Zachary Holloway: What was the work you were conducting at the Victorian Infectious Diseases Reference Laboratory (VIDRL) before the COVID-19 pandemic?

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Dr Julian Druce: VIDRL itself is a public health reference laboratory, with a large focus on virology. For virology there are four main labs: one is a big serology laboratory which tests for antibodies and the footprints that a virus leaves after your immune system has interrogated that pathogen. The other labs are more focused on direct detection of some specific viruses: there’s an HIV-specific lab, a hepatitis-specific lab and then my lab, which focuses on all other viruses. These mostly use very specific PCR (polymerase chain reaction) tests for the detection of the virus.
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Another option for rapidly detecting viruses that might be new is by having tests that, rather than detecting a specific virus, detect a family of viruses at once. They’re called consensus PCRs or pan-viral PCRs. One of those tests was a pan-coronavirus PCR, and that had been sitting in a freezer for thirteen years, only to be brought out at the start of 2020 when SARS-CoV-2 emerged, and that was the test we used to verify that we had the virus by sequencing the PCR product.

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ZH: I know that VIDRL was the first lab outside of China to grow SARS-CoV-2 in culture. What was the process for this, and how did this help in developing a standardised test for COVID-19?

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JD: My boss, Dr Mike Catton, and I had been on WHO [World Health Organisation] teleconference calls all through the preceding weeks where everyone was clamouring for someone to grow the virus. So I immediately put it up for culture on the Friday night when we detected it. This process puts a small amount of patient sample onto cells that may get infected with the virus.  I came in on Sunday to check it, and thought something might be happening so put the flask of cells onto a camera that took photos every fifteen minutes. As soon as I checked this on Monday, I knew that it was growing because there was an obvious pattern in the cells that showed they were changing. 
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In terms of having the cultured virus, it was then just a process of getting it out to other labs and collaborators. We gamma-irradiated some material and that material, which is killed, was a good positive control material for other laboratories to use to verify and validate their testing algorithms. Because at that point, there were only self-designed tests for COVID-19 in a few labs. This material was used to help validate all the labs around Melbourne and Australia as commercial tests became available to get them ready for testing.

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ZH: How important was genome sequencing for our contact tracers to be better able to track and trace the spread of the virus? ​

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JD: In general, roughly every two weeks the virus will generate one mutation somewhere. That mutation can be used to track the lineage – a bit like a family tree – and once that mutation goes from, say, me to you, you might get a new mutation when you pass it on to someone else. That mutation then becomes a key identifier for that strain. That really helped in tracking and tracing in the early days, to understand who was probably giving it to whom even though contact tracing can often work that out. 
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Importantly though, at that very early stage we closed our borders to China, but we left our borders open to America and Europe. So as cases were coming in from those countries, we had to do genomic sequencing to verify what strain, or lineage if you like, with key mutations were showing up. We could then readily identify whether the samples were from Europe, America or the Ruby Princess, or from wherever there were new cases coming in. 

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ZH: Has the increased infectivity of the Delta variant of SARS-CoV-2 beaten contact tracers and made Australia’s “COVID zero” strategy unachievable?

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JD: In terms of “COVID zero”, the national pandemic plan has always been to suppress the virus and flatten the curve, and the public health aim of that is to push the volume of samples down and stretch it out along a timeline axis. You might end up with the same numbers, but it’s stretched out across a year rather than one or two months, which shatters your health system.
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But what we found early was that with a lot of goodwill and effort from the public, we did eliminate the virus. We didn’t necessarily expect to do that, so that was a lucky event. But with the Delta variant, it does seem that it spreads more efficiently: the calculated reproduction rate for this variant is about 3-4 or more, and about 2-3 for the original wild-type.  So this makes it much harder to eliminate.

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​ZH: I think millions of people around the country want to know the answer to this question, but when will lockdowns stop being a viable strategy for containing this virus? Does it come with increasing vaccination, or could it continue after that?

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JD: It very much depends on what happens as we move forward. Of course, vaccination is the pathway out of this. As more people become vaccinated and less susceptible to serious disease and death, we will slowly transform this virus into a common cold, or at least that’s what is likely to happen. 

But I suspect that as we open up, if it all goes badly, we may have to have some level of restrictions to mitigate transmission. Some of this is already being discussed with entry passports, and people not being allowed into pubs, theatres, or wherever else there is close confinement in a natural or urban setting, unless they’re double-dosed.

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ZH: In retrospect, how will we rate the response to this pandemic? Was it proportional to the dangers it posed?

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JD: I think that will be debated for years. Every country has done it a little bit differently, from the worst end of the scale to the best end of the scale. Australia is probably on the better end, in terms of suppressing and eliminating the virus, but we haven’t done as well with the vaccine rollout. We’re getting there now – we’re catching up – but I think, generally, Australia will be viewed favourably as having had a good response. 

In Australia there’s a double-edged sword with vaccination uptake because we didn’t have the carnage that other countries had.. But now that we’ve got the virus circulating again, that has prompted a greater uptake of the vaccine, which is a good thing. 

Outside of Australia, I imagine the World Health Organisation will do an analysis of the generalised responses of different countries: from some of the poorer performers – like America and other countries that decided to let it rip, thinking that herd immunity was the best option – to the responses of other countries, mainly severe lockdowns, who suppressed and eliminated the virus. There are still many types of parameters to look at, from economic and socioeconomic to virological and epidemiological, a lot of elements still to tease apart when this is all done.
 

Dr Julian Druce is the head of the Virus Identification Laboratory at the Victorian Infectious Diseases Reference Laboratory, where he works with a team to detect many of the viruses that infect humans and devises new ways to detect novel viruses. 
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We would like to thank Dr Druce for taking the time to meet with us and discuss his work.