Omicron Update: Dec 22

Well, Omicron continues to show its colors across the globe with case rates surging far beyond what we've seen with any previous waves, like in Denmark and the UK. Other countries, like France, the United States, and Canada have a recent explosion of cases pointing to the beginning of their Omicron wave. Places that put in country-wide restrictions, like the Netherlands and Germany, have altered their Omicron path thus far.

Epicenter: South Africa

It’s clear that Gauteng—Omicron’s epicenter—peaked. It looks like cases in South Africa, as a whole, also peaked.

Why do we have waves? See my previous post here. But this peak is far more interesting than some may think, as it’s a sign that we are missing a fundamental piece of the Omicron puzzle. With R(t)=3, we would expect an attack rate of 90%, so we would expect Gauteng and South Africa to peak much higher. Scientists have offered several hypotheses:

1. Testing. South Africa’s test positivity continues to hoover around 30%, which is very odd because usually this decreases before cases decrease. So this could mean that people aren’t bothering to get tested or South Africa has reached testing capacity.

2. Asymptomatic spread. Somewhat relatedly, the peak could mean there are far more asymptomatic cases that just aren’t detected. So there are far more “true” cases than the epi curves portray. I think this is the most likely scenario.

3. Secondary attack rate. Omicron could have a shorter generation time, so positive cases infect far less people than Delta. In other words, the secondary attack rate is much smaller. Data from the UK, though, shows household transmission higher with Omicron than Delta, so I’m not convinced this is a driving factor.

4. Susceptibility. Omicron is only spreading among certain levels of immunity and/or susceptibility. A running hypothesis is that Omicron and Delta will co-exist with different paths: Omicron will spread through immune evasion and come and go, while Delta could persist onward.

5. Behaviors. Behaviors of people drastically changed due to increasing cases. While, as far as I can tell, national policies on the ground haven’t drastically changed in South Africa, people did go on summer holiday. As South African scientists warned, we need to compare the South African Omicron wave to Beta (not Delta) to account for seasonality and human behavior.

6. Network effects. This plays some sort of role, too (and I think the most interesting). As people see their regular contacts and these networks reassert themselves, Omicron runs out of places to go.

Nonetheless, South Africa showed us that Omicron spread incredibly quickly, and we will continue to see this rate of spread across the globe.

South Africa’s hospitalizations remain about 50% of what they were for the Delta wave. Deaths continue to increase, but also much, much lower than before. Is this because immunity is working or because Omicron is less severe? We don’t know yet. But an important preprint was released yesterday describing Omicron hospitalizations in South Africa. There was a lot in this paper, but, to me, the following was the biggest finding: Once someone got to the hospital, the odds of disease becoming severe was the same as Delta. So if the immune system was breached, Omicron did the same damage as Delta. This is consistent with another robust analysis of hospitalizations from the UK that found Omicron is not less severe than Delta.

On the other hand, lab data is showing that there are certainly physiological differences between Omicron and Delta disease processes (go here for more great details). It will be weeks or months until data crystallizes and we have a clear picture of Omicron severity. What all this means for hospitalizations and deaths in places like the United States remains unknown.

United States

Omicron became the dominant variant in just two short weeks and now accounts for more than 73% of cases in the United States now. By next week Omicron could easily account for 100% of cases. Will Omicron completely overtake Delta or will Delta continue its path among some groups? We should get clarity on this soon.

(CDC) Purple=Omicron; Orange= Delta

With more Omicron will come more cases. The Northeast has, by far, the most cases right now. Washington DC is the leader (134 cases per 100,000) in which cases have increased 440% in the past two weeks. This is followed by New York City with 121 cases per 100K and a 342% increase.

Washington DC (Source NYT)

The state leader is Rhode Island (118 per 100K) followed by New York (100 per 100K) and New Hampshire (88 per 100K). Hawaii (+557%), Florida (+371%), Georgia (+139%), Louisiana (+132%), and Texas (+113%) have the fastest 14-day case growth though.

Nationwide hospitalizations are only up a modest 13% and deaths continue to remain “low” at 1,351 deaths per day. But severe disease patterns lag cases 3-4 weeks, so we will see what happens in a few weeks. While I expect an uptick, I certainly don’t think we will reach levels like we saw in the past thanks to our vaccines and adaptive immune systems. It’s noteworthy, though, that the first Omicron death was reported this week in Houston among a male aged 50-60 years old who previously recovered from COVID19. Do not rely on previous infections to get you through this Omicron wave.

Where will this go?

Throughout the pandemic, the CDC has looked to a consortium of scientific teams across the country to model projections. Recently the teams presented their Omicron projections. One of these teams, University of Texas, made their modeling public over the weekend. Their report looked at 16 omicron scenarios that varied three variables:

1. How quickly Omicron spreads

2. How easily Omicron evades immunity, and

3. How quickly we're able to roll out booster shots

The graphs below display their results for cases, hospitalizations, and deaths. The left and right graphs correspond to the low and high severity scenarios, respectively. Briefly:

• Best case scenario (purple line below; scenario B): By mid-January 190,000 people catch the virus every day—about double what the case rate is today. In this scenario, Omicron would lead to 10,500 hospitalizations per day (a few thousand more than today) and 1,400 deaths (a few hundred more than today).

• Worst case scenario (pink line; scenario C): By January more than 500,000 people would catch the virus every day, which is more than double the peak reached last winter. 30,000 people would be hospitalized per day and 3,900 would die every day. This scenario is the most pessimistic and, in my opinion, won’t happen for two reasons:

  • This model assumes that Omicron is more severe than Delta. This is not the case; in fact, there is considerable debate as to whether Omicron is less severe.

  • This model also assumes that there is no behavior change, which is also not realistic. People change their behaviors when cases increase, whether they realize it or not.

So, like everything in epidemiology, the “truth” lies somewhere between the best and worse case scenario in the United States.

Boosters

Not nearly enough people have their boosters in the United States: 32% of eligible Americans and 55% of those 65+. Omicron has motivated people to get boosted, though. Omicron is convincing 1 in 8 unvaccinated to change their mind, too.

One thing that’s increasingly obvious is how important boosters be in our projections. While we will start seeing an uptick in cases, we will continue to see a distinct pattern between unvaccinated, vaccinated, and boosted. Massachusetts has a great graph illustrating this effect so far.

(MA DPH)

We also really need guidance for the J&J folks. A new study showed the effectiveness of boosters with vaccines distributed in the United States. While 1 mRNA booster (brown squares) after JJ (green dots) helps, it doesn’t help as much as the 3 mRNA series. In other words, it looks JJ people need 2 mRNA shots for full neutralizing antibody protection instead of just one.

Garcia-Beltran et al., mRNA-based COVID-19 vaccine boosters induce neutralizing immunity against SARS-CoV-2 Omicron variant. Source Here

But neutralizing antibodies isn’t the only line of defense. Another study found T-cells among those who received one or two doses of the J&J only dropped with Omicron by 30%. So, people with 1 mRNA booster after JJ should largely stay out of the hospital. I’m really hoping it doesn’t take J&J, the FDA and/or the CDC too long to comment on this. We need guidance now.

Bottom line

As expected, Omicron is taking hold in the United States and case rates will start skyrocketing across the country. What this means for our hospital systems is yet to be seen. As with everything in public health, we prepare for the worst and hope for the best.

Love, YLE

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“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: