How long does it take to bust a COVID cluster?

Tegan Taylor: Hello, this is Coronacast, a daily podcast all about the coronavirus. I'm health reporter Tegan Taylor.
Norman Swan: And I'm physician and journalist Dr Norman Swan, it's Wednesday, 20 January.
Tegan Taylor: And here with us today we have a special guest, ABC data journalist Catherine Hanrahan. Welcome Catherine.
Catherine Hanrahan: Hi.
Tegan Taylor: So Catherine, you've been looking at New South Wales data on the cluster outbreaks that they've had in New South Wales and you've done some data crunching, and what have you found?
Catherine Hanrahan: So what I did was I looked at all the clusters that New South Wales has had since early July when we had the case from Melbourne come and seed the Crossroads outbreak which really started the New South Wales second wave.
So, New South Wales Health defines a cluster as three people who are epidemiologically linked, and what that means is there are three people who have been in physical contact with each other, and also that the genome sequencing of the viruses they have are the same.
So what I found was…I looked at 18 different clusters that we've had in New South Wales since July last year, and regardless of how many cases were in the cluster, what we found is that the clusters last for about the same amount of time, that's three weeks from the first case until the last case is identified. So by the end of three weeks, you're really starting to have found nearly all of the people in that cluster. Now, the problem is, if they miss anyone, that person can then go on and seed a new cluster.
Norman Swan: So while you've got the closure of the Crossroads one, it seeded several clusters, didn't it? I mean, you had the one in the Thai restaurant, the Thai Rock restaurant and various others, and they all trace back to Crossroads eventually. So is it true to say that you close down after three weeks if they have spawned other clusters?
Catherine Hanrahan: In some cases they did identify the source, and in others not. So, for example, the Bankstown area funeral services, the Thai Rock restaurant, Wetherill Park, Batemans Bay soldiers club, they didn't identify the source, but they could tell by looking at the genome sequencing that it probably had originally come from the Crossroads Hotel case, but they never worked out who the individual was that crossed over between the two clusters.
Norman Swan: So in fact then what you're saying, Catherine, is…with the system you've got in place in New South Wales, and presumably Victoria as well now and other states, they all now work on roughly the same basis, you can expect a cluster to be closed at three weeks, but what you don't know is whether you're spawning other clusters which could then get out of control. But if you apply the same methodology, then you just keep on going in three-week cycles.
Catherine Hanrahan: That's right, and that's really what happened in New South Wales. So obviously there were new clusters being seeded, which just rolled from one to the next. But the contact tracers never became overwhelmed by the cases, so they were able to keep each cluster relatively under control and have it shut down after three weeks, but there would always just be one or two escaped cases that would spawn the next cluster.
Norman Swan: So how do we get to doughnut days, 28 in a row, for the state?
Catherine Hanrahan: Yes, it's tricky. I think what we saw happening last year was even though the epidemiologists say it doesn't matter whether you've got a big or a small cluster, it generally last about three weeks. The cluster numbers began getting smaller. So when we got to October last year we had the Oran Park cluster was 23 people, the private health clinic was 13, and so there's just less and less people they need to talk to and I guess they can dig a lot deeper into who those extra cases might be. And in November we got to the end of that last cluster and then we had about a month of no cases, bar one, which was a transport worker.
Norman Swan: One of the controversial things that we were talking about early on in Coronacast coverage of the outbreak in the northern beaches was when it looked like it was spawning other clusters or there were other leaks from overseas was the issue of whether or not to actually lock down for a short, sharp period of time to just get things under control. Is there any evidence that that speeds up cluster resolution?
Catherine Hanrahan: Yes, that's an interesting one because when you look at these 18 clusters, the only one where we had a lockdown, like a real lockdown, was Avalon, Northern Beaches, and yet you didn't see the cluster being shut down any faster than any of the other clusters were. So it's a difficult one to say, and you don't seem to circumvent the process by having a really sharp lockdown, although what you may do is seed less clusters.
Tegan Taylor: So what does the data show about when Sydney's outbreak could end?
Catherine Hanrahan: Well, assuming that there haven't been any new clusters seeded that the New South Wales Health doesn't know about, it would appear from the data that we have about another week of the Berala cluster to run and then it will come to an end.
Norman Swan: Catherine Hanrahan is a data journalist with the ABC. Thank you very much.
Catherine Hanrahan: Thank you.
Tegan Taylor: So Norman, we get heaps of questions about whether when the virus mutates and we've got these new strains popping up globally, whether the vaccines that we are getting are going to be effective against them. And so far we've been hearing from experts that, yes, they will. But there was a Twitter thread by one of the experts in the field in the last couple of days saying that maybe the so-called UK strain, the B117 variant, might not be as effectively targeted by the Pfizer vaccine as we had hoped.
Norman Swan: Yes, this is work done at the University of Cambridge on a small number of people, they basically studied 15 people who had the Pfizer mRNA vaccine. They basically gave them the spike protein with the mutations in it that was modified, so they weren't getting a proper infection. And what they found was that there was a reduction in vaccine efficacy in those small number of people.
And they tried it I think also on the South African mutation…it's unfair to call it South African but the ones that appeared in South Africa, and that also found a little bit reduced level of specific antibody response to that version of the virus. So a very small study, not published yet, but if it's right then there is some reduced effectiveness of the vaccine on these variants. Whether it's enough to make them ineffective, it doesn't look likely from this small study, but it means that there are further variants on top of that and you could get escape from the vaccine.
All is not necessarily lost because the technology platform for the Pfizer and Moderna vaccines allows them to switch virus quite easily, so they think they could do that within about six weeks and they wouldn't need to do further clinical trials because the platform has been tested, a bit like the influenza vaccine. But it would play havoc in countries that have committed to other vaccines that might not be able to turn around that quickly. So at the moment we are still okay, but there are some warning signs.
Tegan Taylor: So let's take a few questions from the audience and, keeping in the theme there about vaccination, someone is asking…she is in her 30s and her partner and she always thought that this was the year to start trying for a baby, but now she is worried that if she gets pregnant now she's going to miss or delay her opportunity to get the vaccine, which she does want to get because she has asthma. Should she delay having a baby or go ahead with it? Does it mean that she can't get the vaccine while she is pregnant or breastfeeding?
Norman Swan: We are yet to see what approval the Therapeutic Goods Administration in Australia is going to give for the Astra vaccine, but at the moment they haven't tested it on enough pregnant women to know whether or not it's safe in pregnancy. It's likely that it is. So you're right to be concerned.
We can't give you advice. The situation of course in Australia is that while you would like to have the vaccine, we've got very little COVID-19 around, and therefore the risk in going ahead with pregnancy unimmunised is much less here than it is otherwise. Let's assume you get pregnant pretty quickly, that takes you through to September, October, which is probably around about the time that the large majority of Australians are going to be immunised, beyond the high-risk groups, so you are actually not going to delay your immunisation by that much because if you waited, it would probably take about then to get immunised anyway. So if you get pregnant now, you'll be done and dusted, and able to get immunised.
Tegan Taylor: Perfect timing.
Norman Swan: Sounds like the perfect solution.
Tegan Taylor: And one more question from Tim. Why is Australia only sourcing two Western vaccines and not all that is available, including the Russian and Chinese ones?
Norman Swan: Let's start with the Russian and Chinese ones. The Russian vaccine could actually be quite a good vaccine. It's not that different in technology to the Oxford University vaccine, and in fact Astra has reportedly started negotiating with the Russians that they might use the Astra vaccine for dose one and the Russian vaccine for dose two because it's a different virus. But they haven't had properly conducted randomised trials.
There are various Chinese vaccines. There is one with a killed version or a neutralised version of the virus, which is a very traditional vaccine, which they've reported has 70% effectiveness. Given that they are not reporting 100% effectiveness and it's 70%, it has the air of reality about it, but again, hasn't had a well conducted randomised trial done and that's why we wouldn't be sourcing those, unfortunately, because they could be quite good vaccines but the data are just not reliable at this point.
And then there are other vaccines. We've got the…it's not just two, we sourced the Novavax vaccine, which could turn out to be very good vaccine, which is a much more traditional vaccine where they inject the spike protein into the body directly, and that is yet to report on its clinical trials, they've had some problems in manufacturing.
And then there are others such as the Johnson & Johnson one which is a single dose, those are just coming through the system now. Really what the Commonwealth did was negotiate with the frontrunner vaccines. The only one they could have negotiated there with a bit more confidence upfront was Moderna and they came to that a little bit late.
Tegan Taylor: Well, that's all we've got time for on Coronacast for today.
Norman Swan: If you've got a question, go to abc.net.au/coronacast, click on 'Ask a Question', and mention Coronacast on the way through. And we will see you tomorrow.
Tegan Taylor: That we will.