DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2
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Author / Producer
Date
2022-04-11
Publication Type
Journal Article
ETH Bibliography
yes
Citations
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OPEN ACCESS
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Abstract
Background
The continued spread of SARS-CoV-2 and emergence of new variants with higher transmission rates and/or partial resistance to vaccines has further highlighted the need for large-scale testing and genomic surveillance. However, current diagnostic testing (e.g., PCR) and genomic surveillance methods (e.g., whole genome sequencing) are performed separately, thus limiting the detection and tracing of SARS-CoV-2 and emerging variants.
Results
Here, we developed DeepSARS, a high-throughput platform for simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2 by the integration of molecular barcoding, targeted deep sequencing, and computational phylogenetics. DeepSARS enables highly sensitive viral detection, while also capturing genomic diversity and viral evolution. We show that DeepSARS can be rapidly adapted for identification of emerging variants, such as alpha, beta, gamma, and delta strains, and profile mutational changes at the population level.
Conclusions
DeepSARS sets the foundation for quantitative diagnostics that capture viral evolution and diversity.
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Publication status
published
External links
Editor
Book title
Journal / series
Volume
23 (1)
Pages / Article No.
289
Publisher
BioMed Central
Event
Edition / version
Methods
Software
Geographic location
Date collected
Date created
Subject
Organisational unit
03699 - Stelling, Jörg / Stelling, Jörg
09490 - Stadler, Tanja / Stadler, Tanja
03952 - Reddy, Sai / Reddy, Sai
Notes
Funding
196348 - Large-scale testing and tracking of SARS-CoV-2 infection and evolution by deep sequencing (SNF)
679403 - Vaccine profiling and immunodiagnostic discovery by high-throughput antibody repertoire analysis (EC)
679403 - Vaccine profiling and immunodiagnostic discovery by high-throughput antibody repertoire analysis (EC)
Related publications and datasets
Is new version of: https://doi.org/10.3929/ethz-b-000528644