The Omicron situation, Week 2

The Omicron situation, Week 2

An update on the escape variant

Noah Smith

Dec 6 

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I’m not going to do one of these every week, but since the situation is still evolving fast, I thought last week’s post about the Omicron variant deserved a follow-up. The reason is that we now have more evidence about the virus than we did just a week ago; South African public health and medical authorities have been providing us with a wealth of epidemiological data, and scientists have been racing to study the new variant. As with last week’s post, this will be a summary of what the experts are saying, followed by my own thoughts. If you want to get the news directly from the experts, check out my list of coronavirus experts on Twitter.

If you haven’t been following the Omicron situation, virologist Muge Cevik has a long and very explanatory thread that’s a good primer to get you up to speed:

Twitter avatar for @mugecevik

Muge Cevik 

@mugecevik

🦠 There’s a lot we don’t yet understand about Omicron, including its impact on immunity and what it means for vaccines. New data will be emerging over the next few wks, which could be misinterpreted w/o context. What we might expect & how to interpret the emerging data? 🧵(1/n)

December 3rd 2021

1,810 Retweets5,006 Likes

But just in the last couple of days, events have progressed, and our data has increased by leaps and bounds.

Point 1: There is going to be a big Omicron wave in the U.S. soon.

Covid has been defined by super-spreader events, and Omicron is no different. An anime convention in NYC has been identified as one important such event. Three apparently unrelated cases have emerged in Washington state. There are reported cases of Omicron transmission between fully vaccinated people. At this point a major U.S. Omicron outbreak is totally unavoidable. It will happen, and it will happen very soon.

Remember, even when a variant spreads fast, it can take months for it to ramp up to a major nationwide outbreak. Trevor Bedford, a top epidemiologist, has a thread in which he argues that we should expect a big Omicron wave in the U.S. and other countries in about eight weeks.

Twitter avatar for @trvrb

Trevor Bedford 

@trvrb

As a broad analogy if it took ~8 weeks for Omicron to grow from initial spark into local epidemic in South Africa, I would expect very roughly 8 weeks from today for secondary epidemics to begin to manifest. 4/6

December 2nd 2021

163 Retweets450 Likes

But when it ramps up, this wave could get bigger much faster than Delta. Bedford has another thread citing South African data to show that Omicron is spreading much faster than Delta did — indeed, even with widespread existing immunity and mitigation measures like masks and social distancing in place, Omicron is spreading as fast or faster than the original Covid did in the U.S. before we had any immunity or any distancing measures!

Twitter avatar for @trvrb

Trevor Bedford 

@trvrb

This estimate of Rt around 3 or 3.5 will become more precise for South Africa in the coming days, but even Rt of 3 is very high. Initial Rt of Delta in South Africa and the US was about 1.5. 16/19

Trevor Bedford @trvrb

A more rigorous analysis of variant-specific Rt by @marlinfiggins that partitions @CDCgov case counts across states in the US by sequencing data from @GISAID shows that Mu was maintaining Rt > 1 in most states in July 2021 when Alpha, Beta and Gamma had dropped below 1. 4/9 https://t.co/LX6BYA6Zwo

December 4th 2021

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So buckle up, folks, we’re in for a bumpy ride here.

Point 2: Omicron has substantial resistance to existing immunity.

Scientists and public health experts strongly agree that Omicron has significant ability to escape the immunity conferred by both vaccines and by prior infection. Initially, this was based entirely on analysis of the mutations in the new variant — and this was powerful evidence, since scientists understand a whole lot about how this virus works.

Now, though, we’re starting to get epidemiological evidence to back up scientists’ theories. For example, Omicron is spreading rapidly in the UK, which has a very high rate of vaccination.

Epidemiologist Christian Althaus has a thread summarizing the emerging epidemiological evidence that Omicron is resistant to existing immunity. He stresses that there’s a lot of uncertainty here — the new variant could be as little as 31% resistant, or as much as 93%.

Twitter avatar for @C_Althaus

Christian Althaus 

@C_Althaus

The mutational profile of Omicron suggests a potentially significant transmission advantage. But can we already say something about increased transmissibility or immune evasion? I'll give it a try. Warning: Preliminary and based on VERY limited data. 1/15 

Image

November 28th 2021

632 Retweets1,683 Likes

And a study found that Omicron is about three times as likely to cause reinfection as Delta.

Twitter avatar for @matthewherper

Matthew Herper 

@matthewherper

COVID-19 reinfection study from South Africa yields ominous data about Omicron  

COVID-19 reinfection study from South Africa yields ominous data about Omicron

New variant is better at evading immunity from past infection—and perhaps from vaccination

science.org

December 4th 2021

14 Likes

And here is a thread from biologist Tom Wenseleers explaining why Omicron’s rapid takeover from the Delta variant is almost certainly due to immune escape. If it were coming only from increased infectiousness (as was the case with Delta), Omicron would have to be 3 times as contagious as the most contagious virus we’ve ever found:

Twitter avatar for @TWenseleers

Tom Wenseleers 

@TWenseleers

Clearly an R0 of 6.5*6.2=40 would be highly implausible. That of measles is 12-18 and that's virtually a record. Immune escape then? What would a priori be most likely: increased infectiousness (R0) or greater immune escape?

December 2nd 2021

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So at this point, it’s very clear that Omicron has substantial escape ability, even if we don’t quite know the exact numbers yet.

Point 3: Omicron is less deadly in South Africa so far, but there are several theories as to why.

Omicron is spreading like wildfire in South Africa’s Gauteng province, but so far there hasn’t been a big wave of deaths to match the big wave of cases:

In previous waves, deaths started rising about a month after cases did. This time, it’s been longer than a month and deaths still aren’t rising, so that’s good. One note of caution here is that hospitalizations in Gauteng are increasing fast:

Twitter avatar for @statesdj

David States 

@statesdj

Hospitalizations in Gauteng SA continue to double weekly 

Image

December 5th 2021

6 Retweets14 Likes

So deaths are pretty sure to rise eventually to some degree. But hopefully the fact that they haven’t risen yet means that the Omicron wave is going to kill fewer of the people it puts in the hospital. And a hopeful sign is that a large percent of the hospitalizations so far are incidental detections in children hospitalized for other reasons (South Africa is testing very vigorously for Omicron).

Some have speculated that this is because Omicron is less deadly than other variants, and this theory is still going around:

Twitter avatar for @HelenBranswell

Helen Branswell 

@HelenBranswell

Lots of caveats; too soon to know. But early info from South Africa provide tantalizing hints that #Omicron may trigger milder illness. With thoughts from @MarionKoopmans, @AmeshAA & @PeterHotez.  

Early South Africa data hints Omicron may cause less severe Covid, but more research needed

Early data from South Africa on Omicron hints it may cause less severe Covid, but more studies are needed for a full picture of the variant.

statnews.com

December 5th 2021

199 Retweets675 Likes

In fact, there might be some lab evidence to support this. Some scientists theorize that Omicron shares genes with the common cold, which they think could make it both more transmissible and less deadly.

On the more pessimistic end of the spectrum, Omicron cases in Gauteng might be milder because they’re skewing much younger so far:

This is pessimistic because it could mean that A) Omicron is so infectious that it’s much more able to infect young people than previous variants, and B) when Omicron finally spreads from the young to the old, severity could increase and death rates could soar again.

But experts seem to be converging on a third explanation for Gauteng’s low death rate: Most people in Gauteng simply had some pre-existing immunity, either from vaccination or from prior infection, and that this is making their illnesses more mild. This is supported by early evidence in the U.S., where people who’ve caught Omicron so far have mild cases and were fully vaccinated. There are good scientific reasons for this — even if the virus can evolve to evade antibodies, it’s harder for variants to escape the additional immunity conferred by T-cells:

Twitter avatar for @EricTopol

Eric Topol 

@EricTopol

Another reason for optimism: the T cell response to vaccines is far less influenced by variants, and is tied to protection from severe illness. The reason why the @BioNTech_Group statement here may well turn out to be true

wsj.com/articles/omicr…

by @bopanc

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November 30th 2021

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