Since my previous post about Omicron just eleven days ago when the news first broke of its existence, we’ve learned what the deal is, thanks to amazing feats of rapid research on a number of fronts by scientists coordinating around the globe and working around the clock. Although much remains to be learned, the broad brushstrokes about what Omicron is and what’s going to happen, things we didn’t know eleven days ago but will still be true and important months from now, have emerged.
Here’s the story with Omicron, as it exists now:
- Omicron has grown to crisis proportions in South Africa in just two months.
- Omicron is spreading explosively all over the world, and may dominate Delta as early as January.
- Omicron evades natural immunity and vaccines significantly, but not completely.
- Boosters help a lot.
- Omicron is probably less transmissible than Delta — ie. Delta is actually more natively contagious.
- Omicron may or may not be less severe than Delta, but it’s not more severe. So the mutation didn’t increase the death rate.
- Omicron is still susceptible to small molecule drugs, but antibodies are a mixed bag.
- Both Omicron-specific booster vaccines, and effective antiviral pills, will be coming in large quantities in March or before.
- You should get ready for a big surge of Omicron in your area.
Omicron has spread all over the world and is growing explosively
As predicted, the speed of events has been dialed up to “fast.”
In South Africa, the COVID-19 case mix is now dominated by Omicron, and has surged in just three weeks to over ten thousand cases a day, over thirty times its pre-Omicron level, and still growing rapidly. And, while deaths lag cases, hospitals are filling up and COVID-19 deaths in hard-hit Gauteng province have already tripled.
All of this has happened in just two months, according to genetic analyses that estimate the emergence date of Omicron.
Despite the imposition of travel bans by the USA and other countries, Omicron is spreading explosively all over the world. It’s been spotted in over fifty countries and over a third of US states, and case numbers in the affected countries are soaring (although estimates of rates of growth are still heavily impaired by ascertainment issues). It’s been confirmed that Omicron was already engaged in community spread in the USA before we even spotted it in South Africa.
That means there’s no realistic prospect of containing it geographically (eg. travel bans) or by contact tracing in the USA or Europe.
In response to this, pharmacies and clinics around the USA have been crushed by a wave of demand for vaccines, with boosters plus first vaccines for children and adults soaring to almost two million a day, and vaccine appointments at many pharmacies are now hard to find.
In the United States, there’s limited evidence that states like New York, Louisiana, and California may have more community spread than most other states, but the geography of COVID-19 caseloads is not a durable phenomenon.
While such estimates are crude and uncertain, some epidemiologists have estimated that at current rates of growth, Omicron may come to dominate COVID-19 outbreaks in major developed countries as early as January. The UK appears to be a candidate to experience Omicron dominance earlier than some others, due to its relatively high rate of Omicron cases so far (over 1% already, according to some estimates). In the USA, the CDC still estimates Omicron accounts for less than one case in a thousand, making it likely that if a major wave does of Omicron does occur here, it would reach crisis proportions somewhat later than in the UK, perhaps several weeks later.
Omicron evades natural immunity and vaccines significantly but not completely. Boosting probably helps a lot.
Several lines of evidence have led to the belief that Omicron is really good at evading immunity. The genetic analyses I mentioned two weeks ago have matured, and the consensus is that Omicron has several mutations likely to individually and collectively help it evade immunity. A large health records analysis in South Africa has confirmed that the percentage of cases attributable to reinfection of previously infected people, normalized for population, has more than tripled since the start of the Omicron wave. And, while estimates of growth rates are still crude, they are much too high to be plausible without significant immune escape.
Taking the estimate of immune escape from the South African health records study at face value (which is dangerous, but bear with me) suggests that natural immunity still has some effect on Omicron, perhaps about 40% (down from 80% to 90% with matched strains). That’s about as bad as Gamma, an escape variant which caused parts of Brazil to go through a second Big Burn.
But while Gamma didn’t escape the vaccines, Omicron does. Scientists suspected this already, as large superspreader events have been observed repeatedly in vaccinated populations, including an anime convention in New York and on a cruise ship in the Gulf of Mexico. On Tuesday night, in-vitro neutralization experiments from two laboratories were released, using different methods. They confirmed that plasma samples from patients vaccinated with the Pfizer-BioNTech vaccine (but not boosted) do neutralize the Omicron spike protein, but have significantly less neutralizing power than they do against the original “wild type” coronavirus. The difference is much larger than with Delta.
Between them, the genetic analyses, DMS data, spread data, and these in-vitro experiments have led scientists to conclude that Omicron significantly evades vaccines. Exactly how these in vitro results play out clinically will take time to emerge.
However, the data show that the greater concentrations of antibodies present in vaccinated-and-infected people do translate directly into greater neutralizing power, and that they retain, on average, neutralizing antibody levels similar to those which have been associated with clinical efficacy in COVID-19 vaccines. This suggests that boosting, which induces similar levels of antibodies in cohort studies, probably helps a lot.
It’s also unclear how this data will translate across vaccines; the Beta variant evades the AstraZeneca vaccine almost completely, but not others. More data should help clear this up in the coming days and weeks.
Omicron might be less inherently transmissible than Delta
There had been speculation that Omicron may have been much more transmissible than Delta, but the latest evidence strongly suggests this isn’t true, and that Omicron may even be less inherently transmissible. It may sound paradoxical that Omicron is spreading explosively relative to Delta while being less transmissible, but it’s all about immune escape.
Trevor Bedford, viral geneticist, explained on Twitter last week that a selective advantage of Omicron over Delta can come from two places: higher transmissibility (R0) and immune escape. Given an estimate for the selective advantage of a population, and its degree of immunity, we can generate a curve of possible values which would explain the data: higher R0 and lower immune escape, or vice versa.
With a responsible estimate of Omicron’s selective advantage, Bedford showed that Omicron would need only about 40% immune escape to spread as well as it has while being no more transmissible than Delta, and if its immune escape were as strong as Gamma, could spread as well as it has with an R0 value substantially lower than Delta. The health records analysis in South Africa, arriving not long after that, suggested that Omicron’s immune escape was, indeed, about this strong.
And another factor pushes in this direction. While Bedford’s math is predicated on the assumption that the serial interval (average time between acquiring and passing the infection) is the same for Delta and Omicron, some data shows Omicron may have a somewhat faster serial interval, which pushes the resulting estimates of R0 down even further. I covered the relationship between serial interval, R, and growth rates, in early 2020.
Omicron is probably less inherently transmissible than Delta; its rapid spread is mainly related to immune escape. This is a good thing, because it means that it will take less effort (masks, social distancing, infections, vaccines) to get it under control than it would if its R0 value were higher.
We’ve talked before about the relationship between R0 and the difficulty of attaining herd immunity.
Omicron may be less inherently severe than Delta, or may not. Vaccination helps.
Both anecotal evidence and a large cohort analysis from a major hospital group in South Africa have suggested that existing cases of Omicron are significantly less serious than cases of Delta in the same populations. While hospitalizations and deaths are seen (contrary to what you may have read in some irresponsible press outlets), they appear somewhat less likely than with Delta cases in the same areas, and patients who are admitted to the hospital are likely to require less oxygen and have shorter durations of stay. However, larger numbers of young people have been admitted with COVID-19 in South African hospitals since the start of the Omicron surge.
Some have said this severity cohort data means Omicron is inherently less severe than Delta. However, this may or may not be true, because Omicron is infecting a different mix of the population. We know that reinfections and breakthrough infections are, on average, less severe than first infections in unvaccinated people, so we would expect to see less severity in a major escape variant even if its inherent severity were the same.
Omicron may or may not turn out to be less severe than Delta, but we can probably feel good that it’s not worse than delta. And having prior immunity almost certainly helps.
Small molecule treatments work. Antibody therapies are a mixed bag.
Scientists have also been investigating whether COVID-19 therapies are likely to work.
All data continues to indicate that small molecule therapies like remdesivir, dexamethasone, molnupiravir, and paxlovid will work as well against Omicron as prior variants. The mutations in Omicron don’t have anything to do with their mechanisms of action.
However, data on antibody therapies have been mixed, with some retaining their efficacy against Omicron in in-vitro experiments, while others appear likely to be significantly reduced in efficacy. More data will clarify matters.
Help is coming early next year, in a big way
As we reported, multiple vaccine concerns are working hard on updating their vaccines for Omicron. Pfizer and Moderna continue to indicate that they will be ready to manufacture an Omicron booster at scale in approximately March. Pfizer has said it will be able to manufacture 80 million doses of an Omicron booster per week.
However, in a surprise, protein vaccine startup Novavax, whose vaccine is already approved in Indonesia and the Philippines and pending in other countries, revealed that it will be ready to manufacture an Omicron booster at scale in January (although precisely what scale remains to be seen). mRNA vaccines have been known as faster to reformulate than protein vaccines, but Novavax’s announcement may be a sign that Omicron boosters will be coming fast from a variety of technologies.
In addition, such boosters appear likely to win approvals quickly, as the FDA has already given manufacturers guidance on what data they need to present, and vowed to process applications quickly.
Additional help will come from antiviral drugs. Both Merck and Pfizer have vowed that their small molecule drugs, which can cut hospitalizations and deaths from COVID-19 by about 30% (Merck) or up to 90% (Pfizer), will be available in March, in quantities large enough to allow routine use around the globe. However, they need to be used within a few days of diagnosis to be most effective.
That is, major help is coming on two fronts just three months from now. The unused fourth line on your vaccine card may have writing on it in just a few months.
Three things you should do right now
- Don’t panic. The world was right to give quick attention when the Omicron news broke, but now science has worked well and we’ve learned it’s only half-bad. The US is likely to see a major wave from Omicron, but we’ve already seen four major waves, and this one is likely to be less deadly due to preexisting population immunity and the fact that vaccines and therapies are coming fast.
- Get vaccinated and boosted. Vaccines are now available and recommended for children from age 5, and the CDC is recommending boosters for all adults. The vaccines clearly help against Omicron (and Delta, by the way, which is currently surging again), and they’re convenient and free. This is one of the best things you can do to protect yourself from Omicron.
- Whatever you’d do to prepare for another major surge, do it now. Rapid exponential growth looks like a sudden slam and takes a lot of people by surprise, and it will be much easier to take any preparations before that happens. In particular, if you have very high risk people in your household, or for whatever other reason really don’t want to get a breakthrough case of Omicron, prepare for the possibility that you’ll have to stay home for a couple months (but likely only a couple months).
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