Accurate Detection of SARS-CoV-2 by Next-Generation Sequencing in Low Viral Load Specimens.
Véronique HofmanJonathan BenzaquenVéronique HofmanElodie Long-MiraSandra LassalleJacques BoutrosChristophe BontouxVirginie Lespinet-FabreOlivier BordoneVirginie TangaMaryline AllegraMyriam SalahJulien FayadaSylvie LeroyMatteo VassalloIrit TouitouJohan CourjonJulie ContentiMichel CarlesCharles Hugo MarquettePaul HofmanPublished in: International journal of molecular sciences (2023)
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.
Keyphrases
- sars cov
- copy number
- mitochondrial dna
- respiratory syndrome coronavirus
- genome wide
- computed tomography
- dna methylation
- end stage renal disease
- single cell
- magnetic resonance imaging
- contrast enhanced
- gene expression
- high resolution
- high throughput
- prognostic factors
- peritoneal dialysis
- label free
- magnetic resonance
- cell free