Clinical and Infection Prevention Applications of Severe Acute Respiratory Syndrome Coronavirus 2 Genotyping: An Infectious Diseases Society of America/American Society for Microbiology Consensus Review Document

Author:

Greninger Alexander L1,Dien Bard Jennifer23,Colgrove Robert C4,Graf Erin H5,Hanson Kimberly E6,Hayden Mary K7,Humphries Romney M8,Lowe Christopher F910,Miller Melissa B1112,Pillai Dylan R13,Rhoads Daniel D14,Yao Joseph D15,Lee Francesca M16

Affiliation:

1. Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA

2. Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA

3. Keck School of Medicine, University of Southern California, Los Angeles, California, USA

4. Division of Infectious Diseases, Mount Auburn Hospital, Harvard School of Medicine, Cambridge, Massachusetts, USA

5. Department of Laboratory Medicine and Pathology, Mayo Clinic, Arizona, USA

6. Departments of Internal Medicine and Pathology, University of Utah, Salt Lake City, Utah, USA

7. Division of Infectious Diseases, Department of Medicine and Division of Laboratory Medicine, Department of Pathology, Rush University Medical Center, Chicago, Illinois, USA

8. Division of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA

9. Division of Medical Microbiology and Virology, Providence Health Care, Vancouver, British Columbia, Canada

10. Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada

11. Clinical Microbiology Laboratory, University of North Carolina Hospitals, Chapel Hill, North Carolina, USA

12. Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA

13. Departments of Pathology and Laboratory Medicine and Microbiology & Infectious Diseases, University of Calgary, Alberta, Canada

14. Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA

15. Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, College of Medicine, Mayo Clinic, Rochester, Minnesota, USA

16. Division of Infectious Diseases and Geographic Medicine, Departments of Pathology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA

Abstract

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged into a world of maturing pathogen genomics, with >2 million genomes sequenced at this writing. The rise of more transmissible variants of concern that affect vaccine and therapeutic effectiveness has led to widespread interest in SARS-CoV-2 evolution. Clinicians are also eager to take advantage of the information provided by SARS-CoV-2 genotyping beyond surveillance purposes. Here, we review the potential role of SARS-CoV-2 genotyping in clinical care. The review covers clinical use cases for SARS-CoV-2 genotyping, methods of SARS-CoV-2 genotyping, assay validation and regulatory requirements, clinical reporting for laboratories, and emerging issues in clinical SARS-CoV-2 sequencing. While clinical uses of SARS-CoV-2 genotyping are currently limited, rapid technological change along with a growing ability to interpret variants in real time foretell a growing role for SARS-CoV-2 genotyping in clinical care as continuing data emerge on vaccine and therapeutic efficacy.

Publisher

Oxford University Press (OUP)

Subject

Infectious Diseases,Microbiology (medical)

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