Will Omicron Save Us?

With the world atwitter over a new coronavirus variant, it seems a good time for armchair epidemiologists to take a look at what is coming. Before we dive into Omicron, lets look back at the Delta surge, and before that Alpha.

The figure above from the New York Times shows US new cases since the start of the pandemic. Pandemics grow exponentially at the beginning of the spread of the disease. The rate of growth is determined by the how many other people a sick individual infects, this number known as R_0, and the average incubation time between infections, R_T. Very quickly into the spread of the pandemic, the reproductive rate of the disease decreases as people get frightened and mitigate spread of the disease. Whether the pandemic grows or shrinks depends and the effective growth rate R_E which combines the effectiveness of the our mitigation efforts with the infectiousness of the pathogen. Seasonal effects add to the confusion with these numbers because our normal behavior in the summer, spending much time outdoors, can lead to low infection rates than when we are inside more in the winter. The pandemic’s history over the last two years illustrates some of these features.

  • Alpha variant emerges with R_0 \approx 3 March 2020.
  • Distancing and masking mitigation efforts reduce R_E to around 1 until November 2020. This implies masking and distancing reduce spread by 1/3 what it would have been without those measures.
  • Pandemic fatigue, holiday gatherings, and winter indoors allows pandemic to grow winter 2020-2021.
  • Improved Spring weather, the vaccine rollout, increasing acquired immunity from infection all lead to a contraction of the pandemic until June 2021.
  • The Delta variant, estimated R_0 \approx 6, simmering below the surface since May 2021, overcomes our relaxed mitigation efforts and spreads quickly especially among the unvaccinated during summer 2021.
  • Delta’s surge encourages more vaccination, infects more individuals which adds to the pool of acquired immunity, and brings back masking and more gathering restrictions so that Delta peak is in remission by October 2021.

Prior to Omicron, this is where we are. The dominant Delta variant with R_0 = 6 can only be brought under control when >80% of the population has immunity to the disease. The fully vaccinated fraction of the population is approaching 60%. SARS-CoV-2 seroprevalence studies show that between 10% and 40% of the unvaccinated population have antibodies for the disease from prior infection. Regions of the country that have been hit hard by the disease, like many of the southern states, are presently reaping the benefits of previous infection with fewer new cases than the rest of the country. But we know that all immunity wanes and natural immunity wanes more quickly than for those vaccinated.

So what do we know about Omicron? Here is what I can find out two weeks after its presence was announced.

  • Omicron emerged from the Delta milieu in South Africa. Preliminary estimates suggest that R_0 for the Omicron variant is about twice that of Delta. So maybe R_0 o \approx 12.
  • In a very small study (just 42 cases), many of the cases were discovered because all patients admitted to the hospital were tested for COVID but otherwise did not present overt COVID symptoms. Of the nine patients that developed pneumonia, eight were unvaccinated and one was a child. The average length of hospital stay for all of these patients was 2.8 days compared to 8.5 days for all patients in the regions hospitals, mostly there with COVID.
  • Many more reinfections are reported with Omicron compared to the earlier variants.
  • Omicron seems to have mysteriously evolved into its present form from a version of the virus that existed about a year ago. Speculations about how this happened include 1) an intermediate animal host that harbored the virus for much of the past year, 2) stealth evolution in an isolated community, 3) evolution inside a single immunocompromised person for much of the intervening time. Or maybe some combination of these possibilities.
  • The WHO reports that Omicron is now found in 38 countries but that there are no deaths associated with the new variant.

Now for the speculation. There seems to be good evidence that the Omicron variant is significantly less dangerous than its predecessors. If we consider the origin stories (and exclude the animal host version) there could be a couple of reasons why this variant is less virulent. First, if the virus was isolated in a single immunocompromised individual for almost a year, then survival of that patient may have been predicated on a mutation to a weakened form of the virus. Virulent COVID for a year should have killed an immunocompromised patient. How about evolution of the virus in an isolated community? There again, if the mutated virus was virulent and caused typical COVID symptoms, even in an isolated community you would have people seeking medical attention and the evolving virus would be detected. However, if the symptoms are mild or nonexistent, then the virus can circulate and mutate stealthily.

What are the implications of a virus with R_0 \approx 12? To stop it you need >90% of the population with immunity. This is just not going to happen outside of a few highly at-risk communities in the United States at this time. This suggests that the Omicron variant is going to rapidly out-compete Delta and more fully infect reservoirs of insufficient immunity. But, the small South African study suggest that the vaccines are likely to moderate the severity of an already mild form of the disease, although significantly more breakthrough cases would be anticipated.

The big question that we have to ask going forward is how much immunity will the Omicron variant provide to offer protection to the Delta and other more virulent forms of the disease? Will Omicron become the mildly benign vector for general COVID immunity, or will COVID branch into more than a single dominant line? There is at least the hope that highly infectious Omicron will quickly infect the non-vaccinated and offer them enough immunity that the pandemic devolves into chronic low level infections that behave much more like the common cold.

The process of a pathogen mutating to less virulent, but more transmissible form, is a common theme in the dance between immunity and pathogens. It is too early to say that this is the path for Omicron, but the hints already suggest that this wave will have a different character than the preceding ones.

I’m not alone with this point of view. Dr. Mobeen Syed seems to think that perhaps the omicron will pave our way out of the pandemic and made this little cartoon.

3 Comments

  1. I hope you are right. Thank you for sharing your thoughts. B

    ____________________________________ Barbara and James Cole Sailing Vessel Complexity

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  2. “we know that all immunity wanes and natural immunity wanes more quickly than for those vaccinated.”

    What are your sources for this claim?

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