Featured researcher: Professor Catherine Bennett

The effective R number estimate and case count graphs: Reff can bounce a lot when case numbers are this low - if we have a low case count for a couple of days then it can appear to jump up after an incubation period (5-6 days) even if numbers are not that different. But remarkably we have only had two occasions when Reff peaked just above one, and the 10-day average is sitting around 0.6-0.7 and in fact has dropped this last week. This probably reflects that case and close contact follow-up is so much more effective when working with such manageable numbers, and working in partnership with the community. So easy for epidemic curve tails to be stubborn or unpredictable, so it’s great to see this steady downward trend continue right through to this end of the curve!

Notes:

• Many interventions were rolled in; we focus on the date where the main intervention became mandatory
• Not all cases are tested – only those with symptoms can be tested in the general community, and not all those will come forward
• When comparing the counts across the 5-6 day incubation period, we use raw new case numbers in the numerator, and the average of the case counts taken from 5 to 7 days previously in the denominator.
• The graph includes a 10-day moving average for the estimated R_eff to highlight the trends

What is R0 and how do we calculate our estimates?

The Reproduction number (R0 or “R naught”) has been talked about a lot during this COVID-19 pandemic. It is an important statistical term that reflects how infectious the virus is in different settings. Each time we change levels of restriction, or mandate masks, we are changing the number of close contacts people have and the risk that they will infect another person, and so R0 changes. We call the specific R0 in any setting R_eff; the effective Reproduction number.

R_eff summarises the average number of people who will be infected by each current positive case and tells us how our outbreak control measures are working. Those secondary infections will be counted as ‘new cases’ after they develop symptoms, seek testing, and when a positive test result is recorded. If the average number of secondary cases linked to particular cases is greater than 1, then R_eff is greater than 1. The number itself tells us how many people are infected by each case. So an R_eff of 3 indicates that each case infects another 3 new people on average, and that the outbreak is growing, with case numbers tripling every incubation period. For COVID-19, the median incubation period is 5 to 6 days.

On the other hand, if existing cases don’t all infect at least one other person, then the number drops below 1 and we know the outbreak is under control and case numbers are shrinking. If R_eff is, say 0.5, then that tells us that we can expect the number of new cases to drop to 50% of today’s new case numbers after one incubation period.

If we make certain assumptions, we can use the publicly available data to come up with a very rough estimate of the reproduction number for Victoria. If we assume that the time from infection to testing is reasonably consistent over time, then we can look at how new case numbers compare across incubation periods to estimate this R_eff. It is likely, however, that the time to testing for people with symptoms may have changed as the outbreak became more serious, and with hardship payments making it a bit easier for people to forgo work and get tested and isolate until they have their result.

Another assumption we’re making is that the proportion of true cases out there that are identified through testing remains reasonably constant as well. If you had only 50 % of cases being tested in one week, and then 100% in the next, it might look like R_eff had doubled, even if the true number of cases per day had not changed. This is true for all modelling where there is likely to be incomplete case capture, but as long as the proportion of cases that are counted stays relatively constant, then comparing even partial counts across incubation periods is still useful.

Case reports tend to come in batches from the outbreak investigations and the labs. For example, we see less reports on Mondays and Tuesdays as these are from tests completed on the weekend. Therefore, it’s useful to take an average of the number of existing cases on any one day. We use a 3-day average to smooth out those reporting fluctuations in the denominator of our calculation when we look at the ratio of new cases to those reported 5-6 days ago.

Finally, it’s important to note that the SARS-CoV-2 virus responsible for COVID-19 does not move through the population evenly. The number of people any one person infects is dependent on their number of close contacts and the environments they live and work in. It may also vary person to person based on their viral load, their symptoms, or other factors that may alter their potential to infect someone else. There have been many super-spreader events, whilst the majority of cases may not infect anyone else at all.

According to Victoria’s Chief Health Officer, Professor Brett Sutton, around one third of our new cases each day are from outbreaks, mostly in aged care and health facilities now. These have a big influence on our daily case numbers until these outbreaks are closed down and we stop seeing new clusters form.

All you need is a large super-spreader event, or a large new outbreak starting when someone takes the virus into their work place, and the reproduction number will change quickly. So, as always, this is not about numbers alone: the epidemic path is determined by where the virus is and who is exposed. Therefore, whilst useful to see how we are tracking, it remains very difficult to predict exactly where R_eff will be in another five days’ time.

Want to know more? What Is R0? Gauging Contagious Infections

Mystery case update (revised):

The CHO, when talking about regional Vic progress at today’s press conference, confirmed zero mystery cases for regional Vic in last 14 days. Our State-wide total count of 21 should be heading down over the next 2 days also as all 7 new cases that were still under investigation yesterday were  today confirmed to be already  linked to outbreaks. So zero mystery cases yesterday, and also the day before. Great news, and the comprehensive follow up and “upstream” tracing of cases is clearly working very well. A total daily case average well below 20 over 14 days, and if mystery cases dropping to none or one or two a day ... that’s where we hoped we would be by the end of lockdown. This will reassure the Health Dept about Step 3, and make that next step announcement more straightforward. Let’s hope its proof that the seeding risk is already so low between metro and regional with no cases detected in workers crossing the border that we can remove that ring of steel, and families and friends can reunite, and business and tourism start to recover. Here’s our glide path for the step 3 metrics. All very encouraging!

The effective R number estimate and case count graphs: Reff can bounce a lot when case numbers are this low - if we have a low case count for a couple of days then it can appear to jump up after an incubation period (5-6 days) even if numbers are not that different. But remarkably we have only had two occasions when Reff peaked just above one, and the 10-day average is sitting around 0.6-0.7 and in fact has dropped this last week. This probably reflects that case and close contact follow-up is so much more effective when working with such manageable numbers, and working in partnership with the community. So easy for epidemic curve tails to be stubborn or unpredictable, so it’s great to see this steady downward trend continue right through to this end of the curve!

Notes:

This graph tracks both daily cases and reported deaths over the second wave. The axis for the cases is on the left, and for the deaths it is on the right and, of course, on a much smaller scale. The reason we have them both in the same graph, even though the numbers are so different, is to highlight the difference in timing between new cases and deaths.

There is on average a week’s lag from someone developing symptoms and being tested and counted as a case, and then developing serious enough illness that might require hospitalisation. It might be a further week before they require intensive care (ICU). Some people can remain in intensive care for a very long time; some might succumb to the virus even without being in ICU. But, on average, there will be a two to three-week lag between peaks in cases and the peak in the deaths that are the terribly sad consequence of those large numbers of new infections.

Cases started to plateau at the end of July, and we saw sustained high numbers for a couple of weeks before the case numbers started to fall in the second week of August. The numbers of reports of deaths finally also started to plateau in mid-August and, whilst fluctuating, has been reasonably stable since; averaging about 15 deaths a day. As we are now at the end of the month, it is expected that we will soon see daily reports decline, and the 7-day average with them. Because the day to day reports can fluctuate a lot, we also show the 7-day average so that you can see the trends over time.

"Unless the pattern changes in what they're seeing when they go out to contact tracing, or unless the proportion of the positives starts to go up, then I think this is a good enough indication that our testing numbers are following the proportion of people with symptoms." Victoria's coronavirus case numbers are declining, but are testing numbers sufficient to be confident about the numbers?

Catherine Bennett talks to ABC NewsRadio Victoria records 45 new Covid-19 cases and 5 deaths

Catherine Bennett said Melbourne’s 14-day average was likely to be “comfortably” within the 30-50 range window by 28 September. Experts expect 14-day average to drop below reopening range next week

"Finally some serology results! 0.28% infection rate detected in elective surgery patients in Syd, Melb and ACT in May-June pre-wave 2. Translates into to ~ 14000 cases for Vic, not the 2000 recorded. That’s about what I have been predicting based on what we know about testing regimens. Also fits in with the possible number of excess deaths (soon to be published). Wave 1 smaller than wave 2 because we went in to stage 3 pretty quickly and that was enough for the virus to die out and did not get into aged care which acted as the accelerator in wave 2. Not sure whether 0.28 was consistent across all regions tested .. more to come. But it will confirm wave 1 and 2 more similar than most allow for, and we can learn from wave 1, particularly how to open up stepwise and safely." Read the study here.

EXPERT Q&A: Victoria records largest number of deaths to date alongside 282 new cases

“Low double digits in our sights...let’s hope the new aged care outbreaks mentioned by the Premier yesterday are rapidly contained to protect lives, and to allow our daily case counts to keep tracking down. The glimmer of light at the end of the tunnel will get brighter.” Magic COVID milestone could be just around the corner

“Deaths may peak 2 to 3 weeks after cases. We saw this in the first wave, and in the data from the previous weeks as I shared before … we must brace ourselves for some days possibly even worse than today over these next couple of weeks.” New coronavirus cases in Victoria may have peaked but deaths expected to rise

“People want to see DHHS’s modelling, but at this stage their value is in COVID-19 scenario testing, not in predicting the case numbers for next week.” Get on top of the outbreaks an the numbers will start to drop rapidly

Restrictions and lockdowns

Daniel Andrews will detail the next step in Melbourne's coronavirus restrictions roadmap today

"If people are taking care and we're moving to step three … [the outbreak] is contained, it's not high-risk" More COVID-19 restrictions may be eased in Victoria on Sunday. Here's what the health experts think

"It's unlikely there is now underlying community transmission in regional Victoria because of the length of the lockdown" Safe for NSW to open up to regional Victoria, experts say

"Victoria's dropping case numbers are "tracking better" than modelling initially suggested and the state's daily figures could warrant fast-tracking the lifting of lockdown restrictions." 'No epidemiological argument for border closure' if case numbers fall at this rate

If you take out the positive cases linked to known outbreaks, the proportion of cases coming back positive dropped to below 0.1 per cent. Victoria should take 'cautious' approach to early easing of coronavirus restrictions, expert says

The lowest 24-hour increase since nine cases were recorded on June 16 brings Melbourne’s rolling 14-day average to 34.4. 11 new cases, two deaths; Melbourne’s harsh lockdown could end weeks early

Common sense must guide us on this road map, and will allow a shift in focus to the important business of evidence-based prevention, early warning systems and testing strategies, backed up by contact tracing and outbreak response readiness, writes Catherine Bennett in The Age Dropping cases should lead to a 'common-sense' rethink on opening up

Catherine Bennett chats to Patricia Karvelas on RN Drive Victoria to boost coronavirus contact tracing

On 6 September, the State Government announced the stage four lockdown would be extended by two weeks, with more significant restrictions to be eased in late October. Experts question model and map as new cases fall to lowest since June

The Victorian Government's roadmap to easing coronavirus restrictions has been met with varied reactions. Victoria's coronavirus restrictions roadmap could exacerbate anxiety and prolong economic pain, experts say

Catherine's thoughts on Victoria's roadmap out of restrictions Steps out will be incremental, frustrating, even arbitrary

The Conversation asked four experts, including Catherine Bennett, what they see as the most important aspects of Victoria’s path out of stage four. Four perspectives on how Victoria should exit stage 4 lockdown

Allowing households to open their doors to one or two close friends and family in a 'germ bubble' is being considered as a possible route out of stage four lockdown and the loneliness that goes with it. The lonely and the learned back 'germ bubbles' as the way to ease lockdown

COVID curfew crunch: Nearly $1 million in fines but medicos are split on its effectiveness

“Evaluation of interventions now will allow us to move from blunt shutdowns to precision tactics in our COVID-19 fight, and help chart our way out of our current lockdown safely.” Stage four lockdown offers a chance to find out path out

“The Stage 5 threat - not the best way to encourage compliance. The compliance engineered into stage 4 should be more than enough to bring this under control. Otherwise, we risk going to even more restrictions to stop people from mixing, or give up on control attempts and live with consequences. Doesn’t bear to think about either, so let’s make this work and work fast!” Stage 5 ahead? What Melbourne could face if COVID cases don’t decline

“Lockdown is the key to killing off clusters that we can’t see, as well as the ones we can. Arguments for a “stage 4” lockdown are lost on me... why use a NZ style shutdown when consensus is that was overkill first time round, (especially as Aus and Melb achieved same outcome) and there is no evidence it will make a difference given current epidemic dynamics. Reduced mobility, more distancing, masks and isolation if symptomatic is the path to shutting this down.” Victorian lockdown high COVID case numbers mean longer lockdown necessary

Masks and face coverings

Watch as Catherine talks to Skynews about Victorian restrictions.Stage three and masks are 'surely enough to manage COVID-19' in Victoria

Research suggests the growing use of alternative face coverings may not be helpful in curbing the spread of COVID-19. Face shields not effective replacements for cloth masks, experts say

“Warning - this story refers to facts and therefore may be considered offensive by some. Congratulations to SBS for pulling together this response.” Fact-checking Andrew Bolt’s claims about Melbourne’s mandatory mask order

Testing

"Testing remains critical, even when our test positive rates are 0.1% or 1 in a thousand. This is especially true whilst a few cases still appear where a source cannot be found. If one person infects two others who are not linked, and that first person does not get tested but the other two do, then we not only miss one case, but we “create” two mystery cases - and these will be more critical in decisions about easing restrictions than +/- one linked case." NSW coronavirus testing rates are plummeting — here's why that's a problem

AusSMC BRIEFING: Genomic testing for COVID-19 - ask the experts

NSW on a knife-edge: experts urge new restrictions to avoid uncontrollable spread of Covid-19

“High rates of positive test results will happen as clusters with high transmission risk are investigated. The positivity rates track closely with the number of linked cases among new reports. This clouds our view of the actual background positive rate in the wider community.” Should I get tested? What if I don't have symptoms? Will it hurt? Your COVID-19 testing questions answered

Community transmission and contact tracing

Catherine Bennett on the ABC’s 7.30 Report Victoria has overhauled its swamped contact tracing system

The Victorian government is implementing changes to its contact tracing system including moving to a suburban hub model similar to New South Wales. A day in the life of Victoria’s Covid contact tracers: ‘The puzzle is blank and once you get it together it's fantastic'

COVID quarantine hotel sex: The rumour that triggered Victoria’s tidal wave of consequences

“Finally! recognition for hardest hit low SES suburbs. I have been telling this story for a while now, but it has been left on the editors chopping block.” Expert on who REALLY should 'be credited for turning Victoria's COVID tide'

“We have known SARS-CoV2 moves in clusters through communities since early on. Comparing Victoria and NSW is a great demonstration of the different outcomes if a new wave of infection is only discovered once multiple clusters have established simultaneously. These events feed more virus back into community that then seed more clusters.” Super-spreaders could be key to controlling COVID-19

“Epidemic curves by LGA grouped in SES quintiles is even more interesting than could be covered in this story. Despite the outbreak being seeded in these communities and large clusters already well formed by the time any restrictions came in, and the fact that people in these areas are less able to work from home or be able to afford to stop working, the rate of drop is proportionally as great in these communities once the excess numbers from local outbreaks start to be contained. These low SES areas not only had the extra serve of bad luck at the start, they have collectively done an amazing job at being part of the public health solution.” 'Past the peak': Cautious optimism as state posts fewer new COVID-19 cases

“Those unlinked COVID-19 community cases … if we can break these unseen chains of transmission.. we will have this beat!” Disease detectives baffled by mystery COVID-19 cases behind tough new lockdown

“More detailed modelling of mobility and distancing data finds that Victoria was best in Australia when the reintroduction of COVID-19 occurred, and the suburbs at the heart of this were no different to others in Melbourne. This report also confirms that COVID transmission via clusters defies normal measures of epidemic potential. This comes back to my previous comments on the element of chance in where the virus lands in the community.. and the impact that this can have.” Victoria’s social distancing best on mainland when second surge hit

"Time to gather the information needed to fuel the difficult but necessary debates about how we live with the virus - we had limited choices when COVID-19 was such an unknown, but all action, and inaction, comes at a cost (lives, health, economic and the myriad of societal impacts), and now we must comprehensively evaluate our strategies." Lockdown is working, but is it excessive?

Health experts question 'incredibly conservative' road map

“More modelling? The Burnet Institute team’s nuanced agent-based model calibrated to our second wave in Vic has more to offer. They found a 41% risk of another wave if we had jumped to the final roadmap step yesterday with our 14-day average at 22 (the previous conservative model said 62% for 14-day av. of 25).
Many are now asking whether we still need the 5km rule. Or when will it be safe to move to step 3, and should the 14-day case count thresholds for this step be updated. These are the kind of scenarios that could be explored using this new model.
The cases seeded into the model should reflect the different mix of case risk we have now (92% are linked and most therefore likely to be in isolation/quarantine when tested), but could be really helpful in guiding decisions on thresholds and timing of steps, as well as whether the 5km rule could be lifted. This is stopping some families from meeting outdoors or permitted businesses opening if clients aren’t local.
It could also help people adapt to the roadmap changes (inc lifting of curfew etc), and help allay fears they may have about opening up. This will be very safe, our detection and response systems too, so we need to bring the people along with us who no longer believe that!” Melbourne's five-kilometre rule: is it really worth it?

“Two months ago there was consensus among epidemiologists that to open up we would need new case numbers in low double digits and mystery cases to single digits. Since then it has all gone a bit crazy, but even after the road map was announced, there has been agreement that 5 cases was too ambitious and 10 cases a day is manageable. Over 70% if Vic’s cases are known to be linked when first reported, and therefore in people already in quarantine, and 85% of our cases under investigation are also linked eventually. We by now must have less than one mystery case a day on average (judging from changes in 14 day total). So why is a small number of contained but persistent outbreaks and 5 community cases a week not manageable? Sure we don’t want months of chasing cases like NSW has had to do, but continuing strict lockdown when we have already had 15 or more incubation cycles under it is clearly not the answer. We need to start easing restrictions, keep testing up, have fast and comprehensive case and contact follow-up, and remember the basics - distance, hygiene and masks. Then we can focus on prevention, early warning systems and monitoring to stay safe." What Australia needs to do to avoid a third Covid wave

Chatting again about all things Covid-19 with Tass and Fiona on Joy radio’s Saturday Magazine Catherine Bennett, Epidemiologist

“Divisive speak is dangerous - true always but particularly so in a pandemic. Opinions are being polarized; open-up completely or strict lock-down, you’re onboard or “you think it’s over because you want it to be over”, this virus is wildly infectious and cant be controlled without complete lockdown or you don’t believe it exists. Anyone with an opinion that doesn’t fit with either extreme is placed in to one to suit the commentator’s argument. These are worrying times. Most recently the narrative at the daily press conference is about regional and peninsula folk being terrified of Melburnians because of their “vastly higher amounts of virus”. Regional Vic’s 12-day av is a very low 1.9 cases/million, and the metro rate is also very low at 7.9 cases/million (half already in isolation). The Health Dept say they can finally see community transmission chains that were there all the time but hidden behind high numbers (data analyses could have shown sooner?). Stage 4 is about suppressing risk of transmission beyond these pockets where infection persists, creating the optimum backdrop for the Dept to do its work. 9 weeks in lock down has not been enough time for this (5-12 incubation periods), let’s hope another couple of weeks is.” - Catherine Bennett's LinkedIn

RMIT ABC Fact Check: Were NSW's coronavirus numbers higher than Victoria's thresholds for lifting curfew, as Scott Morrison said?

Has Australia really had 60,000 undiagnosed COVID-19 cases?

Another week, and we will know more about our October in Melbourne. The Age has taken the lighter moments from today’s press conference to build hope. Also a useful discussion on whether those identified in breach of CHO rules in contact tracing interviews should be fined. Our enforcement strategies have placed us in a difficult situation - respect privacy, open up conversations in order to close outbreaks down, or issue fines. This is part of a bigger public health communication conversation about the way we engage community. Public health communication strategies needs to provide transparency, clarity and certainty, so that people come forward for testing quickly, then have the conversations to allow us to chase any transmission - without rapid testing and information handover, it is that much harder to contain outbreaks. Outbreak control always works better if enforcement is a last resort, and that is something we should try to find ways to avoid going ahead. Premier raises hopes of easing restrictions sooner than planned

What is ‘herd immunity’ and what role does it play in a pandemic? Explainer: Reaching herd immunity in a viral pandemic

“Think before you voice an opinion — consistent messaging is critical in a public health crisis. Expert debate can be valuable, but publicly opposing current interventions on the basis of opinion rather than fact can reduce efficacy by undermining public confidence, and therefore compliance... both of which are already harder to garner in a second wave.” Latest restrictions became a self-fulfilling prophecy