Featured researcher: Professor Catherine Bennett

Today’s updated effective reproduction number estimate graph.

A total of 42 new cases were reported for Victoria on Tuesday, bringing our average R_eff back down to just below 0.7. The metro 14-day average has dropped to 52.9, with 82 cases of unknown source counted in this 14-day window.

The CHO said yesterday that the number of unlinked cases per day has dropped to 4-5, so this cumulative number should keep heading down towards 50 this week if this pattern continues. At this rate of reduction, the metro 14-day average should be close to 35 by next weekend.

Regional Vic 14-day average is 3.6. If no new mystery cases are reported today, regional Vic is set to have their next step out of restrictions announced.

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

Our first day of zero new death reports in 2 months, and hospitalisations, and especially the number in ICU, are now less than a quarter of levels seen at the peak of this second wave. All this is very encouraging news, and tells us that the drop in case counts is real, and not just due to a reduction in testing.

The proportion of tests that are positive also continues to track down, and we now need to test 1000 people to find 3 or 4 that are positive. At the peak, our positive test rate was 10 times this. Keeping testing rates up is critical – this not only helps identify cases and therefore contain spread, but also can identify missing links between known cases and reduce the “mystery cases” that are more critical than overall new cases numbers for decisions on easing restrictions.

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.

"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

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

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

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

“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