The Omicron Variant

There’s already bad news on that front.

…from the article, here is the entire section on incubation periods:

Did anyone click on the study?

Because the study (the only citation provided by the article to back up what it said about a 3 day incubation period) looked only at a cluster of 6 people back in November 24.

I think that it is concerning that the “paper of record” would be so conclusive based on such little evidence. There were 800,000 cases of Covid today. But the article chose to cite a CDC report on a single house-hold cluster of six people from over a month ago.

We have a robust system of Managed Isolation (MIQ) at the border here in NZ. We’ve got plenty of data on incubation periods if you want to look at it. Cases are genomically sequenced so that we can determine if they caught it before they travelled, on the plane, or in MIQ. We have 630 active cases right now in quarantine at MIQ, and we know what day each person tested positive. More accurate data is available, if the NYT wants it. It isn’t hard to find.

And what the NZ data is showing us is that Omicron has an incubation period between 5-15 days. The long tail has been mentioned. But that isn’t an aberration. Not with hundreds of thousands of cases per day.

I just did a google for “what is the incubation period for Omicron” and many of them pointed to that very same CDC study and the three-day figure. There was nothing wrong with the CDC study in itself. It was an investigation into a cluster during the early stages of the variant. But it shouldn’t be used now as the go-to cite for the incubation period of Omicron. That doesn’t make any sense at all.

An update on NZ: as expected, Omicron has broken through MIQ and is now in the community. You can watch the Prime Minister’s press conference yesterday here, as it gives a good amount of information and context of what we will expect in the weeks ahead:

The PM suggests we will hit a thousand cases a day in about two weeks. They are looking at three stages: we are still at the “stamp it out stage”, until we hit 1000 cases per day, which means that we continue with our previous strategy that has been effective against Delta and previous variants. At 1000 cases/day they plan to go into a transition phase, where the focus shifts to those most at risk of severe illness. The third stage would see big changes to contact tracing, close contacts, isolation requirements, and a shift from primarily PCR testing to a mix of PCR and Rapid Antigen Testing.

We are currently at Red Light in the new Alert Protection Framework. That means mandatory masks. Vaccine passports. Gathering limits (based on vaccination status). Mandatory QR code scanning, and physical distancing requirements. MIQ still in operation.

…I’m not going to keep a running total on the NZ numbers, because unlike the NSW numbers the NZ data is spread out over a number of tables and lists, and can be hard to parse.

But on day two of the outbreak, we had:

25 new community cases

Of those 25 cases, 17 of them were Delta, connected to the November outbreak.

8 of them were Omicron, two in Nelson and five in Auckland, all cases epidemiologically linked to the Palmerston North case.

In addition there were 50 new cases in MIQ today.

There are ten people in hospital with covid. No new people in ICU.


Good luck.

I have tons of friends in NZ, having lived there in the late 80’s.

It’ll be interesting to see if NZ figures run in the same way as Australia, it also being a country that has very little natural immunity and a fairly high proportion of the population immunised and boosted.

From the point of omicron taking hold to reaching peak cases seems to be about 4 weeks. The figures for new cases the last 24hr period in NZ was 75, not a huge increase day on day and not yet indicative of the exponential growth seen elsewhere with omicron.
The signal for that will be a rapid doubling in the 3-5 day time period sustained over the course of a couple of weeks.

The question of what the isolation period should be for omicron is a vexed one.

There may be an epidemiological case to be made for a shorter infectious period with omicron but even if not, the sheer number of people infected at the height of the waves may mean that a rethink is required in order to reduce worker shortages and keep the countries running.
The UK has gone for a standard 10 day isolation with the possibility of exiting early with negative testing on day 6 and 7, that seems a reasonable compromise but it certainly will mean that some people that are still infectious will be back into society early as well.

…that 75 includes 50 that arrived and were held at the border in MIQ. They aren’t community cases. As I stated above: there were 25 community cases today, 17 of them Delta, 8 of them Omicron, all of them epidemiologically linked to their respective index cases.

Sure, I did say that omicron is not yet showing exponential growth. It will at some point but that is not seen yet.

…it’s an important distinction in the case numbers. You can’t conflate the total number with the cases in the community because it tells us two very different things.

I wasn’t conflating anything, I’ve seen the figures on the Ministry of Health site and seen the breakdown. At the moment there is nothing that suggests widespread growth. At the point where numbers do climb that’ll be an indication that widespread transmission may be underway and a review of the stratified data will show where it is happening.

It is possible that such high growth could be seen purely in the managed quarantine population but that is unlikely if that population remains stable. Of course even if that were the case such a high number will present a much greater risk of omicron moving to wider community transmission. Containment has not stopped previous variants even at relatively low rates of infection and omicron is a much more slippery beast, more easily passed on and much quicker to spread.

…I mean, yes you were.

The total number says nothing about the current outbreak which was only identified yesterday. We’ve been getting on average about 50 Omicron cases per day at the border for the last month. There are 666 cases at the border right now. But there are currently only 16 Omicron cases in the community. The distinction between cases that have arrived by plane and are being held at the border and those cases in the community should be pretty obvious.

There is plenty to suggest that yes, we have widespread growth. We know where the people that have so far tested positive have been. Hundreds of close contacts have been identified and are self-isolating. Some are already symptomatic.

Containment has stopped previous variants pretty effectively actually. The August Delta outbreak was all linked to a single index case. Everything since then were all genomically linked to the same original cluster. Containment works very well.

At the point that I claim that exponential growth is happening and I neglect to stratify accordingly then feel free to level that accusation.

It is obvious, it is right there in the Ministry of Health figures. I’m genuinely confused as to what you think I am saying.

Well which is it? is it only 16 community cases or is it widespread growth?
The numbers of confirmed cases so far do not show the exponential growth pattern of omicron that has been seen in other countries. If you are suggesting that widespread growth is potentially happening that are not yet confirmed cases then OK, I probably agree (given the nature of omicron) but I clearly referenced the official case numbers and as yet those potential cases has not been reflected in the confirmed cases.
Again, I’m not sure what claims of mine you arguing against.

But containment is not perfect. If it were there wouldn’t have been an August Delta outbreak or a single index case. That is my point, it isn’t perfect and any omicron outbreak is likely to prove more adept at escaping containment and spreading more widely, which you already seem to be admitting.

…the only relevant figure in regard to yesterday’s community outbreak are the community cases. The cases at the border don’t count.

It’s the difference between a proactive and a re-active strategy. We know that there is widespread growth, and we are acting accordingly. You don’t wait for the confirmed numbers, then act. This is pretty fundamental to our strategy. We’ve been doing it since the beginning.

Nothing is perfect. Which is why (as I’ve explained to you over and over again in thread after thread) we have had multiple layers of defence.

The Swiss Cheese Model.

The visual explainers created by Toby Morris and Siouxsie Wiles released under a Creative Commons CC-BY-SA-4.0 licence.

The reason why we have only had 52 deaths so far in two years of the pandemic is because we have had an agile strategy, that has had to adapt multiple times since everything started, that has multiple layers of defence.

Containment has been extremely effective. The numbers say it all. And it will continue to be effective as we move onto the next phase of the pandemic. It is much better to keep those 50 cases a day arriving at the border in Managed Isolation than it would be to just let them into the community. Our new strategy with Omicron is to slow the growth down. To flatten the curve. And our only hope of that succeeding is to continue to try and contain things at the border.

I agree, the community cases will be the best indication of whether omicron is undergoing sustained exponential spread. That isn’t the case yet. It may yet prove to be so.

Sure, proactive is best. The numbers will be a measure of how successful that is.

You say this as if I am somehow unaware of what you have done and the what the success of those measures have been.
You didn’t even have to tell me once seeing as I was poised to take a holiday in NZ during March/April of 2020 and had to pay close attention to what was happening there, what the entry restrictions would be and what the local restrictions would be. The holiday is delayed not cancelled and I’m obviously paying close attention to what is going on, the same as I am for Austria.

Sure, but it will likely be much less effective at preventing community spread of omicron than of other variants, that has been the experience of every other country. Measure that curbed Delta were inadequate to do the same for omicron.

No one is suggesting that knowingly letting them into the community is a good idea but the reality is that managed isolation is imperfect and your caseload of much more infectious cases at the border is likely to increase and an increased challenge to an imperfect system is going run a higher risk of letting more cases into the community.

Sure, “flattening the curve” has been the general aim of most measures taken around the world. The virus can’t really be stopped, you can only slow it. It’ll be interesting to see how the numbers develop in such a “blank slate” situation as NZ.

If you’re interested in a comprehensive breakout of the Australian figures, there’s a very well-structured website here that breaks it all down nicely into the various states’ experiences:

Top-level version - about 9% of Australians have now officially had Covid (probably much more in reality since testing was overwhelmed in the recent Omicron wave), 90% of these in the last month and a half, so almost certainly Omicron. NSW and Vic curves are similar, but Vic kept up more social distancing restrictions so the top of our curve is about half that of NSW.

Numbers are on the way down on the eastern seaboard so we can start to compare the Omicron wave with the Delta one in August/September. Notably, case numbers at the Omicron peak were about 30x what they were for Delta, but hospitalizations only doubled (‘only’ - sigh - but you know what I mean)

…just to be crystal clear on my point here: the New Zealand figure have always made the distinction between community cases and cases at the border. Posting just the total figure, without any additional context, is both unhelpful and misleading.

I said this because you said this:

I’m going to break this down a bit further for you.

We know that containment isn’t perfect. We have always known that containment isn’t perfect. Which is why it is only a single layer in multiple layers of defence. You earlier argued:

Again: we know this. But that doesn’t mean that containment isn’t effective, isn’t a vital part of our strategy, and even though much more slippery beast, more easily passed on and much quicker to spread, it is still an essential.

Not every other country has a system of managed isolation and quarantine at the borders as we do. The goal of MIQ isn’t to “prevent community spread” in the way that you describe it. It is to prevent the seeding of community clusters. Once it gets into the community then we have other measures in place to try and stamp it out.

As I’ve already cited we have developed a three-stage plan that makes allowances for the differences between Delta and Omicron. But that doesn’t mean that Managed Isolation doesn’t work any more, or is no longer effective. The same fundamental epidemiological principles still apply here. Omicron makes containment harder. But it doesn’t make it impossible. The fact that we have been having on average between 20 and 50 cases a day arriving at the border for a couple of months before our first substantial breach should tell you just how effective containment has been.

And that containment has given us time to push our vaccination numbers up even further, allowed time for the booster campaign to step up a gear, allowed time for vaccinations to 5-11 year olds to be approved and for that to start rolling out. After just over a week since the rollout started, 17% of 5-11 year-olds have been vaccinated. (In comparison, after two months in the States the percentage is at 28%)

And that containment means that we can continue at Stage 1 for just that little bit longer. It means we can get more people vaccinated, more people boosted. It means we can still contact-trace, test and isolate and stop people getting sick.

But the thing is…we know this. We’ve been planning for this. We’ve just invented an entirely new strategy to deal with this. Because what containment does is buy us time. Time to look and see what has worked around the rest of the world…and what hasn’t.

Well it was at the start of the pandemic. It isn’t really that way now. I just did a quick google for the term and the algorithm didn’t show me anything posted later than April 2020 on the first page of the general search. On the news tab, the first article that popped up was this one:

Which was a rebuttal to the dangerous ideas being floated here:

(Both links may be paywalled. I could access the first, but couldn’t access the second.)

There has been a shift away from flatten the curve. The general aim of most measures around the world now seem to be to “learn to live with the virus.”

We abandoned “flatten the curve” in the early days of the pandemic because flattening the curve was never going to be enough. Our ICU capacity is a fraction of what is available overseas, and is intently focused on the large cities, leaving many rural areas without coverage.

To give more context on this: our ICU capacity is about a quarter of what NSW has. If we followed the same track as the outbreak there: our ICU’s would have been over-run on January 4th when they hit 105 cases. This should show you just how vulnerable our healthcare system is. Even with the cases where they are at the moment in NSW, even with thousands of hospital staff having to isolate, they still have spare capacity in ICU. We wouldn’t have that. And this is key to our strategic thinking.

What we have now is a highly vaccinated population, just the same as NSW. But NSW abandoned pretty much every mitigation at the start of the Omicron outbreak. They opened internal borders. They removed masking and distancing mandates. Then they encouraged people to celebrate this.

If you go and look at the Swiss Cheese model I posted earlier, you can see the effect that would have. Each layer of cheese is less effective against Omicron: there are more holes for covid to be able to slip through. But just because they are less effective, it doesn’t mean that they stop working. And if you remove several layers completely, you’ve essentially granted Covid a licence to infect as many people as it wants.

Our strategy has always been proactive and adaptive, and things have always been difficult because much of the rest of the world have stopped trying to do things like “flatten the curve”.

And being able to adapt is important here, because we’ve come full circle. Flatten the curve wouldn’t have worked as our primary strategy back in early 2020 against the original variants because it meant our hospitals would have been quickly over-run. But that isn’t the case now.

Y’all heard about Sneaky Omicron (BA.2) yet?

…today’s New Zealand update: 25 new community cases. 15 of those Delta. 10 of those Omicron. In addition to that, there were 37 new cases at the border. There are 10 people in hospital, no covid patients in ICU.

Good news on the vaccine front:

Lab study shows omicron-blocking antibodies persist four months after a Pfizer-BioNTech booster

Please don’t. There is no need and never was. Nothing in your wall of text is news to me. Your main concern seems to be that I am saying things that you agree with and that you already knew.

The starting point here was a simple comment from me that it will be interesting to see how the NZ figures progress and that, as yet, they were not showing the type of exponential growth shown in other affected countries. That is true and remains so.

It is good news indeed. That longer neutralising protection combined with the long-term T-cell response we already suspect should mean that we can get a reasonably high proportion of the population to a point of solid protection.

Interestingly, in that article it also mentions that a fourth dose doesn’t necessarily give any huge benefit over and above the third and that is in line with Albert Bourla’s comments this week about 4th doses.

As Pfizer prep the the omicron variant vaccine for a March release it probably makes sense for countries to focus resources on a Flu-type scenario with a yearly jab against circulating variants rather than having countries scrabbling to boost with a 4th and 5th etc.

That would certainly be a benefit for travel and entertainment. Having a booster that gives 12 month protection that the international community recognises would simplify things enormously.