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Scientists Identify Growing Number of COVID-19 Variants, But Not All Clinical Laboratories Have the Capability to Test for Variants

Fear that immunity-resistant mutations of SARS-CoV-2 will emerge are real and the scientific community is paying close attention

Detection of an increasing number of new variants of the SARS-CoV-2 coronavirus raises the possibility that a new strain of COVID-19 might emerge that brings new problems to the management of the pandemic. Public health officials and clinical laboratory scientists are on the alert to determine if any new COVID-19 variant is more virulent or more easily transmissible.

Pathologists, along with the rest of the scientific community worldwide, are following reports of increasing coronavirus mutations with growing concern. The Alpha variant (Lineage B.1.1.7) accounted for most of the COVID-19 cases in April of 2021 in the US, though it was first identified in the United Kingdom. That was followed by the Iota variant (Lineage B.1.526) first identified in New York City. A series of other variants were to follow. Scientists were not surprised. It is normal for viruses to mutate, so they logged and tracked the mutations.

Then, the Delta variant (Lineage B.1.617.2) emerged during a severe outbreak in India. At first, it did not seem more threatening than any other variant, but that changed very quickly. Delta was different.

“The speed with which it dominated the pandemic has left scientists nervous about what the virus will do next. The variant battles of 2021 are part of a longer war, one that is far from over,” The Washington Post reported, which added, “Today, [Delta] has nearly wiped out all of its rivals. The coronavirus pandemic in America has become a Delta pandemic. By the end of July, it accounted for 93.4% of new infections, according to the Centers for Disease Control and Prevention.”

Why is Delta the Worst COVID-19 Variant So Far?

The Delta variant has two advantages that scientists know about:

  • Stickier spike protein than the spike on the original SARS-CoV-2 coronavirus, as well as on the other, earlier variants. This means that the Delta variant stands a better chance of remaining in a person’s nose or throat long enough to reproduce.
  • Faster replication. When a virus mutation has more opportunity to reproduce, it quickly becomes the main viral strain. This is the case with the Delta variant. Experts say that the viral load in patients with Delta is around 1,000 times higher than in patients with the original virus.
Colorized scanning electron micrograph of an apoptotic cell that is infected with the SARS-COV-2 virus

The image above is a “Colorized scanning electron micrograph of an apoptotic cell (tan) heavily infected with SARS-COV-2 virus particles (orange), isolated from a patient sample,” Newsweek reported. (Photo copyright: National Institute of Allergy and Infectious Diseases/Newsweek.)

Will More Dangerous SARS-CoV-2 Variants Appear?

“The great fear is that nature could spit out some new variant that completely saps the power of vaccines and upends the progress we’ve made against the pandemic. But to virologists and immunologists, such a possibility seems very unlikely,” STAT reported.

That is because, unlike Influenza, which is also a coronavirus, SARS-CoV-2 variants are not able to share genetic materials and recombine into deadlier variants. Thus, scientists are skeptical that a variant could appear and wipe out the progress made with vaccines and treatments.

One of the reasons the Flu vaccine changes every year is Influenza’s ability to recombine into variants that can evade immunity. Therefore, scientists are beginning to suspect that SARS-CoV-2, like the Flu, will likely be around for a while.

“I don’t think eradication is on the table. But I think we could come up with something that’s better than what we have for the flu,” Sharone Green, MD, Associate Professor of Medicine, Division of Infectious Diseases and Immunology and Infection Control Officer at University of Massachusetts Medical School, told Newsweek.

Limiting Infections and Replication

Several factors combined to create the COVID-19 pandemic. But SARS-CoV-2 was a novel coronavirus, meaning it was a new pathogen of a known virus. This meant every person on the planet was a potential host.

The situation now is different. Thanks to natural immunity, vaccines, and treatments that shorten the infection, the SARS-CoV-2 coronavirus has less chance to replicate.

“The pressure is there, but the opportunity is not. The virus has to replicate in order to mutate, but each virus doesn’t get many lottery tickets in a vaccinated person who’s infected,” Jeremy Kamil, PhD, Associate Professor of Microbiology and Immunology at LSU Health in Shreveport, La., told STAT.

Tracking Variants of Interest and Variants of Concern

The World Health Organization (WHO) has been monitoring the viral evolution of SARS-CoV-2 since the beginning of the pandemic. In late 2020, the WHO created categories for tracking variants:

The WHO’s lists of VOIs and VOCs help inform the global response to the COVID-19 pandemic.

According to the CDC’s SARS-CoV-2 Variant Classifications and Definitions:

VOIs are “A variant with specific genetic markers that have been associated with changes to receptor binding, reduced neutralization by antibodies generated against previous infection or vaccination, reduced efficacy of treatments, potential diagnostic impact, or predicted increase in transmissibility or disease severity.”

Current VOIs include:

  • Eta (Lineage B.1.525), detected in multiple countries, designated a VOI in March 2021.
  • Iota (Lineage B.1.526), US, first detected in November 2020, designated a VOI in March 2021.
  • Kappa (lineage B.1.617.1), India, first detected in October 2020, designated a VOI in April 2021.
  • Lambda (lineage C.37), Peru, first detected in December 2020, designated a VOI in June 2021.

VOCs, on the other hand, demonstrate all the characteristics of VOIs and also demonstrate “an increase in transmissibility, more severe disease (e.g., increased hospitalizations or deaths), significant reduction in neutralization by antibodies generated during previous infection or vaccination, reduced effectiveness of treatments or vaccines, or diagnostic detection failures.”

Current VOCs include:

  • Alpha (lineage B.1.1.7), first detected in the UK, September 2020.
  • Beta (lineage B.1.351), first detected in South Africa, May 2020.
  • Gamma (lineage P.1), first detected in Brazil, November 2020.
  • Delta (lineage B.1.617.2), first detected in India, October 2020.

Will Vaccines Stop Working?

With each new variant, there tends to be a flurry of media attention and fearmongering. That a variant could emerge which would render our current vaccines ineffective has the scientific community’s attention.

“There is intense interest in whether mutations in the spike glycoprotein mediate escape from host antibodies and could potentially compromise vaccine effectiveness, since spike is the major viral antigen in the current vaccines,” wrote Adam S. Lauring, MD, PhD, and Emma B. Hodcroft, PhD, in “Genetic Variants of SARS-CoV-2­—What Do They Mean?” published in the Journal of the American Medical Association (JAMA). 

“Because current vaccines provoke an immune response to the entire spike protein, it is hoped that effective protection may still occur despite a few changes at antigenic sites in SARS-CoV-2 variants,” they added.

Future events may justify the optimism that the ongoing effectiveness of vaccines will help with many COVID-19 variants. But pathologists and clinical laboratory leaders may want to be vigilant, because as infection rates increase, so do workloads and demands on critical resources in their medical laboratories.

Dava Stewart

Related Information

‘Goldilocks Virus’: Delta Vanquishes All Variant Rivals as Scientists Race to Understand Its Tricks

Viral Evolution 101: Why the Coronavirus Has Changed as It Has, and What It Means Going Forward

A Doomsday COVID Variant Worse than Delta and Lambda May Be Coming, Scientists Say

Tracking SARS-CoV-2 Variants

Genetic Variants of SARS-CoV-2—What Do They Mean?