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“Kraken,” the newest descendent of the Omicron variant

Lucía Garrido

All viruses, including SARS-CoV-2, which causes COVID-19, change over time. Most changes have little to no impact on the virus’s properties. However, some changes may affect the virus’s properties, such as how easily it spreads, the associated disease severity, or the performance of vaccines, therapeutic medicines, diagnostic tools, or other public health and social measures. 

In June 2020, the WHO Virus Evolution Working Group was established with a specific focus on SARS-CoV-2 variants, their phenotype, and their impact on countermeasures. This later became the Technical Advisory Group on SARS-CoV-2 Virus Evolution. In late 2020, the emergence of variants that posed an increased risk to global public health prompted WHO to characterize some as variants of interest (VOIs) and variants of concern (VOCs) to prioritize global monitoring and research and to inform and adjust the COVID-19 response. From May 2021 onwards, WHO began assigning simple, easy-to-say labels for key variants.

Considerable progress has been made in establishing and strengthening a global system to detect signals of potential VOIs or VOCs and rapidly assess the risk posed by SARS-CoV-2 variants to public health. It remains critical that these systems are maintained as SARS-CoV-2 continues to circulate at high levels worldwide. While monitoring the circulation of SARS-CoV-2 globally, it also remains essential to monitor their spread in animal populations and chronically infected individuals, which are crucial aspects of the global strategy to reduce the occurrence of mutations that have adverse public health implications. In March 2023, WHO updated its tracking system and working definitions for variants of concern, variants of interest, and variants under monitoring.

Viruses naturally mutate over time and lead to new versions or variants.

Variants of viruses naturally merge to form hybrid or recombinant versions. Scientists have identified this process in the COVID-19 virus. A Delta-Omicron recombinant has been detected recently in the USA, U.K., Australia, and parts of Europe, but the number of cases of this version still needs to be higher. The sequencing technology used in B.C. can detect recombinant variants of COVID-19.

Types of Classification

There are multiple ways in which SARS-CoV-2 viruses are classified. Each classification type can be appropriate, depending on the context in which SARS-CoV-2 is being communicated. SARS-CoV-2 is often discussed in the context of lineages (and sublineages). The most commonly used classification system for lineages is Pango. Nextclade may also be used in this context. In a larger context, lineages or groups of related lineages may be classified using Greek letters (such as Omicron) by the World Health Organization (WHO). These classification methods enable scientists to communicate similarities and differences between SARS-CoV-2 viruses.

B.C. aligns with the Public Health Agency of Canada (PHAC) to determine which variants are classified as variants of concern. Currently, the variants of concern include the following:

  • Omicron (B.1.1.529) was first detected in South Africa on November 9, 2021. Omicron has mutations in the spike region, affecting how it spreads and responds to treatments and vaccinations. 
  • The Omicron variants include many lineages, such as BA.1 and B.A.,2*, and sublineages (BA.2.12, BA.1.1*, etc.). Figure 1 in the weekly data report lists the current Omicron sublineages detected in the province.
  • Delta (B.1.617.2) is a subline of B.1.617, first detected in India. Delta spreads quickly and may lead to more severe disease, particularly for unvaccinated people. Delta includes B.1.617.2 and many AY.* sublineages.
  • Gamma (P.1), the variant first reported in Japan but later identified as originating in Brazil, may be able to re-infect people who have had COVID-19. Gamma includes two sublineages, P.1.1 and P.1.2. Some current treatments may not work as well in cases of this variant. 
  • Beta (B.1.351), the variant first reported in South Africa, spreads more quickly than older strains and has numerous sublineages. Some current treatments and vaccines may not work as well on cases of this variant and its sublineages, yet this VoC has yet to become established globally. 
  • Alpha (B.1.1.7), the variant first reported in the U.K., spreads quickly and can cause more severe illness than previous versions. Alpha also includes the Q.* sublineages.

Viruses naturally evolve; some variants can merge to form a hybrid or recombinant version. Scientists have identified COVID-19 recombinants, such as the Delta-Omicron recombinant detected in the USA, U.K., Australia, and parts of Europe. 

WHAT YOU NEED TO KNOW…

  • Omicron has evolved to include many different sublineages.
  • Currently, Omicron (BA.5 and many other sublineages) are the most commonly detected variants in B.C.
  • Public health and researchers are studying the Omicron sublineages closely.
  • Omicron has spread more easily between people than previous COVID-19 variants.
  • People can spread Omicron to others even if they have been vaccinated, especially when they have symptoms.
  • Vaccinated people have a milder case of Omicron and are less likely to end up in the hospital than those who are not vaccinated.
  • Current vaccines provide reasonable protection against severe illness and hospitalizations for Omicron.
    • A third vaccine dose helps to provide more protection from Omicron.
    • Breakthrough infections can occur in people who are fully vaccinated.
  • People who have had COVID-19 can get sick again from new variants.
    • Getting vaccinated is essential even if you have already had COVID-19.
  • Monitoring and research on the new COVID-19 variants are ongoing. This page will be updated often. 
  • More details on the current sampling and sequencing strategies are in the Testing for COVID-19 variants section below.

About the Kraken Covid Variant

This variant is a sublineage of a recombinant of two other Omicron offshoots. That mixing can happen when a person is simultaneously infected with two virus variants or if the two meet in wastewater. 

This one could stand out among the several circulating Omicron variants if it has two advantages that would make it highly infectious—an ability to evade antibodies acquired from past infections or vaccinations and strength in binding to ACE2 receptors, where Covid enters cells and infects people. A preprint posted in early January by Chinese researchers focusing on XBB.1.5 argues that it does, but that paper has not been published or peer-reviewed. 

“It’s kind of a one-two punch of mutations”, says Peter Hotez, co-director of the Texas Children’s Hospital Center for Vaccine Development and dean of the National School of Tropical Medicine at Baylor College of Medicine. “It not only has the immune escape properties, but it was able to do it while preserving its ability to bind to the receptor.” 

It’s also spreading faster because of how people behave: Few wear masks compared to 2020, and many have traveled and gathered indoors to celebrate the holiday season. That’s a recipe for lots of people getting sick, fast. “What we’re having right now is this subvariant that has a lot of immune escape that is also coming into play when we have pretty much removed most, if not all, of our other public health mitigating practices,” says Stephanie Silvera, an epidemiologist, and professor of public health at Montclair State University in New Jersey. 

The variant has been found in 38 countries, according to the WHO. Those include South Korea, Australia, and nations in Europe, where it made up less than 2.5 percent of the proportion of cases during the final two weeks of 2022, the European Center for Disease Control and Prevention said Monday. But the agency notes that the rapid spread in the U.S. doesn’t mean the variant will also become dominant across the Atlantic. 

While most countries have seen Covid waves rise and fall, China is currently dealing with its first massive outbreak after three years of strict containment measures. A hyper-contagious variant could affect that population differently. Experts don’t know yet if the unfettered spread of XBB.1.5 in China could spur the emergence of a “new super variant” or one that’s especially dangerous or transmissible.  

Some variants never live up to initial concerns. Experts watched the Mu variant closely in the late summer of 2021, fearing it would cause breakthrough infections. But it receded quickly. XBB.1.5 could fizzle out without becoming dominant elsewhere, but experts say it’s too soon to know how it will spread. 

Sources: 

https://www.who.int/activities/tracking-SARS-CoV-2-variants
https://www.wired.com/story/kraken-covid-variant-xbb15/

http://www.bccdc.ca/health-info/diseases-conditions/covid-19/about-covid-19/variants

https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-classifications.html

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