COVID-19 Resource Center

COVID-19 Resource Center

Disclosures: Greninger reports having a relationship with Abbott Molecular and has received funding from Gilead Sciences and Merck outside of the submitted work. Lee reports no relevant financial disclosures. Please see the review for all other authors’ relevant financial disclosures.
November 15, 2021
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IDSA, ASM outline role of SARS-CoV-2 sequencing in clinical settings

Disclosures: Greninger reports having a relationship with Abbott Molecular and has received funding from Gilead Sciences and Merck outside of the submitted work. Lee reports no relevant financial disclosures. Please see the review for all other authors’ relevant financial disclosures.
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A joint consensus review from the Infectious Diseases Society of America and the American Society for Microbiology outlined the potential role and challenges of SARS-CoV-2 sequencing in clinical care.

According to Alexander L. Greninger, MD, PhD, MS, MPhil, assistant director of the clinical virology laboratories at the University of Washington Medical Center, and colleagues, no assay is authorized by the FDA for SARS-CoV-2 genotyping, “so any assays developed for clinical use in the U.S. will require validation as a laboratory developed test to be performed in a CLIA (Clinical Laboratory Improvement Amendments) high complexity laboratory.”

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They said allele-specific RT-qPCR has “emerged as a potential solution for identifying SARS-CoV-2 variants with potential therapeutic implications,” because of its fast turnaround time and the ability to focus on mutational hotspots. Additionally, this form of sequencing allows experts to test samples with low amounts of viral RNA.

Whole-genome sequencing allows clinicians to determine the full nucleotide sequence, either for the whole viral genome or for a specific region that contains most of the “known medically relevant mutation sites.”

Alternatively, clinicians could use an RT-PCR test to amplify a region of interest, then use the traditional Sanger sequencing, which derives the nucleotide sequence for the smaller region of the viral genome. Compared with whole-genome sequencing, this approach is less expensive and more widely available, they said.

“Although clinical uses of SARS-CoV-2 sequencing are currently limited, rapidly changing technology and the ability to interpret variants in near real time suggest a growing role for SARS-CoV-2 genotyping in caring for patients as data emerge on vaccine and therapeutic efficacy,” Francesca M. Lee, MD, an associate professor of internal medicine at the University of Texas Southwestern Medical Center in Dallas and a co-author of the review, said in a press release.

Because immunocompromised patients can be infected with SARS-CoV-2 for prolonged periods of time, genotyping results can be returned and potentially aid in treatment with monoclonal antibody therapy.

Whole-genome sequencing can also be used to detect clusters of infections among patients or health care staff, the authors wrote. The cohorting of patients based on viral genotype may be a practical consideration for health care facilities to consider.

“SARS-CoV-2 genotyping has been critical for multiple public health purposes, including epidemiology, vaccine efficacy monitoring, vaccine planning, therapeutic choice and design, and detection of polymorphisms causing therapeutic and/or diagnostic failure,” the authors wrote. “The main current clinical use for genotyping is limited to helping determine if the presence of a mutation will impact the effectiveness of a therapeutic monoclonal antibody.”