COVID-19 – ½ñÈճԹÏ I Championing Mathematical Sciences for Australia’s Advancement ½ñÈճԹÏ Mon, 23 Nov 2020 04:10:55 +0000 en-US hourly 1 https://wordpress.org/?v=5.8.17 /wp-content/uploads/2015/11/cropped-½ñÈճԹÏ_icon-32x32.png COVID-19 – ½ñÈճԹÏ I Championing Mathematical Sciences for Australia’s Advancement 32 32 Professor Adrian Esterman on ABC TV’s ‘Afternoon Briefing’ /2020/11/23/professor-adrian-esterman-on-abc-tvs-afternoon-briefing/ Mon, 23 Nov 2020 03:46:54 +0000 /?p=10338 Expert biostatistician at the University of South Australia discusses the state’s lockdown, how to ease restrictions and hotel quarantine staff working multiple jobs with Patricia Karvelas.

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90% efficacy for Pfizer’s COVID-19 mRNA vaccine is striking, but we need to wait for the full data /2020/11/11/90-efficacy-for-pfizers-covid-19-mrna-vaccine-is-striking-but-we-need-to-wait-for-the-full-data/ Tue, 10 Nov 2020 23:06:36 +0000 /?p=10302 The “interim analysis” is promising, however it’s an early look at the data before a study is complete,

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German biotech company BioNTech and US pharmaceutical Pfizer announced on Monday promising early results from their phase 3 clinical trial for a vaccine against SARS-CoV-2, the virus that causes COVID-19.

These early results are what is known as an “interim analysis”. It’s an early look at the data before a study is complete, to understand if there is any indication of whether the vaccine might work.

Currently, this trial has enrolled , giving half the volunteers . These volunteers then continued their normal lives, but they were monitored for any symptoms that could be COVID-19, with testing to confirm.

Analysis of 94 volunteers with confirmed COVID-19 suggests the vaccine has an .

This means that if you took ten people who were going to get sick from COVID-19 and vaccinated them, only one out of ten would now get sick.

 

Can we get excited yet?

There is more data to come. This is a press release and the data have not undergone “peer-review” through scientific publication, although it has been assessed by an independent monitoring board. The study also won’t be complete until 164 volunteers have confirmed COVID-19, and the estimate of efficacy may therefore change. Finally, the volunteers must be monitored for a defined period of time after vaccination for any side effects and this must be completed.

Important questions also remain. It’s unclear how long protection will last, as this study has only been underway for three months. It’s unclear if this vaccine protects against severe disease or if this vaccine will work equally well in everyone. For example, a with this vaccine showed that immune responses were lower in older people.

But 90% efficacy is striking. To give some context, the US Food and Drug Administration indicated they would licence a SARS-CoV-2 vaccine with . The flu vaccine often provides around and the mumps vaccine, which is currently the at four years, provides around .

The BioNTech/Pfizer vaccine could outstrip that, after just nine months of development. This level of efficacy means virus transmission could be very effectively controlled.

That has the . It bodes well for other vaccines currently being tested for SARS-CoV-2 and we could end up with multiple successful vaccines. This would be great because some might work better in certain populations, like older people.

Multiple vaccines could also be manufactured using a broad range of established infrastructure, which would accelerate vaccine distribution.

Producing mRNA on a commercial scale

The BioNTech/Pfizer vaccine is what’s called an mRNA vaccine.

As by Associate Professor Archa Fox, an expert on molecular cell biology from the University of Western Australia, explains:

mRNA vaccines are coated molecules of mRNA, similar to DNA, that carry the instructions for making a viral protein.

After injection into muscle, the mRNA is taken up by cells. Ribosomes, the cell’s protein factories, read the mRNA instructions and make the viral protein. These new proteins are exported from cells and the rest of the immunisation process is identical to other vaccines: our immune system mounts a response by recognising the proteins as foreign and developing antibodies against them.

A problem for Australia is that it can’t make mRNA vaccines onshore yet.

The Australian government has an agreement for . Since this vaccine requires two doses, this agreement is sufficient for five million Australians. It’s unclear how long it will take until any vaccine is widely available, but we may hear more about this in the coming weeks and months.

The vaccine requires storage at a temperature below -60℃. This will certainly be a challenge for shipping to Australia and local distribution, although not impossible. One solution to this problem is to form vaccination centres to roll out the vaccine once it becomes available. In a briefing by Pfizer, the company said it will use ultra-low temperature shipment strategies and the vaccine can then be distributed on “dry-ice”.

Currently, Australia has no capacity to produce mRNA on a commercial scale given the technology’s novelty. But we (the authors) and others have been working to coordinate and build the manufacturing capacity in Australia for future mRNA vaccine and therapeutics. With financial support aimed at private-public mRNA manufacturing collaboration, Australia can equip itself with this vital technological asset.

, Bioengineer and Research Fellow, ; , Professor of Pharmaceutical Biology, , and , Vice-Chancellor’s Research Fellow, School of Health and Biomedical Sciences,

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Zeroing in on Victoria’s suppression success /2020/11/09/zeroing-in-on-victorias-suppression-success/ Mon, 09 Nov 2020 01:01:03 +0000 /?p=10292 “Victoria has only done what all the other states and territories have been able to do apart from NSW – which is get to zero and keep it there”: UniSA’s Adrian Estermann commentary in .

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Australian Academy of Science announces latest Regional Collaborations Programme grants /2020/10/30/australian-academy-of-science-announces-latest-regional-collaborations-programme-grants/ Fri, 30 Oct 2020 00:34:37 +0000 /?p=10234 These Australian Government grants administered by the Academy support projects utilising digital methods of collaboration in addressing shared regional challenges that either directly or indirectly relate to the COVID-19 pandemic response and recovery in the Asia–Pacific region.

Grants of up to $10,000 are available to support digital collaborative research projects with Asia–Pacific regional partner economies for Australian early- and mid-career researchers.

Learn more from the .

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‘The Random Sample’ – ACEMS podcast: From Maths to the Media /2020/10/29/the-random-sample-acems-podcast-from-maths-to-the-media/ Thu, 29 Oct 2020 05:18:40 +0000 /?p=10228 What can you do with a mathematics education? For Casey Briggs, he’s turned it into a career with the ABC. , Casey talks with ACEMS’s Tim Macuga about his role in communicating data, especially when it comes to a story like the COVID-19 pandemic. Casey also talks about the challenges of presenting statistics and data to a TV audience.

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Melbourne is almost out of lockdown. It’s time to trust Melburnians to make their own COVID-safe decisions. /2020/10/19/melbourne-is-almost-out-of-lockdown-its-time-to-trust-melburnians-to-make-their-own-covid-safe-decisions/ Mon, 19 Oct 2020 00:29:43 +0000 /?p=10163 Deakin University epidemiology chair Professor Catherine Bennett commentary in .

After days of speculation, today’s by Victorian Premier Daniel Andrews was pretty much as we expected: a significant lifting of restrictions, albeit only a half-step out of lockdown.

From 11.59pm tonight, Melburnians will be able to travel up to 25km from home, with no time limits on exercise or recreation, bringing the chance to play a round of golf or visit the hairdresser.

Even more encouragingly, we may only have to wait a week until the lockdown is lifted, the “four reasons” to leave home are removed, and retailers and other businesses can once again open their doors.

Andrews said the planned move to step three of the COVID-19 roadmap could be brought forward a week from its provisional date of November 1 if case numbers — now tracking at 7.5 new cases a day for metropolitan Melbourne and just 0.5 in the regions — remain favourable.

“Victorians have stayed the course, and we just have a little longer to go,” he said.

I agree Victorians can rightly be proud, because this lockdown was a very big ask. In fact, I see no reason why we can’t remove blanket rules such as the 25km radius and Melbourne’s “ring of steel” immediately.

Buying time

The blanket restrictions in Melbourne, which have been in place since early July, have bought time to rebuild our public health response, with stronger measures for testing, contact tracing and isolating outbreaks. The idea is to “bring the restrictions to the virus”, meaning we can now contain it wherever it might appear.

As a result, restricting the general public’s movements with the help of blanket rules makes less sense, because many Melburnians now have a minuscule risk.

I don’t understand why we need to impose a 25km limit. It’s such a big radius but will still exclude people who live at opposite ends of the city from seeing each other. Perhaps the fear is too many people will congregate in popular or scenic places. But surely that can be managed by scrutinising those particular places.

In contrast, when Singapore was coming off its second wave, it lifted restrictions when COVID-19 cases were at 60 per million people, per day. Melbourne’s current average is just over 1 case per million people, per day. If Andrews were to promote Victoria’s strategy to the rest of the world, I’ve no doubt they would agree it’s been a success, but they would probably also wonder why it is taking so long.

We had an extended blanket lockdown that was enough to quash the virus multiple times over in households. But we weren’t able to contain it in aged care, certain workplaces, and complex households.

With cases now so low, the idea that all public movement equals viral spread is not true. There’s a lot more to this virus than this sort of reductionist approach. We know probably 70% of people don’t even pass it on, and that many cases are the end of a chain of infection. If we do get a cluster, we will likely pick it up. This gives me confidence Melbourne will be able to open up fully next weekend.

The wholesale rebuilding of our contact-tracing means we are now very much on the front foot. Health authorities should continue urgently interrogating and isolating new cases, particularly mystery ones.

But for the wider public, it is now important to instil a sense that the government trusts people to be sensible for themselves. The more rules we have, the harder it is for people to have a sense of agency.

The rules should now be focused on areas where there is greatest risk. Unnecessary blanket rules might get in the way of people buying in. For instance, the ring of steel shouldn’t be necessary, given the testing and tracing measures we now have in place. What’s more, I think it will be a long time before people go back to their old patterns of movement, given that people have become acclimatised to staying at home.

This also means it’s easier to consider lifting border restrictions. While we’ve been busy fighting off the second wave we’ve built the health response to a point where we can live with the virus. So things like borders become less crucial.




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If authorities aren’t busy policing things that don’t make much of a difference, such as the 25km rule, it will free up resources and also mean people have one less rule, and one less fine, hanging over them.

I would also urge authorities to allow people to wear masks only in situations where it makes a real difference, as opposed to everywhere. It’s easier to trust the public to do that when they’re not being told to wear them all the time.

Over more than three months, Victorians have grown used to being told what to do in intense detail. Now it’s time for people to get back some control, and I’m hopeful we can do that in a way that’s safe.The Conversation

, Chair in Epidemiology,

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So, Victoria, what do we do now? /2020/10/14/so-victoria-what-do-we-do-now/ Wed, 14 Oct 2020 05:51:52 +0000 /?p=10150 It’s now mathematically impossible that Melbourne will reach its COVID-19 case target to release to Step 3 of the Roadmap soon, but how might we open up a little and beat the disease modelling?

University of Melbourne’s Professor Tony Blakely in ‘The Age’ and .

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When Does A Second COVID-19 Surge End? /2020/09/25/when-does-a-second-covid-19-surge-end/ Fri, 25 Sep 2020 02:08:15 +0000 /?p=10114 Australian mathematicians Nick James and Max Menzies have published what they believe is the first analysis of COVID-19 infection rates in US states to identify turning points in data that indicate when surges have started or ended.

The new study is published today in the journal ‘Chaos’, published by the American Institute of Physics.

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Has Australia really had 60,000 undiagnosed COVID-19 cases? /2020/09/21/has-australia-really-had-60000-undiagnosed-covid-19-cases/ Sun, 20 Sep 2020 23:32:00 +0000 /?p=10082 A preliminary study, posted online this week by researchers at the Australian National University and elsewhere, estimates 71,000 Australians had COVID-19 by mid-July — 60,000 more than official number of cases diagnosed by that stage. Biostatistics , and from in .

A , posted online this week by researchers at the Australian National University and elsewhere, estimates 71,000 Australians had COVID-19 by mid-July — 60,000 more than official number of cases diagnosed by that stage.

The study involved testing 2,991 elective surgery patients in ten hospitals across four states, to see whether they had antibodies against SARS-CoV-2, the virus that causes COVID-19.

The study initially found 41 positive patients (1.4%), but then adjusted for the false positives that would arise due to the imperfect specificity of the antibody test, which the researchers estimate would produce 11 false positives for every 1,000 tests. This yielded an estimated prevalence of 0.28% — or eight “true” positives from the 2,991 people sampled.

The researchers then extrapolated this estimate, including its uncertainty parameters, to the Australian population as a whole. They ultimately concluded the number of Australians with SARS-CoV-2 antibodies — and who have therefore presumably been infected with COVID-19 — is somewhere between zero and 181,050, and most likely about 71,000.

This begs two main questions: should this alter our view on how best to contain the spread of COVID-19, and are there any limitations to the study that we should be aware of?

Let’s begin with the latter question. Here are four key things to consider when interpreting the results.

1. False positives

In countries with very low COVID-19 rates, such as Australia, the key requirement of an antibody test is to be highly specific — that is, to avoid false positives. This is even more important than being highly sensitive (avoiding false negatives).

The antibody test used in the new study reportedly has a specificity of 98.9%, and a sensitivity of 100%. This means, for every 1,000 tests, we can expect 11 false positives and no false negatives.

Imagine a place with high prevalence of the virus, such as New York City, where of people are estimated to have had COVID-19. A sample of 1,000 would, on average, contain 200 COVID-19 positive people, of whom the test would correctly identify all 200, with no false negatives. It would also find 11 people positive who were actually negative, giving an estimated prevalence of 211 out of 1,000, or 21.1% — which is close to the true figure.

Now imagine a sample of 1,000 Australians, with a COVID-19 prevalence of, say, 0.2%.

Just two people in this sample would correctly test positive, but again we would expect the test to deliver 11 false positives. This gives an estimated prevalence of 13 out of 1,000, or 1.3%, which is several times higher than the true figure.

Even if you revise your estimate to account for the expected false positives, as the authors did, we can see how hard it is to estimate low prevalences accurately. The small number of real cases is liable to be lost in the noise.

2. Sample size

A larger sample size could provide improved precision. The small sample size is why the study’s estimated range is so wide. In fact, it stretches all the way down to zero, even though we know there can’t possibly have been zero COVID-19 cases in Australia. But no matter the size of the study group, the false positive problem never really goes away as long as the prevalence is low.

3. Testing method

One solution would have been to retest the samples with currently available commercial with specificities of 99.9%. This would have offered a way to overcome the problem with false positives.

The suspicion that the sample included a substantial proportion of false positives is supported by the fact only one COVID-19 positive patient had contact with a known COVID-19 case, and none of those who tested positive had reported any COVID-19-like illness.

4. Extrapolation

There are also questions over how reliably the results can be generalised to the entire Australian public. The study involved people undergoing elective surgery, who may have had different risks of exposure to the virus.

It is hard to say from the available data whether any adjustment was made for variables such as age, sex and state of residence when extrapolating to the wider Australian population.

So what can we say for sure?

What can we determine from this study about the number of people exposed to COVID-19 in Australia? Unfortunately, without a much larger sample, wider sampling of the population, and a more reliable test, we know little more about the prevalence of exposure to COVID-19 than we already did.

This means it would be unwise to use these new findings to claim COVID-19 is any less dangerous or deadly than we thought.

Rather than take these estimates at face value, what we really need is more comprehensive testing of the prevalence of SARS-CoV-2 antibodies, including studies that track this prevalence over time.

In any case, Australia can consider itself fortunate to have low enough case numbers that the issues of false positives becomes a major caveat in interpreting studies such as this. Sadly, in many other places, false positives are buried in a landslide of genuine COVID-19 cases.


Editor’s note: Ian Cockburn, one of the study’s lead authors, told The Conversation false positives are indeed more likely to be a significant factor when trying to estimate low prevalence rates, but described the study as a “best estimate” based on two separate statistical analyses, which both arrived at the same result. He added the research team plans to use further statistical methods to check the study’s results before it is accepted for full publication.

He said the study sample “is not a perfect cross-section” of the population, and the ideal study size would be 6,000-10,000 people, but obtaining blood samples from the general population poses significant logistical and cost obstacles.

He added it can be difficult to verify commercial companies’ claims to have antibody tests with higher specificities, and that patients who register a false positive may also test false positive with another test if it works in the same way.The Conversation

, Professor of Biostatistics, and , Scientia Professor and Head, Viral Hepatitis Clinical Research Program, Kirby Institute,

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Virus modelling far from perfect: University of Melbourne maths and medicine /2020/09/21/virus-modelling-far-from-perfect-university-of-melbourne-maths-and-medicine/ Sun, 20 Sep 2020 23:16:28 +0000 /?p=10080 Mathematical biology Professor James McCaw and Medical Dean Shitij Kapur in .

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