Single-Amplicon Multiplex Real-Time Reverse Transcription-PCR with Tiled Probes To Detect SARS-CoV-2 spike Mutations Associated with Variants of Concern-Reference-Cited by-同舟云学术

Single-Amplicon Multiplex Real-Time Reverse Transcription-PCR with Tiled Probes To Detect SARS-CoV-2 spike Mutations Associated with Variants of Concern

Published:2021-11-18 Issue:12 Volume:59 Page:
ISSN:0095-1137
Container-title:Journal of Clinical Microbiology
language:en
Short-container-title:J Clin Microbiol

Author:

Babiker Ahmed¹²^ORCID,Immergluck Katherine¹³,Stampfer Samuel D.¹,Rao Anuradha³⁴⁵,Bassit Leda³⁴⁵,Su Max¹,Nguyen Vi¹³,Stittleburg Victoria¹,Ingersoll Jessica M.²³,Bradley Heath L.²,Mavigner Maud³⁴^ORCID,Schoof Nils³⁴,Kraft Colleen S.¹²^ORCID,Chahroudi Ann³⁴⁵^ORCID,Schinazi Raymond F.³⁴⁵^ORCID,Martin Greg S.³⁶,Piantadosi Anne¹²^ORCID,Lam Wilbur A.²³⁷⁸,Waggoner Jesse J.¹³⁹^ORCID

Affiliation:

1. Emory University School of Medicine, Department of Medicine, Division of Infectious Diseases, Atlanta, Georgia, USA

2. Emory University School of Medicine, Department of Pathology and Laboratory Medicine, Atlanta, Georgia, USA

3. The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA

4. Emory University School of Medicine, Department of Pediatrics, Atlanta, Georgia, USA

5. Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta and Emory University, Atlanta, Georgia, USA

6. Emory University School of Medicine, Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Atlanta, Georgia, USA

7. Aflac Cancer & Blood Disorders Center at Children's Healthcare of Atlanta, Atlanta, Georgia, USA

8. Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia, USA

9. Rollins School of Public Health, Department of Global Health, Emory University, Atlanta, Georgia, USA

Abstract

To provide an accessible and inexpensive method to surveil for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations, we developed a multiplex real-time reverse transcription-PCR (rRT-PCR) assay, the Spike single-nucleotide polymorphism (SNP) assay, to detect specific mutations in the spike receptor binding domain. A single primer pair was designed to amplify a 348-bp region of spike , and probes were initially designed to detect K417, E484K, and N501Y. The assay was evaluated using characterized variant sample pools and residual nasopharyngeal samples. Variant calls were confirmed by SARS-CoV-2 genome sequencing in a subset of samples.

Funder

Doris Duke Charitable Foundation

Emory University

HHS | Centers for Disease Control and Prevention

HHS | NIH | National Institute of Allergy and Infectious Diseases

HHS | NIH | National Institute of Biomedical Imaging and Bioengineering

HHS | National Institutes of Health

Publisher

American Society for Microbiology

Subject

Microbiology (medical)

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