Where Omicron might take us

This is quickly written ( poor structure and typos etc.) because I have lot going on, but this topic is important and things are changing very quickly.

Omicron is spreading crazy fast in South Africa, and can cause severe illness. How likely that latter is is unkown. We don’t have good data on how virulent (dangerous) an Omicron infection is, and in something this transmissible, the horse is out of the barn by the time we do. Here are three facts that I elaborate on below:

1) Omicron is far more contagious than Delta and will create a more dramatic rise in cases in the US than any other time in the pandemic
2) We are more likely to experience breakthrough infection with Omicron (meaning post vaccination or post reocvery from another COVID infection)
3) Omicron does have the ability to make some people very ill including children which might mean it is more severe an infection for everyone. Read below to understand why I believe them to be true. There are links in each section.

Now, there is not much science on this yet. It takes time to do a careful study and this is moving very quickly, so we do the best we can with what we know now.

1) Omicron is FAR more contagious

See the plot at OurworldInData here . (The arrows and notes on the plot are mine) Of note is this is a 7 day moving average. This is done to smooth out noise in the data and also testing and reporting trends driven by the 7 day workweek cycle (people work less on weekends, or maybe are more likely to get tested then, etc). Today’s data point is an average of the past 7 days. That means today South Africa is about 3.5 days further down the road than that data point. With that slope thismeans the country is already up to about 170 cases per million people per day

The plot is a log graph. On a log graph, the slope is proportional to the transmission rate. The slope in South Africa over the past 2 weeks is far steeper than at any time during the pandemic. It is more transmissiable than
Delta which was hands down the COVID contagiousness champ so far.

Transmission rate includes three factors that are hard to separate:

1. Inherent properties of the virus (how much it takes to infect a new host and how much virus the host puts into the environment) and
2. The amount of mixing in the population a(if everyone keeps to themselves it cant spread. If people are mixing more , something spreads faster)
3. How many people in the population are susceptible to reinfection.

That second one is hard to quantify at all. We can look at the Delta slope though for comparison . It is steeper. There is nothing special about the US that suggests the US will avoid a steeper slope with Omicron. This means when it starts to climb it will do so VERY quickly.

See the plot at OurworldInData here . You will see that in the non-log view South Africa total case counts do not look so bad since totaldaily cases are still lower than that peak. The graph might look this way if you are looking at it prior to December 5th. That log slope has predictive power. By December 6th or 7th, South Africa new daily cases should be at Delta peak levels, assuming they don’t run out of tests. ( I wrote this on the morning of December 3rd).

A side note: the US is starting to tick up also. Is this Omicron driven? I doubt it at this point. We just don’t have enough Omicron here yet for it to have a notable impact, though with its ability to spread, that will change within 3 weeks. I think the US uptick is behavior change and cold weather driven. (I believe that divot between 11/24 and 12/2 is due to a Thanksgiving testing fall off).

[Late edit: A COVID control champion, Hawaii, has now detected its first case of community transmission of Omicron. Yikes.

2) Omicron is likely to cause more breakthrough infections

Antibodies gum up the virus and make it so it can’t enter cells. They are not the only part of the immune system, but if the antibodies are not effective then at least a mild infection can ensue before the body reacts effectively. Omicrons has enough mutations in the parts that antibodies can easily get at that antibodies made for other versions of COVID are not effective. This means even someone recently convalescent, chock full of antibodies, or recently vaccinated, can get infected.

This finding is still preliminary, but careful experiements are being conducted right now to test this. It will take a week or so, and Omicron spreads so quickly, I am forced to lean forward and assume the preliminary will be borne out. This makes sense because the spike protein is what sticks out of the viruses encapsulation layer of fats so it is a prime target for antibodies. Omicrons’ spike protein has dozens of mutations which means it has chemical changes that make it harder for an antibody built for the old spike protein to stick to it and gum up the works.

Covid-19 Antibody Drugs Are Challenged by Omicron, Preliminary Testing Indicates

Scientists say it will take weeks to tell how dangerous omicron really is. Here's why

The good news here is, anecdotally, at least some folks who have been vaccinated have mild cases. The immune system is many layered so this could mean that a vaccinated individual’s body is able to learn to make Omicron countering antibodies more quickly. How severe the Omicron infection is and how much difference vaccination makes is not known at this time. That will take a few weeks of watching the first folks getting sick, but there is one disturbing warning sign.

3) Omicron can get people pretty sick

Lots more children are ending up in the hospital than at any other time in the pandemic in South Africa. It is particularly bad in the wholly unvaccinated under 5 set. It is unclear if this is because cases overall are rising very quickly and the percentage of children who get sick need a hospital is the same as any other time (so there are so many infected kids all at once even a small percentage needing hospitalization is still a big number) or if Omicron infection is more dangerous to kids.

So far in the pandemic children have generally fared better with COVID infection than adults, but it could be this one is particularly worse for kids and less so (or even easier) on adults. This news is troubling in that it might mean Omicron is more dangerous, and particularly scary for vaccinated parents who now have to seriously fear bringing a breakthrough case home to their children. We don’t know that it is more dangerous. It might even be less dangerous to adults or even children since we don’t know the entirety of what is behind the rise in more children showing up in the hosptial in South Africa.

What we do know for sure is that Omicron can cause hospitalization level illness. Omicron is not the pandemic ender I have fantasized about: a VERY transmissible variant that squeezes out other variants but only gets people a little ill. At the least, this one can really impact small children seriously. It is not unreasonable to wonder if this means Omicron is more dangerous to adults than prior variants because children tended to become less ill with those. I hope the dramatic increase in hospitalization of kids in South Africa is because nearly everyone has it and it just is not making the adults as sick. If that is true then we will see case counts start falling soon in South Africa (the mythical herd immunity that has never materialized anywhere). I am pessimistic on that, but that is just a hunch by hoping the same thing many times before during the pandemic.

Omicron spikes hospitalisation among kids under 5 in South Africa

Closing thoughts

I hate that there is little hard science on this yet. Using anecdotes (news stories) is fraught with peril but this is moving so quickly we have to make decisions and news stories are the best I can do. I did go as far to confirm these news stories in multiple sources and rely more on quotations from experts rather than what the journalists write. I am going to watching Israel and England closely, which are similiarly vaccinated as the US and probably a bit ahead of the US in the Omicron infection curve.

For me Omicron means 1) I am watching for notable upticks in my area and will revert to extreme caution when I see it (early morning grocery shopping. Keeping more to myself, etc.) 2) I am going to be flexible in my plans. I have some upcoming travel I am looking forward to (exciting conference and side trip to my gf) and I am ready to cancel it if things look risky.

I am quite vaccinated, and I still do not want this thing in my body. I am also enjoying getting out in the world a bit more, going to open mics, my dad and gf coming to visit in late December, not wearing masks when I pass someone on a hiking trail, going to somewhat crowded outdoor areas, going to stores just for fun sometimes. I am mentally preparing myself to not do things that are upcoming that I REALLY want and change how I move in the world.

I hope in a week, South Africa new daily cases have crested and is clearly on the downslope. I am prepared for it being on fire and what that means for us.

— — — — — — — — — — — — — — — — — — — — — — — — — —

* Steeper except for the early days when slope was driven by new test availability more than transmission. At the beginning of the pandemic a lot of cases were undetected and as tests became available the number of cases went up quickly making a steep slope.