Sequencing Approaches" Viruses 14, no. 8: 1674. https://doi.org/10.3390/v14081674