Omicron Update: Nov 29
In an attempt to keep you up to speed, here’s an Omicron update.
1. All U.S. adults should get a booster.
Before today, this was CDC’s recommendation for boosters in the US:
The CDC changed its recommendations today. Now, all adults should (not may) get a booster. Like I posted yesterday, we have reason to believe that boosters will help protect against Omicron. (Parents: no word yet on 12-17 year old boosters).
2.
WHO Update
Last night the WHO provided an update, which basically said we still have more questions than answers: Is Omicron more transmissible? How do vaccines work against Omicron? Does Omicron cause more severe disease? We don’t know, but we’re working on it. There were a few sentences worth highlighting, though:
“Preliminary evidence suggests there may be an increased risk of reinfection with Omicron (ie, people who have previously had COVID-19 could become reinfected more easily with Omicron), as compared to other variants of concern, but information is limited.”
So, infection-induced immunity (some are calling it “natural immunity”) may not work well against Omicron. This isn’t a surprise because we saw this with Delta too: Those with infection-based immunity were 5 times more likely to be reinfected than those with vaccines. Time for the unvaccinated to get vaccinated.
3. What’s happening on the ground in South Africa?
As expected, cases are rising. Omicron has been identified in each region in South Africa, so exponential spread is well on its way. A South African epidemiologist estimated that by next week there will be 10,000 new cases per day in South Africa.
An increase in cases means Omicron is spreading. This does not necessarily mean Omicron is more transmissible (i.e. more contagious/ higher R(0)) than Delta. We have to marry lab data (what are the specific mutations doing) with “real world” data (does Omicron outcompete Delta in places with high rates of Delta, like the US) to see.
Keep in mind that there is a possibility (some say strong) that Omicron will be less transmissible than Delta. That’s because there’s a trade-off between immune escape (or immune corrosion) and transmissibility. We’ve seen that with other variants of concern. In the figure below, transmissibility (or contagiousness, or R0) is on the horizontal axis and antibody effectiveness on the vertical axis. The higher in either direction, the worse. To know where Omicron is on this chart is a complex, scientific guess at this point.

Back to South Africa... Test positivity rate (TPR) is also increasing. TPR has consistently been an early indicator of what’s to come. TPR indicates whether a community is testing enough to catch the virus. We decrease TPR by increasing testing: People learn they are positive, they isolate, and stop spreading the virus. Early in the pandemic, the World Health Organization advised countries to strive for a 5% TPR. As of November 27, TPR in South Africa is at 9.77% (3,220 cases from 34,880 tests). This is not terrible, but not great.

We are also seeing a rise in wastewater tests. Wastewater is actually an incredibly accurate, early indicator of case rise. The figure below shows wastewater tests in the city of Tshwane (near South African epicenter) alongside lab confirmed cases. Detection of COVID-19 in wastewater is almost as high as it was with Delta. So, this could mean a rise in cases is coming. This also could mean that cases are mild so they are going undetected. Time will tell.
On a national level, we don’t see a rise in hospitalizations in South Africa. But hospitalization trends lag case trends 2-4 weeks, so this may be coming. This pattern has been consistent throughout the pandemic.
However, if we zoom in on South Africa’s epicenter— Gauteng— we start seeing a rise. Below is a graph from the National Institute for Communicable Disease. The bars are hospitalizations per week (Monday - Sunday). Last week, there were 580 COVID-19 hospitalizations, which is a 110% increase from the previous week. This week just started, and there are 71 hospitalizations so far.
It’s important to note that this increase in hospitalizations isn’t necessarily because Omicron is more severe than other variants. It could just reflect the fact that more people are getting infected. Parsing this out is key to understanding Omicron.

In the past 24 hours, there’s been news about “mild presentation” of Omicron, leading some to the conclusion that that Omicron is not severe. I sure hope this is the case, but be cautiously optimistic. Those were only ~100 mild cases among young people and do not represent country-level demographics.
4. What’s happening in other parts of the world?
As expected cases are starting to pop up all around the world— 5 continents, 21 countries, and 195 confirmed cases. At some point there’s no point to tracking this, but for now it’s fascinating for epidemiologists to follow.

When you hear about cases in the news, it’s important to distinguish whether these cases are from travel or from the community. If a case has no travel history or no contact with someone who has traveled to South Africa (like the 3 cases in Israel), this is a clue that Omicron has already been spreading.
5. Why haven’t we found a case in the United States?
We hypothesize that Omicron is already in the States; it’s just been flying under the radar. We don’t have a confirmed case yet.
Our genomic surveillance system is suboptimal given our large population. While it’s getting better, it’s ranked 20th in the world.
Regardless, we have 68 Public Health Labs sequencing 15,000-20,000 specimens to search for variants like Omicron. We also have commercial labs, CDC contract labs, and academic labs. Nationally, ~5% of all specimens are sequenced. This means our system can detect down to 0.01% of circulating variants. So, Omicron can be found…eventually.
We can also identify Omicron on PCR tests. Usually a swab would have to go to a special lab for genome sequencing to know which variant caused the infection. However, it looks like Omicron has a special signal on the PCR directly. For example, when the PCR is positive it lights up two channels instead of three channels, indicating that it’s Omicron instead of Delta, for example. So why haven’t PCR tests caught Omicron in the U.S. either?
It may be that testing centers don’t know this handy trick yet
Maybe we have a positive PCR but it was sent to a lab for confirmation
Maybe we aren’t testing enough to detect a small number of cases
Or, there’s the possibility that it’s just not here yet
6. What about holiday plans?
During the onslaught of interviews today, many asked me about what Omicron means for the holidays. Can we still fly? What about holiday parties? Is Christmas cancelled? People… Let’s get through this next week. Once we have the data, we will know how to approach holidays smartly. But I have a hunch that it will include—can you guess?—masks, testing, ventilated spaces, and vaccines.
Love, YLE
“Your Local Epidemiologist (YLE)” is written by Dr. Katelyn Jetelina, MPH PhD— an epidemiologist, biostatistician, professor, researcher, wife, and mom of two little girls. During the day she has a research lab and teaches graduate-level courses, but at night she writes this newsletter. Her main goal is to “translate” the ever-evolving public health science so that people will be well-equipped to make evidence-based decisions, rather than decisions based in fear. This newsletter is free thanks to the generous support of fellow YLE community members. To support the effort, please subscribe here:
Katelyn,
Going back to your 11/15 post "State of Affairs: Europe", I think it deserves some follow-up in light of recent developments with Omicron.
It's been 19 days since Der Spiegel created the infographic showing how much better Portugal, Spain, Malta, and Denmark were doing than the rest of Europe thanks to their high vaccination rates. What has happened since? Cases spiked in the cited "doing it right" examples.
- Spain is clearly in their 6th wave, which is on track to have surpassed their 1st and 4th waves. Additionally, Omicron is detected, but unlikely the cause of their 6th wave. Restrictions being added back in.
- Portugal cases rose since publication as well, now higher than their 1st and 4th waves. 13 cases of Omicron detected at a fully vaccinated soccer team in Lisbon. Restrictions back in place.
- Denmark is now at an all-time high in cases for the entire pandemic. Omicron detected in a few people as well. Finland, Iceland, and Norway are at all-time highs as well, all having very high vaccine rates - curiously I just noticed that Der Spiegel left off Norway and Iceland when they made their original scatterplot - I surmise because it didn't help the correlation they were framing as their rates were already skyrocketing in the Nov 1- Nov 7 snapshot they chose to make their argument.
- Malta, same story as the others.
- Vermont, already at its highest level of infection throughout the entire pandemic when this piece was published, has soared even higher. Excess deaths continue to be elevated by 20% throughout the state, though that data lags by 6 weeks, so our insight ends late October.
Experts appear to be pivoting, and now we are getting (in my opinion) disingenuous stories proclaiming "this isn't surprising", or "this is what we have been saying all along".
Example:
"There’s another factor at play that could help explain why Vermont, in particular, has seen such high case counts in recent weeks: Only a small proportion of residents have had a COVID infection. That’s not the case across the country."
From:
https://www.vpr.org/vpr-news/2021-12-01/why-vermonts-covid-surge-isnt-surprising
Which goes against what the CDC has claimed, that the vaccine is 5x more effective at preventing breakthrough infections. Now we need 3 doses and to get the infection anyway?
_________
Where am I going with all this?
Science evolves. I get that. It feels to me that some are sticking by hypotheses that data appears to reject, but we aren't evolving along with that data.
The original hypothesis for the vaccine was that it would end the pandemic. I'm too lazy to dig up quotes, but Dr. Fauci, Dr. Wallensky, et al, repeatedly stated that at 50%, 60%.... 70% vaccination levels we would no longer see cases rise like before. That while there may be the odd breakthrough case here or there, but cases would never reach levels like they did before. That deaths would decline.
It's been a year. Does this hypothesis hold up? Should it be discarded? What updates can be made to salvage the hypothesis without falling into a sunk-cost fallacy?
What are some competing hypotheses to explore?
As a lay person, it looks like the Covid 19 vaccines are about as efficacious as flu vaccines, not nearly the 95% promised. And flu vaccines are notoriously not very good.
And it is perfectly "Ok" that flu vaccines, and possibly Covid vaccines aren't very good. Science can't be rushed. We are barely at 100 years of so many tremendous breakthroughs in medicine, so I dont have unrealistic expectations, but at the same time, I don't want to be bullshitted to either. (which is why I subscribe to you :) )
And I'm skirting with "correlation doesn't equal causation", but it feels like these variants are in answer to our vaccines. Alpha dominates until we rolled out first set of vaccines. Delta bypasses those (I'm aware Delta was around prior to our roll-out, but clearly it was the lineage of all the other ones that seemed to thrive among our vaccinated population). Now we are boostering people, and Omicron, at least very early, looks like the candidate selected to bypass those. If not Omicron, I assume something else will step up, no?
Throughout my life I have been told not to overtake antibiotics because bacteria will create new strains. Does this carry over to respiratory viruses/ILI? Is this why Michael Osterholm responded "It's much more complicated than we thought...I know less about influenza today than I did 10 years ago." When quizzed on why Flu Vaccines fail so frequently in 2017? [1]
Is it possible we are at war with something which can't be out-vaccinated? Are we ready to embark on a multi-year campaign of quarterly vaccines, always a step behind the next greek alphabet letter? Could this potentially make things worse than they are now? I'm getting chills of George Carlin's warning that our obsession with germs is going to create superbugs...
If we haven't stopped the flu after 80 years of vaccines, can we realistically expect this to go differently?
The US has spent/printed somewhere between 4 - 10 trillion dollars combating this pandemic, and it seems like we have little results to show from an ROI perspective. For perspective, the total amount spent by the govt, pharm industry, and various charities for oncology research is around 60 billion a year. 100 years of potential cancer research spent on Covid.
What is the end game here?
/rant, thanks for all the work you put into to gathering so much info and simplifying it for us
[1] https://www.sciencemag.org/news/2017/09/why-flu-vaccines-so-often-fail
This article is similar to the story of the origin of the Omicron variant.
"Summary (100 words)While most people effectively clear SARS-CoV-2, there are several reports of prolonged infection in immunosuppressed individuals. Here we present a case of prolonged infection of greater than 6 months with shedding of high titter SARS-CoV-2 in an individual with advanced HIV and antiretroviral treatment failure. Through whole genome sequencing at multiple time-points, we demonstrate the early emergence of the E484K substitution associated with escape from neutralizing antibodies, followed by other escape mutations and the N501Y substitution found in most variants of concern.This provides support to the hypothesis of intra-host evolution as one mechanism for the emergence of SARS-CoV-2 variants with immune evasion properties."
Article from the University of South Africa
https://www.krisp.org.za/manuscripts/MEDRXIV-2021-258228v1-deOliveira.pdf