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Capturing SARS-CoV-2 from patient samples with low viral abundance: a comparative analysis
Juliana Pipoli da Fonseca1, Etienne Kornobis1,2, Elodie Turc1
1Institut Pasteur, Université Paris Cité, Plate-Forme Technologique Biomics, 75015, Paris, France.
Scientific Reports
|November 12, 2022
Summary
Capture-Seq effectively detects SARS-CoV-2 genomes in patient samples, even at low viral loads. This hybridization technique is crucial for monitoring mutations and variants during the ongoing coronavirus pandemic.
Area of Science:
- Virology
- Genomics
- Molecular Biology
Background:
- Genome sequencing is vital for tracking SARS-CoV-2 mutations and variants.
- The emergence of variants of concern necessitates robust methods for viral genetic analysis.
Purpose of the Study:
- To evaluate the efficacy of the Capture-Seq hybridization technique for detecting SARS-CoV-2 genomes in patient samples.
- To assess the performance of Capture-Seq across different viral loads and panel types.
Main Methods:
- Analyzed 20 patient nasal swab samples with viral loads ranging from CT25 to CT36+.
- Tested three multi-virus panels and two SARS-CoV-2-specific panels with varying probe compositions (ssRNA, ssDNA, dsDNA).
Main Results:
- SARS-CoV-2-only panels demonstrated high efficiency, with a significant percentage of reads mapping to the target genome.
- Multi-virus panels struggled with low-abundance targets and showed a high rate of off-target reads, likely due to host sequences.
- Capture-Seq proved effective for low-abundance samples up to CT values of 35.
Conclusions:
- Capture-Seq is a highly effective method for studying SARS-CoV-2 in patient samples, particularly those with low viral loads.
- SARS-CoV-2-specific panels are superior to multi-virus panels for accurate viral genome detection using this technique.
