DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2

Alexander Yermanos; Kai-Lin Hong; Andreas Agrafiotis; Jiami Han; Sarah Nadeau; Cecilia Valenzuela; Asli Azizoglu; Roy Ehling; Beichen Gao; Michael Spahr; Daniel Neumeier; Ching-Hsiang Chang; Andreas Dounas; Ezequiel Petrillo; Ina Nissen; Elodie Burcklen; Mirjam Feldkamp; Christian Beisel; Annette Oxenius; Miodrag Savic; Tanja Stadler; Fabian Rudolf; Sai T Reddy

doi:10.1186/s12864-022-08403-0

DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2

Alexander Yermanos^*, Kai-Lin Hong, Andreas Agrafiotis, Jiami Han, Sarah Nadeau, Cecilia Valenzuela, Asli Azizoglu, Roy Ehling, Beichen Gao, Michael Spahr, Daniel Neumeier, Ching-Hsiang Chang, Andreas Dounas, Ezequiel Petrillo, Ina Nissen, Elodie Burcklen, Mirjam Feldkamp, Christian Beisel, Annette Oxenius, Miodrag SavicTanja Stadler, Fabian Rudolf^*, Sai T Reddy^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

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. Graphical abstract: DeepSARS uses molecular barcodes (BCs) and multiplexed targeted deep sequencing (NGS) to enable simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2. Image was created using Biorender.com.[Figure not available: see fulltext.]

Original language	English
Article number	289
Journal	BMC Genomics
Volume	23
Issue number	1
DOIs	https://doi.org/10.1186/s12864-022-08403-0
Publication status	Published - 11 Apr 2022
Externally published	Yes

Keywords

COVID-19/diagnosis
Genomics
Humans
Mutation
SARS-CoV-2/genetics
Whole Genome Sequencing

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10.1186/s12864-022-08403-0Licence: CC BY

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Yermanos, A., Hong, K.-L., Agrafiotis, A., Han, J., Nadeau, S., Valenzuela, C., Azizoglu, A., Ehling, R., Gao, B., Spahr, M., Neumeier, D., Chang, C.-H., Dounas, A., Petrillo, E., Nissen, I., Burcklen, E., Feldkamp, M., Beisel, C., Oxenius, A., ... Reddy, S. T. (2022). DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2. BMC Genomics, 23(1), Article 289. https://doi.org/10.1186/s12864-022-08403-0

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title = "DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2",

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. Graphical abstract: DeepSARS uses molecular barcodes (BCs) and multiplexed targeted deep sequencing (NGS) to enable simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2. Image was created using Biorender.com.[Figure not available: see fulltext.]",

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author = "Alexander Yermanos and Kai-Lin Hong and Andreas Agrafiotis and Jiami Han and Sarah Nadeau and Cecilia Valenzuela and Asli Azizoglu and Roy Ehling and Beichen Gao and Michael Spahr and Daniel Neumeier and Ching-Hsiang Chang and Andreas Dounas and Ezequiel Petrillo and Ina Nissen and Elodie Burcklen and Mirjam Feldkamp and Christian Beisel and Annette Oxenius and Miodrag Savic and Tanja Stadler and Fabian Rudolf and Reddy, {Sai T}",

note = "Publisher Copyright: {\textcopyright} 2022, The Author(s).",

year = "2022",

month = apr,

day = "11",

doi = "10.1186/s12864-022-08403-0",

language = "English",

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Yermanos, A, Hong, K-L, Agrafiotis, A, Han, J, Nadeau, S, Valenzuela, C, Azizoglu, A, Ehling, R, Gao, B, Spahr, M, Neumeier, D, Chang, C-H, Dounas, A, Petrillo, E, Nissen, I, Burcklen, E, Feldkamp, M, Beisel, C, Oxenius, A, Savic, M, Stadler, T, Rudolf, F & Reddy, ST 2022, 'DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2', BMC Genomics, vol. 23, no. 1, 289. https://doi.org/10.1186/s12864-022-08403-0

TY - JOUR

T1 - DeepSARS

T2 - simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2

AU - Yermanos, Alexander

AU - Hong, Kai-Lin

AU - Agrafiotis, Andreas

AU - Han, Jiami

AU - Nadeau, Sarah

AU - Valenzuela, Cecilia

AU - Azizoglu, Asli

AU - Ehling, Roy

AU - Gao, Beichen

AU - Spahr, Michael

AU - Neumeier, Daniel

AU - Chang, Ching-Hsiang

AU - Dounas, Andreas

AU - Petrillo, Ezequiel

AU - Nissen, Ina

AU - Burcklen, Elodie

AU - Feldkamp, Mirjam

AU - Beisel, Christian

AU - Oxenius, Annette

AU - Savic, Miodrag

AU - Stadler, Tanja

AU - Rudolf, Fabian

AU - Reddy, Sai T

PY - 2022/4/11

Y1 - 2022/4/11

N2 - 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. Graphical abstract: DeepSARS uses molecular barcodes (BCs) and multiplexed targeted deep sequencing (NGS) to enable simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2. Image was created using Biorender.com.[Figure not available: see fulltext.]

AB - 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. Graphical abstract: DeepSARS uses molecular barcodes (BCs) and multiplexed targeted deep sequencing (NGS) to enable simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2. Image was created using Biorender.com.[Figure not available: see fulltext.]

KW - COVID-19/diagnosis

KW - Genomics

KW - Humans

KW - Mutation

KW - SARS-CoV-2/genetics

KW - Whole Genome Sequencing

U2 - 10.1186/s12864-022-08403-0

DO - 10.1186/s12864-022-08403-0

M3 - Article

C2 - 35410128

SN - 1471-2164

VL - 23

JO - BMC Genomics

JF - BMC Genomics

IS - 1

M1 - 289

ER -

DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2

Abstract

Keywords

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