It’s hard to believe it’s been one week since Omicron broke the news. While we continue to wait on lab evidence, we’re getting a substantial amount of epidemiological data every day. Here’s an update since my last…

1. Reinfections are high against Omicron

We got our first piece of solid scientific evidence yesterday (here). A group of South African scientists leveraged a national dataset of all positive COVID19 tests over time. This dataset includes data regardless of the reason for testing or type of test (PCR or antigen). Using this dataset, they assessed the reinfection rate in South Africa from March 2020 to November 27 2021.

The key findings of their analysis are in Panels A and C in the figure below. Both graphs are infections plotted over time. Panel A is primary infections, so someone who never had a positive test ever before. Panel C is reinfections, so someone who had a positive test (at least 90 days) before. The colored background corresponds to different waves. This is what we see:

Purple was South Africa’s first COVID19 wave. This was all primary infections, as reinfections were impossible at this stage.
During the Pink and Orange wave, primary infections and reinfections largely reflected each other. They had a similar pattern but at different magnitudes.
Then you get to Omicron at the tail end of these graphs. While primary infections are increasing, reinfections have substantially more exponential growth. In fact, that blue line is almost as high as the previous Delta wave.

Pulliam et al., Increased risk of SARS-CoV-2 reinfection associated with emergence of the Omicron variant in South Africa. Preprint here.

This is the first evidence to show us that the rate of reinfection with Omicron is high—3 times higher than Delta. In other words, infection-induced immunity is not doing a great job at stopping Omicron.

We now know this is the preliminary evidence WHO based their recommendation on earlier this week: People who have previously had COVID-19 could become reinfected more easily with Omicron. This is also another example of South Africa’s incredibly swift work at finding early signals so the rest of the world can prepare.

2. South Africa State of Affairs

South Africa is having explosive spread. Yesterday they had 16,055 new cases in one day. Using Delta’s doubling rate, we hypothesized South Africa would break 10,000 daily cases by next week. Omicron has far outpaced this. The test positivity rate in South Africa is 24%, which is bad as Omicron is spreading faster than we can detect it.

If we zoom into South Africa’s epicenter—Gauteng—case acceleration for this new wave (black line) is just unbelievable. The spread is near vertical compared to other waves.

Hospitalizations in South Africa have started to slowly rise. Because hospital trends lag case trends by 3-4 weeks, we still don’t know if, and how, Omicron impacts severe disease and death. We are at the mercy of time.

We got a little peak into these hospitalizations during a brief yesterday hosted by the National Department of Health (South Africa). South Africa is actively investigating the vaccination status of patients in hospitals. Unfortunately there is still lot of “unknown” data, but the data they do have shows that among 1,351 hospitalized 23% patients are unvaccinated and 2% of patients vaccinated. Until we can get more complete data, I wouldn’t come to sweeping conclusions with this. But it’s welcoming news that the vaccinated aren’t piling up at the hospital.

National Department of Health (South Africa)

During the briefing, South Africa also presented the age distribution of hospitalized patients. It’s apparent that younger people are going to the hospital at a higher rate during this Omicron wave (orange bars below) compared to the Delta wave (blue bars below). This pattern is specifically apparent with kids less than 5 years old.

National Department of Health (South Africa)

South Africa is actively investigating why. I think there are a few things that could be explaining this:

Kids aren’t vaccinated and may be the last group for the virus to reach. Parents may have avoided infection by altering behaviors until now.
Adults around these kids aren’t vaccinated. Infection-induced immunity doesn’t protect well against Omicron while it largely did before. So parents could be bringing the virus home and infecting kids.
Because so little is known about Omicron, kids may be hospitalized out of precaution at a higher rate than before.
Omicron induces more severe disease for kids than previous variants.
A combination of all of the above.

My guess is a combination of #1-3. Keep in mind what happens in one country doesn’t always happen in others. Landscapes between countries are very different: vaccination rates, behaviors, environment, genetics, and unknown unknowns. We need to carefully track epidemiological data by age to see if this is a generalizable signal. As a parent, I don’t really want to wait to find out though.

3. United States State of Affairs

This virus is well on its way as it has reached more than 11 states. Some cases have no ties to South Africa travel indicating (and confirming) that Omicron is spreading throughout our communities. The key question we have in the States is: Does Omicron outcompete Delta? We need more data to see whether this is happening.

Nonetheless, we’re seeing case growth across the nation with 94,926 new cases per day. Hot spots are clustered in the Northern states who were largely untouched by Delta during the summer, but all geographic areas in the United States are increasing.

Delta and the Thanksgiving holiday are largely driving spread right now. Omicron may be adding a little fuel, but certainly not a main factor yet.

Not nearly enough people are fully protected going into the Winter months. Only 59.7% of the United States is fully vaccinated (which the CDC defines as not having a booster, which really needs to change). Only 22% of 18+ are boosted and, even more concerning, only 46% of those aged 65+. I found the graph below useful in displaying poor booster coverage in the United States. If you know someone that’s 65+, call them right now and encourage them to get a booster if they don’t already have one. It’s not too late.

Bottom Line: Previous infections are largely not protective against Omicron. Omicron is in the United States and spreading quickly. Let’s take advantage of this warning from South Africa to mount a proactive (rather than reactive) response.

Love, YLE

P.S. I typically get many messages asking what I’m doing with my girls who are under 5. We haven’t changed our behaviors with Omicron news just yet. We are already boosted, wear masks inside, and avoid large indoor events. The girls are still going to child care (but all teachers are fully vaccinated and wear masks). We still have our plane tickets to CA for Christmas. But my husband and I got on the same page last night and both agreed that we need to closely watch how this unfolds in the coming weeks. This may mean cancelling Christmas plans with unvaccinated family members or cancelling plane tickets last minute. The name of the game is flexibility.

“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:

Subscribe now

Your Local Epidemiologist

Omicron Update: Dec 4