You would think a new variant of concern could not be a good thing, but it fact it is possible. The update (Dec 5th) is that while is is clear a variant could help, that variant may not be Omicron.
Although this page will record data on omicron over time, given how long the virus have now been followed, already at this early time already there is significant data to work with, although some of the content here focuses on the possibility that a new variant could be a good thing.
- What We Do Know About Omicron, And What Is Not Yet Known.
- How Could A Variant Help?
- What makes a ‘Perfect’ Variant?
- Could We Make A Designer “Ideal” Variant?
- What could possibly go wrong?
What We Do Know About Omicron, And What Is Not Yet Known.
Just over two weeks ago since three people in Botswana were found to have a new variant of SARS-Cov2, with a significant number of mutations. It is highly unlikely this number of mutations occurred at once, or within a short span of time. The virus would have had a way of evolving undetected until now. The possible origins include:
- an isolated community.
- an individual with a compromised immune system where the virus could exist and evolve over a long time.
- the variant evolved in another species and then spread to humans.
The B.1.1.529 variant was first reported to WHO from South Africa on 24 November 2021. The epidemiological situation in South Africa has been characterized by three distinct peaks in reported cases, the latest of which was predominantly the Delta variant. In recent weeks, infections have increased steeply, coinciding with the detection of B.1.1.529 variant. The first known confirmed B.1.1.529 infection was from a specimen collected on 9 November 2021.WHO: Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern 26 November 2021
- It is not yet clear whether Omicron is more transmissible.
- It is not yet clear whether infection with Omicron causes more severe disease compared to infection with other variants.
- Preliminary evidence suggest there may be increased risk of reinfection with Omicron.
In summary, it is seen as possible that that major contribution to increased spread, could be through bypassing level 2 immunity. Update: At least, this did seem to be case initially, but now things are not so clear.
Clearly, we know Omicron is sufficiently more contagious than delta under the conditions prevalent in South Africa. Which also suggests high levels of level 2 immunity in South Africa, despite low levels of vaccination.
The chart at the head of this page and that to the left, shows just how rapidly omicron has taken over, suggesting an even larger increase in spread over delta, than delta represented over its predecessors. However, the rate of new cases is not only faster than with new variants, it is also fast that than recorded with the first wave.
Update: The chart to the left (with omicron as the time red spike) was produced showing that the rapid takeover of being the dominant strain occurred when cases were low. However, just two days after this chart was produced, the case numbers were those shown to the right, see here for details.
However, so far it has only ‘taken over’ during spring season, communities where vaccination rates are low, and HIV rates are high. Given delta is already highly contagious, what is required to spread even more effectively, and under what conditions is the spread so effective?
This is yet to be answered, but there are some concerning possibilities.
Vaccine And Immunity Resistance.
All evidence points to omicron evolving in an environment with low levels of vaccination, so it is unlikely to have evolved specifically to bypass vaccines. But it may have evolved to bypass immunity, and that may be independent on whether the immunity came from previous infection or vaccination. Vaccines trigger an immune response to the spike protein that resembles the the spike protein on the virus, so a new strain that looks different could bypass immunity.
There are however, several different mechanisms of immunity. One that is active in the body only when actively disposing of the virus, and fades withing weeks. Another that activates very rapidly and can significantly reduce spread, but fades after about two months. A third activates too slowing to be as effective in preventing spread, but usually reactivates the other mechanisms in time to prevent serious disease for around 6 months from previous immune response. All that is required to increase spread is to get around the second mechanism (level 2), so spread can be increased substantially, with the same increase in the prevalence of serious illness among those with immunity, either through vaccination or infection. So spread can also increase even among vaccinated populations, without vaccination becoming less effective against severe disease.
There are early suggestions that cases so far have been quite mild, but the cases have all occurred in a young population who even if unvaccinated, may have strong immunity from recent infection to other strains. If the spread In essence, there is hope, but it is just too early and data so far is inconclusive.
How Could A Variant Be Helpful?
What makes a ‘Perfect’ Variant?
Imagine a variant that takes over and replaces all other variants, but is less virulent. Perhaps that is what we already have with omicron?
Could We Make A Designer “Ideal” Variant?
If omicron has the potential to be beneficial, why can’t we make out own ‘designer’ variant, that takes over, but which like the sterile mosquitoes, at some point becomes unable to reproduce?
What could possibly go wrong?
Have you head the song “there was an old lay who swallowed a fly?
What happens if we need to create another variant to replace the first one we made?
To early. Come back in a few weeks.