Accurate Detection of SARS-CoV-2 by Next-Generation Sequencing in Low Viral Load Specimens

As new SARS-CoV-2 variants emerge, there is an urgent need to increase the efficiency and availability of viral genome sequencing, notably to detect the lineage in samples with a low viral load. SARS-CoV-2 genome next-generation sequencing (NGS) was performed retrospectively in a single center on 17...

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Bibliographic Details
Published in:International journal of molecular sciences 2023-02, Vol.24 (4), p.3478
Main Authors: Ilié, Marius, Benzaquen, Jonathan, Hofman, Véronique, Long-Mira, Elodie, Lassalle, Sandra, Boutros, Jacques, Bontoux, Christophe, Lespinet-Fabre, Virginie, Bordone, Olivier, Tanga, Virginie, Allegra, Maryline, Salah, Myriam, Fayada, Julien, Leroy, Sylvie, Vassallo, Matteo, Touitou, Irit, Courjon, Johan, Contenti, Julie, Carles, Michel, Marquette, Charles-Hugo, Hofman, Paul
Format: Article
Language:English
Subjects:
Analysis
Copy number
Coronaviruses
COVID-19
Disease transmission
DNA sequencing
Genexus
Genomes
Genomics
Health aspects
High-Throughput Nucleotide Sequencing
Humans
low viral load
Metropolitan areas
Next-generation sequencing
Nucleotide sequencing
Pandemics
Retrospective Studies
SARS-CoV-2
Scientific equipment and supplies industry
Severe acute respiratory syndrome coronavirus 2
Viral infections
Viral Load
Workflow
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Summary:As new SARS-CoV-2 variants emerge, there is an urgent need to increase the efficiency and availability of viral genome sequencing, notably to detect the lineage in samples with a low viral load. SARS-CoV-2 genome next-generation sequencing (NGS) was performed retrospectively in a single center on 175 positive samples from individuals. An automated workflow used the Ion AmpliSeq SARS-CoV-2 Insight Research Assay on the Genexus Sequencer. All samples were collected in the metropolitan area of the city of Nice (France) over a period of 32 weeks (from 19 July 2021 to 11 February 2022). In total, 76% of cases were identified with a low viral load (Ct ≥ 32, and ≤200 copies/µL). The NGS analysis was successful in 91% of cases, among which 57% of cases harbored the Delta variant, and 34% the Omicron BA.1.1 variant. Only 9% of cases had unreadable sequences. There was no significant difference in the viral load in patients infected with the Omicron variant compared to the Delta variant (Ct values, = 0.0507; copy number, = 0.252). We show that the NGS analysis of the SARS-CoV-2 genome provides reliable detection of the Delta and Omicron SARS-CoV-2 variants in low viral load samples.
ISSN:1422-0067
1661-6596
1422-0067
DOI:10.3390/ijms24043478