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- Title
Accurate Detection of SARS-CoV-2 by Next-Generation Sequencing in Low Viral Load Specimens.
- 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
- Abstract
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, p = 0.0507; copy number, p = 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.
- Subjects
SARS-CoV-2 Delta variant; SARS-CoV-2 Omicron variant; VIRAL load; SARS-CoV-2; NUCLEOTIDE sequencing; COVID-19; VIRAL genomes; DNA copy number variations
- Publication
International Journal of Molecular Sciences, 2023, Vol 24, Issue 4, p3478
- ISSN
1661-6596
- Publication type
Article
- DOI
10.3390/ijms24043478