INSIDE AN OMICRON WAVE
You’ve seen the vertical line: Australia, the US, the UK. It’s probably coming to a town near you. But, as Keith Lynch explains, there’s a sliver of hope in the avalanche.
An almost vertical line reaching towards the sky. You’ve seen that line in South Africa, in the UK, the US, in Australia. That’s what an Omicron outbreak looks like.
But what goes up must go down. We’ve seen case numbers plunge in South Africa; the same dynamic now appears to be at play in the UK.
There are several characteristics that appear to explain Omicron’s bewildering ability to find new hosts. The first is its prowess at sidestepping the protection from infection induced by vaccination and previous infections.
According to a UK analysis: 10 weeks after third doses, the Pfizer booster was only 30 per cent effective in preventing symptomatic infection in those over 65. (Do keep in mind the vaccines hold up very well against severe illness.)
Omicron’s propensity to replicate in the airways and not the lungs may also help explain its spread.
The newest iteration of the coronavirus is also more likely to cause asymptomatic infections, South African data shows. The knock-on effect is obvious: if people don’t know they’re sick they’ll just get on with life.
Throughout the pandemic the public has not only been exposed to the virus but also to a wide range of epidemiology ‘‘speak’’ that expresses how those microscopic particles that have, at times, brought the world to its knees actually behave.
The virus itself doesn’t have an agenda, it doesn’t care about you or me, it’s probably even fairly ‘meh’ about the 1pm Covid updates, it just makes more of itself within the biological parameters of its existence.
At those Covid press conferences, you may well have seen Prime Minister Jacinda Ardern or directorgeneral of health Dr Ashley Bloomfield speak about the R number. This is a mathematical expression that expresses how many people, on average, a person with the virus goes on to infect.
To help understand why an Omicron wave seems to rise like Apple stock but fall like Kodak, I spoke to Covid-19 modeller Michael Plank. He explained what we know so far and why there may be some good news (and this is all relative) hidden in the staggering rise and dizzying fall.
Understanding the basics
The exciting thing for R number fans is there is more than one R number. There’s R0 which expresses how many people an infected person goes on to infect if, for instance, there were no public health measures or vaccines dampening down spread. Delta’s R0 is about 6 and that was, and is, bad news.
Which brings us to Re (sometimes written as Reff) – this is how many people an infected person passes the virus on to in the real world.
In the New Zealand community right now, the Reff is probably below 1.
An R number above 1 means Covid is in the ascendancy. When it drops below 1, the outbreak is withering and dying out. Keep this in mind for later.
R is a somewhat limited measure though, as the UK’s Covid Dashboard helpfully explains. ‘‘Different diseases with the same R can generate epidemics that grow at very different speeds. For instance, 2 diseases, both with R=2, could have very different lengths of time for 1 infected individual to infect 2 other people; one disease might take years, while the other might take days.’’
Which brings us to the temporal aspect of a virus’ spread. First up, there’s something called the ‘‘generation time’’ – the time between when the first person is infected and when they infect someone else.
There’s another measure called the ‘‘serial interval’’ – which is defined as the length of time between the start of Covid-19 symptoms in Person 1 and Person 2, who is infected by Person 1.
The Omicron advantage
Right now, as Plank told me, it’s really hard to work out if Delta or Omicron’s R0 is higher, as very few people haven’t been vaccinated or infected.
You’d really need to run an awful ‘‘survival of the fittest’’ experiment that sees both variants unleashed in an immunologically naive population without telling anyone.
But what we do know is that Omicron’s Reff looks to have reached shocking highs in much of the world, with daily case numbers doubling in days.
There is some research from South Korea that suggests Omicron’s serial interval is 2.2 days. According to the World Health Organisation, Delta’s serial interval was somewhere
between 2.5 and 3.3 days. And we thought that was fast . . .
As you have probably picked up, while serial intervals and generation times are different things, they do go hand in hand.
The Journal of the Royal Society
explains this nicely: ‘‘The timing of symptom onset is more easily observed; generation times are therefore often estimated based on serial intervals.’’
What that means in real life
To understand why Omicron’s R number and generation time matters, Plank offered up this simple example.
Say there are two variants: A and B. A has an R0 of 4 and a generation time of 5 days (this is an average, by the way, it’d be different in real life, but you get the idea).
Day 0 = 1 infection.
Day 5 = 4 new infections. Day 10 = 16 new infections. Day 15 = 64 new infections. Day 20 = 256 new infections. Day 25 = 1024 new infections. Day 30 = 4096 new infections. Day 35 = 16,384 new infections. (now we’re seeing some real exponential growth).
Day 40 = 65,536 new infections.
Now, let’s look at Variant B. Let’s say it has an R0 of 2 and a generation time that’s much quicker at 2.5 days. Its R0 is much lower, but it moves much more quickly. This still means after 40 days (or 16 generations) you still end up with 65,000 new infections.
‘‘So variant A and B spread equally quickly and infect the same number of people right?’’ Plank says.
To start with yes, that’s what happens but as time goes on it’s harder for both to find hosts.
‘‘Once half the population has been infected, someone with variant B ‘tries’ to pass it on to 2 other people, but one of them is immune so only one gets infected. This means the R number is now 1 and the wave has peaked and starts to come down,’’ he explains.
Now let’s go back to variant A. Its R0 is 4, so it’s ‘‘trying’’ to pass the virus on to four other people. But now that half the population has been infected two of them are immune and two still get infected.
‘‘This means the R number is now 2 – smaller than it was to start with (variant A had R0=4) but still easily high enough for cases to continue to increase very quickly to a much higher level.’’
In this particular scenario, cases don’t start to come down until three-quarters of the population has been infected.
Keep in mind though that even when the R number is below 1, people are still getting infected as the daily numbers are falling.
So, as Plank outlines, at the end of the wave, Variant A would have infected almost 100 per cent of the population whereas Variant B would have infected around 80 per cent.
Why does this matter?
Well, the hope is that Omicron is more like variant B, incredibly fast but with a lower R number.
New UK modelling suggests, as The Guardian reports. ‘‘Scientists may have also overestimated the growth advantage of Omicron over Delta’’ because of it having a shorter generation time.
And that brings us back to population or herd immunity, a term you likely heard in 2020.
Let’s quickly remind ourselves what it means: As the Mayo Clinic in the US outlines: ‘‘Herd immunity occurs when a large portion of a community [the herd] becomes immune to a disease, making the spread of disease from person to person unlikely. As a result, the whole community becomes protected – not just those who are immune.’’
Early last year, Plank’s modelling suggested that between 80 and 85 per cent of the population would need to be vaccinated before New Zealand would reach that tipping point.
Remember, as outlined in the variant A and B scenario above, the threshold is a product of the R number. That is, the higher a disease’s R number, the more people it needs to infect before the herd immunity tipping point is reached.
The ‘‘85 per cent target’’ was for the Alpha variant. Its R0 was about 4.5. That target was, it appeared, achievable.
When Delta came along, our dreams of herd immunity were dashed. It was thought that about close to 100 per cent of the New Zealand population would need to be vaccinated as an infectious person, on average, passes the virus on to six others.
Before we go on it is important to keep in mind that any herd immunity from Covid19 is likely temporary. If we, for example, vaccinated 100 per cent of the population all at once against Delta, we’d have reached that threshold.
But we know antibody numbers wane and there’s no guarantee Omicron antibodies will provide long-term protection from re-infections or from a new variant. (Although it should help our immune system fight off severe disease.)
This is just about understanding why Omicron rises so fast and then crashes down in what seems like a two-month period. What happens after that is a story for another day.
Mathematician and epidemiologist Adam Kucharski said there was still some uncertainty in this area, but a change in generation time may well explain Omicron’s speed.
‘‘If it’s entirely down to generation time you’d expect Omicron to go up very quickly but also come down very quickly because it’s not inherently more transmissible, so it goes through the susceptible population much faster.’’
‘‘If it is more transmissible that growth would be sustained for a longer period of time because it would really be that R number driving it.’’
Dr Stephen Kissler, an infectious disease expert from Harvard University, agreed. ‘‘To get a rapid spread and rapid turnaround you really just need a lot of generations very quickly.’’
The hope, as Plank explains, is that Omicron’s R0 is lower than Delta’s. That may offer some cold comfort (again, it’s all relative) that, as an uncontrolled Omicron wave rises, it doesn’t infect everyone.
At the moment, Plank is working to model an Omicron wave in New Zealand.
Essentially the question is this: if we do see that vertical rise on our shores, how many people will get it before the waters recede?
‘‘Once half the population has been infected, someone with variant B ‘tries’ to pass it on to 2 other people, but one of them is immune so only one gets infected. This means the R number is now 1 and the wave has peaked and starts to come down.’’
Professor Michael Plank