Omicron Update: Dec 2
There are a few Omicron details for you since my last update…
1. CDC announced the first confirmed case in the U.S.
Omicron was confirmed in San Francisco, California yesterday. A vaccinated individual (Moderna series but not boostered) returned from South Africa on Nov 22, developed symptoms three days later, and tested positive for the virus on Nov 29. Because of the travel history, the swab underwent genomic sequencing at University of California San Francisco and was confirmed yesterday as Omicron. The individual still has mild symptoms, but is improving.
There were a few things I noticed in between the lines here:
Omicron arrived before Thanksgiving. Last year Thanksgiving was a series of mini superspreader events across the country. The timing of Omicron’s arrival could additionally springboard us into a Winter surge.
Because this was a travel case, this isn’t necessarily the “proof” we need to say Omicron is spreading in our community. But we can certainly assume it by now.
Notice this case landed exactly 1 week before the Biden travel ban. Travel bans to a few select countries do not work; it is not an evidence-based public health solution. It does a lot of damage too. It not only perpetuates disease related stigma, but now scientists in South Africa are running out of reagents needed to answer the lab questions we are all desperately waiting for.
Nonetheless, it shouldn’t be a surprise that Omicron in the U.S. Once we identify a variant (even if it was very early like Omicron), it’s already spreading under our radar. We live in a very globalized and connected world.
We actually saw this prediction with flight patterns. Dr. Dick Brockmann and his team did some interesting calculations based on the world aviation network from August 2021. They estimated the likelihood of a passenger from South Africa or Botswana traveling to another country and exiting the airport (i.e. not a layover). Based on their calculations, U.S. had the second highest probability of a traveler (3.355%) in the world behind Zimbabwe. This means that out of 1000 passengers from South Africa/Botswana, 34 were expected to land in the U.S. You’ll also notice that San Francisco airport made it in this figure too. There are a ton of limitations to this analysis, but interesting nonetheless.
CA not only has a lot of flights, but it also has a fantastic genomic surveillance system. CA has sequenced 288,535 tests since the beginning of the pandemic, which accounts for 5.74% of all sequenced tests and far outpaces other states. This probably means that Omicron is other places, but CA was just the first to successfully find it. This is considered “finder’s bias”.
2. Lab data
We’re still waiting on lab data to evaluate, at the micro-level, how Omicron’s mutations influence transmissibility, immunity effectiveness, and disease severity. There are rumors of lab data but nothing has been shared publicly. It’s coming soon. Unfortunately, it takes time for cells to grow in a lab. Once we have enough growth, then Omicron will be tested against our antibody protection. I’m particularly interested in if, and how, 3 mRNA doses compares to 2 doses.
3. Epidemiological data
It’s incredibly important to marry lab data with epidemiological data. What happens in the lab (a highly controlled environment) can be different from what happens in the “real world” (environment and genetics). Integrating both sources gives us a “true” picture.
Thankfully (or not), we’re getting more and more data in the real world.
Cases continue to exponentially increase in Gauteng (black line)—the Omicron epicenter. There were 6,168 new cases today with the 7-day average up 424%. The doubling time is every 3.5-5 days. This is compared to a doubling time of 11 days in the beginning on the Delta wave. Test positivity rate is also increasing (9% to 15% in two days), which means that this increase is not just because Gauteng is testing more. This thing is spreading.
With this preliminary data, we can start measuring the reproductive number or contagiousness of Omicron: How many people will catch the disease from a single infected person?
There are two types of reproductive numbers: R(0) and R(t)
R(0) is the spread of disease if nothing was in it’s way: No vaccine or infection-induced immunity, no screening, no quarantining, etc. For Delta, the R(0) is ~6.
R(t) is the “effective” transmissibility: the actual transmission rate right now on the ground. This takes into account things that slow transmission like immunity, human behavior, etc. We want R(t) to be less than 1, which would represent a decrease in spread.
Through mathematical models, we can calculate these numbers. Three separate science groups have done this (here, here, here) and all came to roughly the same conclusion: In Gauteng, the R(t) was 0.8 (during the tail end of Delta) and is now 2.33 (during Omicron). This means in the same environment that Delta faded away, Omicron found traction by 3-fold. In other words, there seems to be in less in the way (like reduced immunity protection or easier/faster access into cells) for Omicron than for Delta. We’ll get confirmation from the lab studies.
Tom Wenseleers (a biostatistician) plotted the number of tests sequenced by variant over time in South Africa. What he found was the number of sequenced tests identifying Delta dramatically decreased (purple line), while the number of sequenced tests identifying Omicron dramatically increased (red line). This is another angle showing that Omicron is outcompeting Delta—Omicron is highly transmissible.
I’m a little less confident in this data because South Africa didn’t have much Delta in the first place—they were at very low transmission when Omicron was introduced. It will be interesting to see what happens when Omicron gains traction somewhere with very high rates of Delta (like the United States).
4. World Health Organization travel update
Yesterday the WHO released a strong recommendation regarding international travel:
“Persons who are unwell, or who have not been fully vaccinated or do not have proof of previous SARS-CoV-2 infection and are at increased risk of developing severe disease and dying, including people 60 years of age or older or those with comorbidities that present increased risk of severe COVID-19 (e.g. heart disease, cancer and diabetes) should be advised to postpone travel to areas with community transmission.”
This doesn’t mean those who are boosted and over the age of 60 shouldn’t travel within the United States. You still can. If you plan to do so, though, I would certainly upgrade your mask. Time for N95’s.
If anyone’s traveling to visit high risk family or friends (like 60+ years old, comorbidities), please test through a series of rapid antigen tests. Here is a previous post showing how to do so.
Bottom Line: Omicron is in the United States and we’re not surprised. As more epidemiological data accrues, transmissibility of Omicron is not looking good. Stay vigilant and do your part to reduce infection and spread.
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:
To anyone also thrown for a second by seeing Summer surge 2021 just starting on the graph for Guateng-it's the beginning of summer now in the Southern Hemisphere.
You do realize it's unfair that I have to read your citations before adequate coffee? Thank you for another informative post. I've reached the same conclusions. I'm concerned for R(t) but I'm still waiting for both my network of clinicians (rather ad hoc) and published info from case studies on the severity and mortality. I'd already started the morning with the Twitter epidemiology updates (and filtering the cruft) and your piece here added significant content making my life easier.