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Clinical Organizations Release SARS-CoV-2 Variant Sequencing Guidelines

The rapid communication provides laboratory professionals with guidance on sequencing COVID-19 variants

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Miriam Bergeret, MSc

Miriam Bergeret, MSc, is Today's Clinical Lab's managing editor.

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Published:Apr 30, 2021
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On April 28, 2021, the Association for Molecular Pathology (AMP), Infectious Diseases Society of America (IDSA), and Pan American Society for Clinical Virology (PASCV) released a rapid communication concerning SARS-CoV-2 variant testing and sequencing in clinical settings. The communication lists SARS-CoV-2 variants with CDC classification and covers key questions including:

  • When should SARS-CoV-2 sequencing be used or requested, and for whom?

  • What samples are used for next-generation sequencing (NGS) sequencing to identify variants?

  • Which laboratories offer variant testing? (See the list of AMP members’ laboratories.)

The document was developed to guide lab and health care professionals by providing specific recommendations, but the communication notes it should not be taken as standard of practice.

SARS-CoV-2 is an RNA virus that mutates as it passes from person to person, and different strains or variants of the virus can arise based on a common set of genetic mutations. Several SARS-CoV-2 variants are currently circulating around the world. 

Tracking variants involves tracking their genetic fingerprint via NGS or reverse transcriptase (RT)-PCR. It’s important to track variants as some are more infectious and pathogenic than others, and can interfere with COVID-19 diagnostic tests, potentially producing false negative test results.