Targeted Hybridization Capture of SARS-CoV-2 and Metagenomics Enables Genetic Variant Discovery and Nasal Microbiome Insights-Reference-Cited by-同舟云学术

Targeted Hybridization Capture of SARS-CoV-2 and Metagenomics Enables Genetic Variant Discovery and Nasal Microbiome Insights

Published:2021-10-31 Issue:2 Volume:9 Page:
ISSN:2165-0497
Container-title:Microbiology Spectrum
language:en
Short-container-title:Microbiol Spectr

Author:

Nagy-Szakal Dorottya¹²,Couto-Rodriguez Mara¹,Wells Heather L.¹,Barrows Joseph E.¹,Debieu Marilyne¹,Butcher Kristin³,Chen Siyuan³,Berki Agnes⁴,Hager Courteny¹,Boorstein Robert J.⁵,Taylor Mariah K.⁶,Jonsson Colleen B.⁶^ORCID,Mason Christopher E.¹⁷⁸⁹¹⁰,O’Hara Niamh B.¹²¹¹^ORCID

Affiliation:

1. Biotia, Inc., New York, New York, USA

2. Department of Cell Biology, College of Medicine, SUNY Downstate Health Sciences University, New York, New York, USA

3. Twist Bioscience, South San Francisco, California, USA

4. School of Natural Sciences, College of Natural, Behavioral and Health Sciences, Caldwell University, Caldwell, New Jersey, USA

5. Lenco Diagnostic Laboratories, Inc., New York, New York, USA

6. The University of Tennessee Health Science Center, Memphis, Tennessee, USA

7. Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, Cornell University, New York, New York, USA

8. HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA

9. WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, New York, USA

10. Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York, USA

11. Jacobs Technion-Cornell Institute, Cornell Tech, New York, New York, USA

Abstract

This is the first FDA emergency-use-authorized hybridization capture-based next-generation sequencing (NGS) assay to detect the SARS-CoV-2 genome. Viral metagenomics and the novel hybrid capture NGS-based assay, along with its research-use-only analysis, can provide important genetic insights into SARS-CoV-2 and other emerging pathogens and improve surveillance and early detection, potentially preventing or mitigating new outbreaks.

Publisher

American Society for Microbiology

Subject

Infectious Diseases,Cell Biology,Microbiology (medical),Genetics,General Immunology and Microbiology,Ecology,Physiology

Link

https://journals.asm.org/doi/pdf/10.1128/Spectrum.00197-21

Reference55 articles.

1. Centers for Disease Control and Prevention. 2020. COVID Data Tracker. CDC Atlanta GA. https://covid.cdc.gov/covid-data-tracker/#datatracker-home.

2. Johns Hopkins. 2020. Track reported cases of COVID-19. Johns Hopkins Coronavirus Resource Center. https://coronavirus.jhu.edu/map.html.

3. COVID-19 diagnostic approaches: different roads to the same destination

4. A Recurrent Mutation at Position 26340 of SARS-CoV-2 Is Associated with Failure of the E Gene Quantitative Reverse Transcription-PCR Utilized in a Commercial Dual-Target Diagnostic Assay

5. Butler D Mozsary C Meydan C Danko D Foox J Rosiene J Shaiber A Afshinnekoo E MacKay M Sedlazeck F Ivanov N Sierra M Pohle D Zietz M Gisladottir U Ramlall V Westover C Ryon K Young B Bhattacharya C Ruggiero P Langhorst B Tanner N Gawrys J Meleshko D Xu D Steel P Shemesh A Xiang J Thierry-Mieg J Thierry-Mieg D Schwartz R Iftner A Bezdan D Sipley J Cong L Craney A Velu P Melnick A Hajirasouliha I Horner S Iftner T Salvatore M Loda M Westblade L Cushing M Levy S Wu S Tatonetti N Imielinski M et al. 2020. Shotgun transcriptome and isothermal profiling of SARS-CoV-2 infection reveals unique host responses viral diversification and drug interactions. bioRxiv. doi:10.1101/2020.04.20.048066.

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