DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2.
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
11 Apr 2022
11 Apr 2022
Historique:
received:
27
10
2021
accepted:
21
02
2022
entrez:
12
4
2022
pubmed:
13
4
2022
medline:
14
4
2022
Statut:
epublish
Résumé
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. 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. DeepSARS sets the foundation for quantitative diagnostics that capture viral evolution and diversity. 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 .
Sections du résumé
BACKGROUND
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
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
CONCLUSIONS
DeepSARS sets the foundation for quantitative diagnostics that capture viral evolution and diversity. 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 .
Identifiants
pubmed: 35410128
doi: 10.1186/s12864-022-08403-0
pii: 10.1186/s12864-022-08403-0
pmc: PMC8995413
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
289Informations de copyright
© 2022. The Author(s).
Références
Euro Surveill. 2021 Jun;26(24):
pubmed: 34142653
PLoS One. 2012;7(8):e42543
pubmed: 22900027
Nat Rev Microbiol. 2021 Jul;19(7):409-424
pubmed: 34075212
PLoS Comput Biol. 2019 Apr 8;15(4):e1006650
pubmed: 30958812
Nat Microbiol. 2020 Oct;5(10):1299-1305
pubmed: 32651556
Nat Commun. 2021 Mar 3;12(1):1405
pubmed: 33658502
Clin Microbiol Rev. 2000 Oct;13(4):559-70
pubmed: 11023957
Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):228-33
pubmed: 23248286
Cell. 2021 Apr 29;184(9):2523
pubmed: 33930298
Proc Natl Acad Sci U S A. 2021 Mar 2;118(9):
pubmed: 33571105
Curr Issues Mol Biol. 2021 Jul 30;43(2):845-867
pubmed: 34449545
Sci Transl Med. 2020 Dec 9;12(573):
pubmed: 33229462
Bioinformatics. 2004 Jan 22;20(2):289-90
pubmed: 14734327
PLoS One. 2021 Feb 17;16(2):e0247115
pubmed: 33596239
Exp Mol Med. 2020 Jun;52(6):963-977
pubmed: 32546849
Sci Adv. 2020 Sep 11;6(37):
pubmed: 32917716
J Transl Med. 2021 Jun 5;19(1):246
pubmed: 34090468
Nat Med. 2021 Apr;27(4):622-625
pubmed: 33654292
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Nat Commun. 2021 May 25;12(1):3132
pubmed: 34035246
Cell. 2021 Apr 29;184(9):2384-2393.e12
pubmed: 33794143
JAMA. 2020 May 19;323(19):1967-1969
pubmed: 32250394
Nat Rev Genet. 2021 Jul;22(7):415-426
pubmed: 33948037
Sci Transl Med. 2021 May 26;13(595):
pubmed: 33941621
Nat Biomed Eng. 2021 Jul;5(7):657-665
pubmed: 34211145
Nature. 2021 Jul;595(7869):707-712
pubmed: 34098568
Science. 2021 Apr 9;372(6538):
pubmed: 33658326
Bioinformatics. 2018 Dec 1;34(23):4121-4123
pubmed: 29790939
Euro Surveill. 2017 Mar 30;22(13):
pubmed: 28382917
Nature. 2021 Aug;596(7871):276-280
pubmed: 34237773
Nucleic Acids Res. 2019 May 7;47(8):e47
pubmed: 30783653
Sci Transl Med. 2021 Apr 14;13(589):
pubmed: 33619081
Nat Biotechnol. 2021 Dec;39(12):1556-1562
pubmed: 34188222
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Nature. 2021 May;593(7857):130-135
pubmed: 33684923
Science. 2021 Mar 26;371(6536):1306-1308
pubmed: 33766871