People wearing masks

As COVID-19 case counts fluctuate, public health bodies continue to find new SARS-CoV-2 mutations that often account for local and global surges. With each new variant comes concerns over how pandemic mitigation efforts might be impacted by different viral genetics and infection characteristics. In addition to considering how the efficacy of treatments and vaccines could be affected, test reliability has been called into question. Accurate detection of positive COVID-19 cases remains critically important to public health measures aimed at reducing transmission and spread.

Dr. Vin Gupta, Critical Care Pulmonologist and Professor at the University of Washington’s Institute for Health Metrics and Evaluation, agrees that reliable detection is an important measure and says test makers have a key role ensuring testing remains a constructive tool. According to Dr. Gupta, “As various organizations around the world track and monitor variant activities closely, test manufacturers must continue to evaluate their assays to ensure they remain robust even as the virus evolves.”

What are virus variants, and why do they occur?

A variant of a virus is defined by a specific set of genetic changes, or mutations. It’s common for viruses to mutate, with some being more likely to undergo these genetic changes than others. Coronaviruses generally mutate less often than other well-known viruses such as influenza and human immunodeficiency virus (HIV), but genetic changes can and do occur as we have seen with the noteworthy SARS-CoV-2 variants Alpha, Delta, Omicron (BA.1 and BA.2).

Vin Gupta, MD

“We still need to be able to detect coronavirus so an individual who is actually positive will test positive, regardless of variant.”

-Vin Gupta, MD

Why do variants matter to the COVID-19 pandemic?

Not every genetic mutation is significant, as most will not change a virus’s structure or behavior. There is, however, the potential for a set of mutations to result in a variant that improves a virus’s ability to spread, cause more severe illness, or compromise the efficacy of existing protections. The Delta variant, for example, was believed to be at least twice as contagious as previous versions of the virus while also increasing the likelihood of hospitalization with infection [1]. Omicron BA.1 and BA.2 subvariants have followed, each more contagious than the previous dominant strain [2].

Dr. Gupta highlights the role variants have played in prolonging or worsening the pandemic. “The surges we are seeing are the direct result of the ways in which this coronavirus has changed. If we had been dealing with the original version of the virus this entire time, we would be long done with this pandemic,” he says. “One of the big concerns as we continue to see this lethal respiratory virus change, is that the more it changes, the more it can evade the body’s natural defenses and the protection we get from vaccines.” Thus far, vaccines have thankfully maintained some level of protection against SARS-CoV-2 variants, but it's hard to predict if that could change with future mutations.

To ensure timely and appropriate mitigation efforts and alignment of clinical resources with anticipated disease spread and severity, detecting and tracking new variant activity will remain an ongoing focus as long as the spread of COVID-19 continues within communities. “The emergence of variants should concern us all,” Dr. Gupta emphasizes. “They are a constant threat to our way of life and to the number of people who might be in harm’s way.”

How are variants identified and monitored?

Standard antigen and molecular diagnostic tests look for a specific viral protein or examine a targeted area of the viral genome, respectively. These tests are designed to detect the presence of SARS-CoV-2   in a sample, but does not detect which variant is present. In addition to ongoing diagnostic testing, the World Health Organization recommends routine genetic sequencing of positive samples to get a more complete picture of the virus — and any new variants that might have emerged — at any given time [3]. “It’s really important to know when a variant has arisen through genetic sequencing and other efforts that help us understand the virus at a very granular level, how it’s changing and the way it’s actually morphing under a microscope,” says Dr. Gupta. These comprehensive measures are done through surveillance programs.

From local public health laboratories to the World Health Organization, teams across the globe are collecting more detailed information on a subset of COVID-19-positive samples to identify and track new mutations. This data is then aggregated to provide insight into how specific changes are affecting virus characteristics, as well as where variant spread is happening.

How do variants affect the reliability of diagnostic tests?

Standard antigen and molecular diagnostic tests look for a specific viral protein or examine a targeted area of the viral genome, respectively. These tests are designed to detect the presence of SARS-CoV-2   in a sample, but does not detect which variant is present. In addition to ongoing diagnostic testing, the World Health Organization recommends routine genetic sequencing of positive samples to get a more complete picture of the virus — and any new variants that might have emerged — at any given time [2]. “It’s really important to know when a variant has arisen through genetic sequencing and other efforts that help us understand the virus at a very granular level, how it’s changing and the way it’s actually morphing under a microscope,” says Dr. Gupta. These comprehensive measures are done through surveillance programs.

From local public health laboratories to the World Health Organization, teams across the globe are collecting more detailed information on a subset of COVID-19-positive samples to identify and track new mutations. This data is then aggregated to provide insight into how specific changes are affecting virus characteristics, as well as where variant spread is happening.

Do variants affect the Accula SARS CoV-2 Test?

Thermo Fisher Scientific’s Accula SARS CoV-2 Test, offering rapid PCR technology in CLIA-waived settings, was designed to tolerate genetic variation in the virus. Shortly after the Delta variant emerged, Thermo Fisher’s evaluations along with studies conducted by the National Institutes of Health (NIH) demonstrated robust coverage and uncompromised sensitivity in the Accula test’s ability to detect SARS-CoV-2 in samples with known variants [4]. Thermo Fisher Scientific conducts routine surveillance of global SARS-CoV-2 sequences to determine if any mutations are present that could impact test performance.  In silico analysis of available sequences indicates that the Omicron subvariant known as BA.1 or BA.2 will not impact the performance of the Accula SARS-CoV-2 Test.

“Knowing that the Accula device retains its clinical sensitivity is vital information, because all of the organizations that rely on it right now will have the confidence to know that they can continue to rely on it, recognizing the fact that the virus may look different in the months and years ahead,” says Dr. Gupta. “Because we are dealing with a changing virus, we have to make sure the tools we have at our disposal today remain valid and clinically sensitive months down the road. Continued investments and prioritization of these important testing workstreams will remain vital.”

Accula-Dock-and-Accula-SARS-CoV-2-Test-tfs

“Knowing that the Accula device retains its clinical sensitivity is vital information, because all of the organizations that rely on it right now will have the confidence to know that they can continue to rely on it.”

-Vin Gupta, MD

Disclaimer: This test has not been FDA cleared or approved but has been authorized for emergency use by FDA for use by laboratories certified under the Clinical Laboratory ImprovementAmendments (CLIA) of 1988, 42 U.S.C. §263a, that meet requirements to perform high, moderate, or waived complexity tests. The test is authorized for use at the Point of Care (POC),i.e., in patient care settings operating under a CLIA Certificate of Waiver, Certificate of Compliance, or Certificate of Accreditation. This test has been authorized only for the detectionof nucleic acid from SARS-CoV-2, not for any other viruses or pathogens. The emergency use of this test is only authorized for the duration of the declaration that circumstancesexist justifying the authorization of emergency use of in vitro diagnostics for detection and/or diagnosis of COVID-19 under Section 564(b)(1) of the Federal Food, Drug, and CosmeticAct, 21 U.S.C. § 360bbb-3(b)(1), unless the declaration is terminated or authorization is revoked sooner.

Regulatory and Intended Use: For Use under the Emergency Use Authorization (EUA) Only. For prescription use only. For in vitro diagnostic use.

Style Sheet for Komodo Tabs
Style Sheet for Global Design System