This week, a new strain of the SARS-CoV-2 virus was identified and sequenced in South Africa, enhancing our understanding of its characteristics. The World Health Organization was informed about this variant on November 24th, and it has been named Omicron (B.1.1.529) as part of the Greek alphabet system. This development is particularly alarming to scientists globally.

In response to this news, several nations have promptly closed their borders. Israel has enacted a strict ban on all entrants, while the U.K. and the U.S. have opted for a more moderate response, restricting access specifically from South Africa, where the variant was first identified.

Governments are rushing to implement measures, and some experts express concern that it may be too late to effectively manage the variant's spread if the worst-case scenarios materialize.

Why is there such concern among experts?

The Current Data Landscape To grasp the reasons behind this anxiety, we need to consider the situation in South Africa prior to the discovery of Omicron. We must also acknowledge that viruses typically emerge in waves, a pattern that is evidently true for SARS-CoV-2, the causative agent of COVID-19.

The virus initially surges through a population, rapidly spreading before moving on to another group. This pattern can be observed in historical outbreaks, including the Bubonic Plague, which had several waves following its initial emergence in the 14th century.

Before the emergence of Omicron, South Africa was recovering from a particularly severe wave caused by the Delta variant. An analysis of daily new COVID-19 cases and fatalities reveals three distinct peaks.

These peaks represent individual outbreaks, akin to those witnessed during the Black Death and other pandemics.

As the virus has adapted, it has become increasingly transmissible, which is evident in the rising daily case counts with each new wave.

The rapid increase in cases seen at the far right of the charts signifies the emergence of the Omicron variant. This alarming uptick occurs much faster than previous waves.

Typically, the speed of infection spread in each wave serves as a strong indicator of the outbreak's overall impact. This is why border closures and efforts to slow transmission are critical — they provide the necessary time to prepare.

In military terms, a swift surprise attack poses significant challenges for defense before troops can establish their positions.

Currently, the Omicron variant appears to be spreading more quickly than Delta, with initial reports indicating many of the first patients affected were younger individuals, although the available data is still limited.

Is Omicron More Contagious or Deadly? Regarding its contagiousness, preliminary data raises concerns. The Omicron variant seems to have rapidly proliferated in South Africa, with early reports indicating that it constitutes the majority of sequenced cases in the country.

It is important to note that this information may evolve as virologists and epidemiologists continue their analyses. The swift spread could potentially result from a superspreader event or multiple events, rather than intrinsic transmissibility of the variant.

At this point, we lack sufficient data to draw definitive conclusions. However, experts are particularly concerned about the numerous mutations present in Omicron, which may enhance its transmissibility.

Notably, mutations like E484K, N501Y, and D614G on the spike protein have been observed, along with R203G and G204R on the nucleocapsid protein.

All these mutations pose risks.

The E484K mutation impairs the ability of antibodies to recognize the virus, allowing it to spread before the immune system can respond effectively.

Laboratory studies suggest that the N501Y mutation enhances the binding affinity of the viral spike protein to human cells, facilitating replication and widespread infection. This mutation has also been linked to increased transmissibility in the Alpha and Gamma variants of SARS-CoV-2.

The D614G mutation, associated with the U.K. variant, seems to enhance the virus's ability to attach to and infect human cells.

Another significant mutation is Q498R, which Israeli researchers predicted in a published study in August 2021, suggesting it could amplify the infectivity by 50 times when combined with N501Y and E484K.

In laboratory settings, the Omicron variant appears formidable. However, as with past predictions, laboratory findings do not always translate to real-world scenarios.

Before jumping to conclusions, it is prudent to exercise caution, take preventive measures, and await further data.

Will Our Vaccines Remain Effective? Beyond the question of transmissibility, a crucial concern is whether the virus can evade vaccines to a concerning degree. If so, to what extent can it bypass the immunity our vaccines provide?

Scientists are particularly apprehensive given the over 30 mutations present on the Omicron spike protein.

Most COVID-19 vaccines (e.g., Pfizer/BioNTech, Moderna, Johnson & Johnson, and AstraZeneca) are designed to target the spike protein for eliciting immunity. These vaccines introduce genetic material into cells, prompting them to produce the spike protein.

The immune system recognizes these proteins as threats, triggering antibody production, essentially preparing the body for future encounters with the actual virus.

So, why the alarm?

The issue lies in the virus's evolution; mutations have occurred in the genes responsible for producing the spike protein that binds to ACE2 receptors on human lung cells.

As a result, the immune system, primed to respond, may struggle to recognize the newly mutated spike proteins on the Omicron variant.

Additionally, the efficacy of monoclonal antibody treatments for infected individuals is uncertain under this scenario.

However, it is important to note that we currently lack definitive evidence to support these concerns; they remain hypothetical. Thus, there is no immediate cause for panic. We should remain vigilant and take appropriate precautions as we adapt to the evolving situation.

Thank you for reading. If you're interested in staying updated with my insights, consider signing up for my email list. For more information on mutations and viral evolution, I recommend exploring the article linked below and following the research of Shin Jie Yong.

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