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SARS-CoV-2 Sequencing Explained

Viruses like SARS-CoV-2 continuously evolve as a result of changes in the genetic code that take place during the replication of the genome. These changes might be produced by genetic mutations or viral recombination. A group of virus variations that have a common ancestor and are genetically connected is called lineage. One or more modifications that set a virus’s variant apart from other SARS-CoV-2 variants are required for a virus to be considered a variant. A recombinant is a variant produced when genetic code from two different variants is combined to create a new variety.

During this epidemic, researchers in the United States and elsewhere have discovered several SARS-CoV-2 strains, as expected. Scientists evaluate the genetic variations between viruses to find variants, including recombinants, and how they are linked to one another to inform local epidemic investigations and comprehend national trends.

Points To Remember on SARS-CoV-2 Sequencing

  • Since the onset of the COVID-19 pandemic, new genetic lineages of SARS-CoV-2 have been forming and circulating worldwide.
  • The genetic lineages of SARS-CoV-2 in the United States are continuously tracked through epidemiological research, monitoring based on virus genome information, and laboratory studies.
  • Omicron was given the “Variant of Concern” designation by the SARS-CoV-2 Interagency Group (SIG) of the United States government on November 30, 2021. (VOC).
  • The SARS-CoV-2 Interagency Group (SIG) of the United States government moved Delta from the “Variant of Concern” category to the “Variant Being Monitored” type on April 14, 2022.
  • The SIG Variant classification scheme defines four classes of SARS-CoV-2 variants: Variant Being Monitored (VBM), Variant of Interest (VOI), Variant of Concern (VOC), and Variant of High Consequence (VOHC).
  • The SARS-CoV-2 Interagency Group (SIG), established by the United States Department of Health and Human Services (HHS), was to improve coordination between the various entities involved.
  • The SIG has frequent meetings to assess the danger posed by SARS-CoV-2 variations circulating in the United States and provide recommendations concerning the classification of variants.

SARS-CoV-2 sequencing Key Terms


A viral genome (the genetic code) that has undergone one or more mutations is a variation. A viral genome (the genetic code) that has experienced one or more mutations is a variation. In certain situations, public health organizations may classify a collection of genetic variants that share similar alterations as a Variant Being Monitored (VBM), a Variant of Concern (VOC), or a Variant of Interest. These classifications are based on the genetic changes shared by the variants in the collection (VOI). A shared set of characteristics and qualities might necessitate intervention from the public health system.


A single alteration in the genome of a virus is referred to as a mutation (genetic code). Even though mutations are common, the virus’s properties only sometimes shift due to them.


A process in which the genomes of two SARS-CoV-2 variants merge during the process of viral replication to generate a new variant that is distinct from both of its parent lineages and has the potential to infect other people.


A group of closely related viruses that have a common ancestor is referred to as a lineage. There are multiple lineages of SARS-CoV-2; they all induce COVID-19.

SARS-CoV-2 Sequencing Explained
SARS-CoV-2 Sequencing Explained

SARS-CoV-2 Sequencing Results Report Guide

Understanding the genetic variety, dissemination, and evolution of SARS-CoV-2, including variant viruses, is of the utmost importance for the nation’s COVID-19 pandemic response. This includes variant viruses.

The Centers for Disease Control and Prevention (CDC) requests that labs that process and are sequencing SARS-CoV-2 positive specimens send such data to the state, local, tribal, or territorial public health departments. According to the technical guidelines, the SARS-CoV-2 sequencing results must be reported to the appropriate state, local, tribal, or territory public health authority according to the precise instructions and examples.

The Centers for Medicare & Medicaid Services (CMS) published information that enables services that conduct SARS-CoV-2 sequencing on recognized samples to notify patient-specific results to local, state, tribal, or territorial public health departments. These facilities can be either CLIA-certified or not certified by the Clinical Laboratory Improvement Amendments (CLIA). The public health department can get reports on any sequencing data. Laboratories should report results to patients when:

  • When the methods used to perform the sequencing have satisfied the CLIA requirements.
  • For having established performance specifications and have been granted Emergency Use Authorization (EUA) from the United States Food and Drug Administration.

The test has to be carried out at a laboratory or other facility that has been granted CLIA certification, and it has to comply with all CLIA and FDA rules that are relevant when:

  • The SARS-CoV-2 sequencing is provided to the ordering provider.
  • Relayed to the patient
  • This can be found in the patient’s medical file.
  • It is designed to be utilized for diagnosing, preventing, treating, or evaluating a person’s health.

An amendment to the Policy for Coronavirus Disease-2019 Tests in the Course of the Public Health Emergency was published on November 15, 2021. Before providing a test for diagnostic use or disclosing test findings to a healthcare practitioner, a patient, or a medical record, the FDA mandates that makers of COVID-19 diagnostic tests first submit a EUA request for evaluation and authorization. And so, for example, when the test is still current and in use before the update of November 15, 2021, FDA does not plan to oppose or protest against the continued availability of a COVID-19 diagnostic test without EUA.

SARS-CoV-2 Sequencing Results and Public Health Departments

This guidance describes how to include a SARS-CoV-2 genetic sequencing result in an already-existing electronic laboratory report so that the state, local, tribal, or territorial health authorities can receive that data. Once a positive virus test result has been reported, the sequencing results for SARS-CoV-2 should also be reported to the same public health authority. In the electronic transmission of the sequencing data, all of the patient’s initial demographic information should be included, together with the material of the viral test report and the results of the second test that was ordered, which should identify the viral bloodline.

The sequence data should be uploaded to a public database by laboratories or institutions with SARS-CoV-2 positive samples and plan to publish SARS-CoV-2 lineages, including variations.

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