New Review Article Outlines Potential of SARS-CoV-2 Genetic Sequencing in Patient Care

Nov. 3, 2021

Washington, D.C. – November 3, 2021  The rise of more transmissible variants of SARS-CoV-2 has spurred growing interest in harnessing information about the genetic sequences of these variants to help treat patients. A new joint consensus review from the American Society for Microbiology (ASM) and the Infectious Diseases Society of America (IDSA) outlines the potential role of SARS-CoV-2 sequencing in clinical care and the challenges in implementing this process in laboratories. The review is published today in Journal of Clinical Microbiology and Clinical Infectious Diseases.
“Although clinical uses of SARS-CoV-2 sequencing are currently limited, rapidly changing technology and the ability to interpret variants in near real-time suggests a growing role for SARS-CoV-2 genotyping in caring for patients as data emerge on vaccine and therapeutic efficacy,” said Francesca M. Lee, M.D., an author of the review and a member of IDSA’s Diagnostic Committee. Dr. Lee is also an associate professor in the Division of Infectious Diseases and Geographic Medicine in the Departments of Pathology and Internal Medicine at the University of Texas Southwestern Medical Center in Dallas.
With more than 2 million SARS-CoV-2 genomes sequenced so far during the pandemic, this testing has provided critical information about the lineages and evolution of the virus that has supported the public health response. The new review publishing today describes several potential clinical applications of this testing process, including for screening immunocompromised COVID-19 patients being considered for monoclonal antibody therapy and for infection prevention efforts in health care facilities using whole genome sequencing.
The new IDSA-ASM article also outlines related issues, from assay validation and regulatory requirements to clinical reporting for laboratories and emerging challenges in clinical SARS-CoV-2 sequencing. Key considerations for implementing whole genome sequencing, including clinical/epidemiological and laboratory issues, such as accuracy and reproducibility, quality control, workflow and ordering decisions, and billing and reimbursement, are also summarized.
The consensus review, “Clinical Applications of SARS-CoV-2 Genotyping,” is available online now. In addition to Dr. Lee, authors of the review include Alexander L. Greninger, M.D., Ph.D., M.S., MPhil; Jennifer Dien Bard, Ph.D.; Robert C. Colgrove, M.D.; Erin H. Graf, Ph.D.; Kimberly E. Hanson, M.D., M.H.S.; Mary K. Hayden, M.D.; Romney M. Humphries, Ph.D.; Christopher F. Lowe, M.D., M.Sc; Melissa B. Miller, Ph.D.; Dylan R. Pillai, M.D., Ph.D.; Daniel D. Rhoads, M.D.; and Joseph D. Yao, M.D.
The following conflict of interest disclosures are included in the review: Dr. Rhoads has received funding from Cepheid, Cleveland Diagnostics, Luminex, Qiagen and Talis Biomedical outside the submitted work. Dr. Pillai has a relationship with Illucidx Inc. outside the submitted work. Dr. Greninger has a relationship with Abbott Molecular and has received funding from Gilead and Merck outside the submitted work. Dr. Miller receives fees and funding from Cepheid, Luminex Molecular Diagnostics, QIAGEN, Talis Biomedical, Werfen, Agena Bioscience, Sherlock Biosciences, Abbott Molecular and ArcBio outside the submitted work. Drs. Lee, Bard, Lowe, Colgrove, Graf, Hanson, Humphries and Hayden have no conflicts of interest to declare.
About ASM
The American Society for Microbiology is one of the largest professional societies dedicated to the life sciences and is composed of 30,000 scientists and health practitioners. ASM's mission is to promote and advance the microbial sciences.
ASM advances the microbial sciences through conferences, publications, certifications, educational opportunities and advocacy efforts. It enhances laboratory capacity around the globe through training and resources. It provides a network for scientists in academia, industry and clinical settings. Additionally, ASM promotes a deeper understanding of the microbial sciences to diverse audiences.

About IDSA
The Infectious Diseases Society of America (IDSA) is a community of over 12,000 physicians, scientists, and public health experts who specialize in infectious diseases. Its purpose is to improve the health of individuals, communities and society by promoting excellence in patient care, education, research, public health and prevention relating to infectious diseases. Learn more at

About the Journal of Clinical Microbiology
Journal of Clinical Microbiology publishes the most current research related to the laboratory diagnosis of human and animal infections and the role of the laboratory in both the management of infectious diseases and the elucidation of the epidemiology of infections. Learn more at
About Clinical Infectious Diseases
Clinical Infectious Diseases is a leading journal in the field of infectious diseases with a broad international readership. The journal publishes articles on a variety of subjects of interest to practitioners and researchers. Topics range from clinical descriptions of infections, public health, microbiology, and immunology to the prevention of infection, the evaluation of current and novel treatments, and the promotion of optimal practices for diagnosis and treatment. Clinical Infectious Diseases is an official publication of the Infectious Diseases Society of America. Learn more at

Author: ASM Communications

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