An Exploration of Key Topics Shaping the Future.

From Covid-Zero to Worlds Worst Outbreak? Tracking Omicron, and The Australian ‘Pandemic-Over’ Experiment.

NSW Cases following removal of restrictions, prior to the collapse of collecting case numbers.

On December 16th, I wrote on how, despite the world facing a looming Omicron surge, Australia and one state in particular in Australia (NSW), opened up as others introduced restrictions.

The result is case numbers effectively an experiment, moving to “The Pandemic Is Over” and we can “live with the virus” position, and no longer need ongoing measures beyond vaccination to control spread.

This has taken the situation in NSW, to currently arguably the world’s worst outbreak.

With Australia mostly, at least until mid 2021, having escaped the impact of Covid-19 through strict border controls, the shift to move the nation, starting with the state of NSW, from “zero covid” to post-Covid-19 world on the basis of a high vaccination rate alone, represents quite an experiment.

This page will track the progress of the experiment in NSW Australia in specific, and Omicron in general.

  • Tracking the NSW, Australia: Vaccinated, so “Pandemic Over” Experiment.
    • Latest Update (5th Jan 2022)
    • Background:
      • Significance Of The Australian Experient.
      • Politics and political convictions.
    • Phase 1: Cases Vs Projections.
    • Forget Cases: They Are Irrelevant Or Just Embarrassing.
  • Tracking Omicron Globally: Updates to be added.
    • South Africa.
    • to be added
  • Omicron The Variant: Transmission & Severity.

NSW, Australia: “Pandemic Over” Experiment.

Latest Update (9th Jan 2022)

The test positive rate even reached 40%, but has become largely academic. The real positive test percentage is no longer collected, and even the real positive test numbers are currently no collected. People at test centres are now either given a rapid antigen test (RAT) if they qualify, or told to buy one if they do not. In either event, whether the person is positive or not is not reported.

Hospitalisations and ICU numbers continue to climb, with both now setting new records each day. Despite daily case numbers no longer being measured, there level remains higher than it was when people already in hospital become infected, so hospitalisations would be expected to continue to rise.

The NSW system is now overloaded, and that could be the reason the rate of people in ICU dying is increasing, but no matter what the reason, it is a disturbing trend. It is likely there are now health consequences for all ICU patients, no just those admitted for Covid-19.

Unless cases start falling soon, the experiment could be headed towards failure. But without a clear plan to return to collecting case numbers, even seeing a fall if there is one would be a problem. There is a plan to enable people to record RAT results within a week, but as this would be voluntary, it would take at least another week to understand trends from this very different data. Just capturing the tests is one thing, but given there seems to be little incentive to pay the costs undertake a test, what numbers mean will be questionable.

Update (5th Jan 2022)

The test positive rate has now reached 1 in 3, and even despite suppression of testing, official case numbers per day per capita are 2nd highest in the world.

Hospitalisations looks to track positive test percentage, but correlation is not causation, and a delay of between two weeks and four weeks between cases and hospitalisation would be required to establish any link. Hospitalization are above the previous 1,266 record set in September, but ICU numbers are below the previous 144 record.

Background:

Global Significance And Risks Of The Australian Experient.

Australia is the first country to go from “zero-covid” to “let it rip”. Having been “zero-covid” previously, Australia has insignificant immunity from previous infection. Most countries have a mix of a known level of immunity from vaccination, together with a difficult to determine level of immunity from previous infection, resulting in infection. Australia provides one of the few places where the level of immunity in the community is sufficiently well known that outcome of “letting it rip” is known to be reproducible.

The results are not “corrupted” by an unknown level of immunity though infection. Whatever results occur in Australia, can be reproduced through ensuring the same level of vaccination. No level of exposure to the virus is required to reproduce the results.

The Risks vs Mitigations and Justifications.

Conducting the experiment involve significant risks:

  • Countries with similar immunity levels to Australia, have felt the need have need to reintroduce measures to prevent spread as cases rose following opening up, even before Omicron.
  • The severity of Omicron is unknown, and although early data suggests less initial severity, it is possible the long term effects are more serious.
  • Early data suggest children are more at risk from Omicron, and there are reasons this could be real and relevant.
  • As Omicron results in more community infection, it is possible that typical initial viral loads for those infected will increase, leading to an increase in severe infections.

Despite the increased risks, there are several factors that could possibly mitigate the risks, or mean that the threat is overstated:

  • It is Winter in most countries where similar immunity levels, but summer in Australia.
  • If Omicron does reduce death rates, it could have come at just the right time.

Politics and political convictions: Pandemic Over.

The balance of “belief vs science” in NSW has shifted. Science and data so far shows best economic outcomes are achieved by solving health care problems, but belief that solving health care problems comes is detrimental to economic outcomes is strong. While belief may be in the ascension in the Australian national government, the balance moved far more strongly to belief in NSW following the recent leadership change. The key beliefs are:

  1. Best health practice comes and economic cost and the the balance has been too far to health.
  2. Once people are vaccinated, the pandemic is over.

These core believes drive all else.

While the official position is “we have to learn to live with Coivd-19”, the actual response is not so much a set of adjustments to live with Coivd-19, but more “we can learn to live with the consequences of ignoring Coivd-19”, and that the high vaccination rates enable a “if we let it rip” approach.

The new approach is very much driven by a long held philosophy of some political leaders, that there is a trade off between health and the economy. All measures to prevent spread are seen as the enemy of the economy.

The approach is that solving the health crisis is at odds with best economic policy. For example:

  • Working from home:
    • Reduces consumption of fuel.
    • Reduces spending on commuting
    • Moves the making of many coffees and preparation of meals from a economic activity, to an unpaid activity.
  • Mask Wearing Requirements:
    • Further Encourages working from home.
    • Reduce gatherings at bars and entertainment venues.
    • Encourage outdoor gatherings with self catering in place of gatherings commercially catered.
    • Encourage “do it yourself” activities with reduced commercialisation of labour.
  • Treatment for All Under The Pandemic
    • Prevents enterprises capitalising commercial opportunities such as testing kits and services at surge pricing.

Productivity may actually go up as it did in Australia, but it does not feel right to those who worship ‘economic activity’. Many things are still done without a corporate ‘cut’, and sometimes without taxable activity. I have previously felt that putting economics first would mean learning to accept a death rate comparable to other counties with a similar level of immunity, but as mortality rates continue to fall, and a government has better access to modelling than I do, it is not certain how this will end. My task to predicting the future? I am nervously hopeful, but do expect higher long term death rates than Australian current experience from Coivd-19 becoming the normal. Daily deaths of between 30 and 80 per day seem likely, but creative statistics could find a way to lower the numbers.

As discussed here in “why let it rip?”, the NSW government took a step to the right with appointment of a new state leader, providing for the first time in Australia an alignment of a Trump leaning national leader, and a Trump leaning state leader. This dose not mean the bold experiment cannot not work, at all, but past evidence suggests a few things:

  • Commuting central business districts will not return to pre-pandemic levels.
  • The economic benefits from trying to “wind back the clock” and fight any measure to reduce infections, will lower standards of living, even if there is some artificial economic activity.
  • The ideology driven aspects of the NSW experiment will fail, even if it turns out that with some winding back of the ideology, hospitals manage to cope.
  • The ideology will lead to unnecessary loss of life, and economic cost.

None of this will stop the results of the experiment from providing guidance worldwide as to what works, and what does not work.

Phase 1: Cases Vs Projections

Cases Prior To Tracking and Projections:

Phase 1 is all about dealing with rising case numbers, while weaning the public and the medical system away from case numbers as a source of information on what is happening. Testing people is not part of the “post pandemic vision”.

In the 5 days between starting the page “Omicron Doom” and publishing that page, cases in NSW grew over four fold (>4x), which represented doubling around every two days.

Day fin Dec 2021Sa11Su12Mo13Tu14We15
Cases Tested and Positive4855368041,3601,742
Cases Tested and %91k 0.53%75k 0.71%87k 0.96%105k 1.3% 144k 1.2%
Note: date is date of testing, number are released later, so 15th is data released on 16th.

Projections, It Is Not Difficult.

I did some very simply modelling. Clearly the government would have access to far more detailed modelling. Rather than doubling every 2 days, I used The more sustainable, doubling every 3 days was used as a projection going forward, with the projections calculated for the two weeks following December 16th:

Day from Dec 81821242730
Predicted Positive Cases if Tests Keep Up3,0006,00012,00024,00048,000
Actual cases could rise at this rate, but testing could never keep up, so official numbers from testing should be be lower.

I stated at the time:

This would be close to 50,000 cases per day by year end. Of course, in a country where the previous maximum was less that 3,000 it is unlike the testing system can adjust to test and verify this number of positive tests with 2 weeks, so it is unlikely the official figure will reach 50,000. The higher the numbers, the greater the under reporting. Prior to a rethink of testing, around 25,000 cases would be maximum to be reported, as that would represent around 20% or all people tested being positive

Tracking, Numbers As Expected?

The government seemed to react with some surprise to cases, and on December 21, did backtrack slightly, and finally mandated masks for indoor venues such as shopping centres. QR code checking was also reinstated, but given tracking of cases has stopped, this seemed a very token gesture.

What I had not expected, was the speed at which the government acted to limit testing. Results quickly went from being available within 24 hours, to 72 hours or longer. There were complaints that testing required for travel was overloading the system, and testing centres closing the queues for being tested even before the testing centre opened. Arriving at 7:00am for a testing centre that would open at 9:00am was too late to be tested even if prepared to wait the full day. People were queuing form 5:00am.

Testing centres operated reduces hours, or even closed over the holiday period.

Updating the table as predicted back on December 16th:

Day from Dec 81821242730
Predicted Positive Cases if Tests Keep Up3,0006,00012,00024,00048,000
Actual Positive Test Numbers(added as updates)2,5665,715**6,394**11,201**22,577**
Number Tested – Percent Positive( part of updates)149k 1.7%160k 3.6%110k 5.9%158 7.1% 19%
Actual cases could rise at this rate, but testing could never keep up, so official numbers from testing should be be lower.

** note, case numbers reported with one additional day delay. So numbers for a day, became those reported not the next day, but the day far (eg 23rd December for 21 Dec) , as it is stated test results now take 48 to 72 hours.

So how accurate were the predictions? I predicted around 50,000 cases, and testing only revealing half of all case by year end. This sounds very accurate, but two mistakes cancel out. Testing was even less effective than I expected, which means actual cases would be higher than I expected.

Most experts estimate 100,000 cases per day by year end 2021.

Based on our experience from overseas, and experience from 2020 survey when the positivity detection rate was very low, I don’t think it unreasonable at this point to speculate that we are missing at least two-thirds or four fifths of the cases.

Professor John Kaldor UNSW Kirby Institute.

My prediction of cases being double official numbers, has clearly turned out to be an underestimate.

Phase 2: Ignore Cases, Only Hospitalisations & Deaths Matter.

Context.

For reference, consider that the only deaths from Covid-19 in the first six months of 2021, were people who were infected elsewhere and arrived already infected. Non one died from catching the virus in the state in that time. For much of the pandemic, life was relatively normal for those in NSW.

Then in July 2021, Delta arrived. Despite efforts to use previous social distancing and lockdowns, a significant wave resulted. As waves do, the wave subsided, and full credit for the wave subsiding was allocated to vaccinations. Records for daily cases and deaths plus total hospitalized and ICU cases were all set during this period. These records provide the reference for the people experiencing the “pandemic is over” experiment.

The record daily high is 15 deaths first set on 28 September 2021, and repeated on 30 September.

From Wikipedia: COVID-19 pandemic in New South Wales as at Jan3 2022.

By 11 September new locally acquired cases of COVID-19 rose to 1,599, a NSW and Australian record high, and brought total new cases reported, during the state’s Delta outbreak (since 16 June) to 36,374.[222] The record of 1,599 stood until 4 October when Victoria had 1,763 new cases

From Wikipedia: COVID-19 pandemic in New South Wales as at Jan3 2022.

Doctors, nurses and administrators are concerned about staff shortages as the number of people hospitalised with COVID-19 in NSW surpasses 1000. … At the peak of the Delta outbreak, on September 21, there were 1266 people hospitalised with infections, and 244 in intensive care.

The New Daily. Fears grow for hospitals and healthcare workers as daily cases surpass 32,000

World’s Worst Outbreak? NSW, January 2022.

Note: When first written NSW had 2,800 cases per million, put in 7th in the world, but this has since risen to 4,400 cases per million per day, placing NSW at 2nd behind only Aruba.

The worst outbreak? Really? Here are the points supporting this suggestion:

  • Despite list in 7th 2rd in the world on the basis of tests, case numbers are recognised as being 3x to 5x higher, moving case numbers above case numbers from elsewhere.
  • Australia is in mid summer, when cases should be lowest, so this performance relative to other countries in mid winter is relatively a bigger problem.
  • All other stats/countries on the list have responded to the surge with measures to reduce spread, while NSW is is staying with the plan to remove all restrictions despite cases.
  • No other location has transitioned so quickly from zero local cases of covid-19, to anywhere close to top of the list.

As a rebuttal, here are the points against this claim:

  • While no other contender has reduced and blocked testing in response to the surge, overwhelmed testing systems may be under reporting cases elsewhere, making it impost to determine who is the true champion.
  • While Ireland, Demark, etc are similar in population of less population to NSW, France and Span are much larger, so the worst region from those counties, or the worst performing state from the USA should also be considered.
  • Vaccination rates in Australia are relatively high, which could mean the high case numbers translate to less hospitalisations and deaths.

Which argument do you find more compelling?

In January 2021, a single case of a person in NSW catch Covid-19 was national news. Yes, infected people arriving from else and went into quarantine. But Covid-19 in the community was so rare that all restrictions in the community were relaxed, there were no death or serious illness in the lead up to June 2021, and life was normal aside from travel and associated quarantine. Crowds at sport, unrestricted gatherings etc.

NSW 7th(2nd on Jan5) worst officially on Jan 1, now but only through suppressed testing

The start of 2022 is so different. Now 27% of people test positive, and despite testing being completely overrun running on restricted access, and even actively discouraged by the government. For NSW to in reality have more cases per capita than Ireland, testing in Australia would need to be reporting on 60% of cases relative to Ireland.

Official data puts NSW in the top 7 states, and despite being a state, at the mid point of the group in terms of population.

Country /StatePopulation(M)Offiicial New Cases (000)Tests%
Ireland5.01744
Greece10.5
Denmark5.7
Spain46.7
France65.367.5
Montenegro0.6
NSW8.022

Testing: Public Enemy?

Donald Trump once said, if you want less cases, stop testing.

Is it beyond coincidence that now the Trump supporting leader of NSW is in place, testing has collapsed.

“COVID-19 testing sites shut down as PM rules out universal free rapid kits”

Sign about testing in NSW

Testing numbers rose as cases rose, but then testing became restricted, so that despite more people wanting to be tested, testing numbers fell.

Earlier in the surge, as cases climbed to 6,000 per day between December 22nd to 25th testing numbers were above 160,000 per day with less than 4% positive. Now at time of writing Jan 4th 2022, with positive tests above 20,000 per day, less than 100,000 tests were completed on each of the previous 3 days. It is not that more cases results in less tests, just that the government is completing less tests.

Official advice is for people to purchase and conduct their own rapid antigen tests. The result is that rapid antigen tests are completely sold out, so people do not have that option either.

With ideology coming into play again the Australian Prime Minister declared that government supplying free rapid antigen tests would represent unfair competition to retailers. So, there are retailers who normally generate significant revenue from rapid antigen tests? Or is the Prime Minister protecting the right to “surge pricing” and retailers a capitalizing on natural disasters?

Notably, the main relevant retailers are saying they would prefer that the tests were available and this is not their usual business.

The Prime Minister went on to say people should not expect free things from Government that could be delivered by private enterprise. Perhaps Australia may not be the place to be in future, if you expect to wander for free down a government owned footpath, in order to enjoy a free walk in a government owned park?

If the the pandemic really is over, because high vaccination rates do mean being infected is no longer a threat, then testing would become as senseless as queuing to be tested for the common cold. Ok, although undeclared, NSW is conduction is an experiment. However, moving to effectively shut down testing while the experiment is still underway seems a lot of confidence in the outcome of the experiment. Influenza and other diseases have case numbers monitored by other means than testing individuals, but the relevant protocols for Covid-19 are not yet in place.

To be Added:

Tracking health outcomes. How severe in practice in the highly vaccinated Australian context.

International Tracking & News.

South Africa: First Response.

I wrote “Omicron Alert” in response to the alarming rate of growth of case numbers of Omicron in South Africa in early December 2021, but case numbers have since fallen.

Cases peaked on December 12th, at a new record for South Africa after the steepest climb of the pandemic. However since that time cases fell, creating what could be the shortest wave of the pandemic. As with an “case numbers” figure, actual case numbers are far high than verified and tested case numbers, but deaths have only risen to 3x the level of between waves.

The rapid growth in case numbers suggested from the beginning that Omicron could “burn quickly” due to exhausting the potential new people to infect and creating local “herd immunity” zones, and this may be what is happening in South Africa.

Europe and the USA.

Both Europe and the USA experienced record case numbers over the Christmas new year period, but reported cases have fallen in the few days since. Is this due to reduction of reporting over the holidays, or a genuine stabilisation?

The reality varies from country to country in Europe, and state to state in the US. Some states may be experiencing peaks already, but that would be hidden by aggregate numbers.

I will update as more data becomes available. within the week.

Omicron The Variant: Transmission & Severity.

Transmissibility.

New information is that Omicron is more likely to infect the upper respiratory system.

My original assumption was that, as given there is no new ability for the virus to travel through the air, the increased rates of transmission must result from a smaller viral load being required with Omicron to trigger an infection detected by testing. This would mean the same number of particles in the air would result in more people with sufficient infection to test positive. While this still may be true, there is now another know possible reason, and an infected person may shed more virus. These two factors could both be present simultaneously.

Severity.

The data does not all point to he same conclusion. Clearly more people who are exposed to Omicron go on to count as cases. But conclusions on severity can depend on whether the sample group is those exposed to the virus, on only those who become infected.

Relative to that larger sample group of infected people with Omicron, there are a smaller percentage of hospitalisation and death, at least initially, when a significant number of people has some existing immunity. However, relative to the full sample of people exposed to infection, the percentage of hospitalisations increases. Overall, the virus has worse outcomes, but being ‘infected’ means less because while greater number infected includes more people who will have a severe case, it also includes a far bigger number of insignificant, who with previous straisn would not even be considered cases

So far it seems possible that more of the people initially exposed to Omicron, end up in hospital, or are at risk of death, despite the percentage, because so many more people become a “case”.

There is also evidence that Omicron infects different tissue than earlier strains, and infects the upper respiratory system more, and the lungs less. This is problematic, as the immune system is less effective for the upper respiratory system. The bigger worry is that given Covid-19 infects other organs such as heart, brain, intestines etc, it is possible the upper respiratory system is not the only area subject to worse infection, so “long Covid” could in fact be worse.

Resources.

New research this week seems to affirm the suspicion that the coronavirus can infect many parts of the human body, not just our respiratory system. It also found that the virus can sometimes linger in the body even after a person’s initial symptoms have abated. The preliminary findings may also shine a light on the complex chronic condition known as long covid that some survivors experience.

The Coronavirus Can Persist for Months in Brain, Heart, and Intestines, Major Study Finds

https://www.gizmodo.com.au/2021/12/reckless-and-dangerous-cdcs-new-shorter-covid-19-isolation-guidelines-disturb-some-health-experts/

https://www.gizmodo.com.au/2021/12/rapid-tests-may-be-less-accurate-for-omicron-fda-warns/

A growing body of evidence indicates that the Omicron Covid variant is more likely to infect the throat than the lungs, which scientists believe may explain why it appears to be more infectious but less deadly than other versions of the virus. Six studies – four published since Christmas Eve – have found that Omicron does not damage people’s lungs as much as the Delta and other previous variants of Covid. The studies have yet to be peer-reviewed by other scientists.

“The result of all the mutations that make Omicron different from previous variants is that it may have altered its ability to infect different sorts of cells,” said Deenan Pillay, professor of virology at University College London.

“In essence, it looks to be more able to infect the upper respiratory tract – cells in the throat. So it would multiply in cells there more readily than in cells deep in the lung. This is really preliminary but the studies point in the same direction.”

If the virus produces more cells in the throat, that makes it more transmissible, which would help to explain the rapid spread of Omicron. A virus that is good at infecting lung tissue, on the other hand, will be potentially more dangerous but less transmissible.

Guardian: New studies reinforce belief that Omicron is less likely to damage lungs

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Covid-19 & Vaccination Deaths: Statistically, Coincidences will distort reported deaths.

I read recently about reasonable people protesting over post vaccination deaths in South Korea, echoing stories from around the globe about the underreporting of deaths following vaccination.

Can most of these deaths be just coincidences? This question has me seeking the real story on what is happening, not just with deaths following vaccination, but also with deaths from the virus. Almost one year after my initial exploration of vaccine efficacy and safety, now there is data, not just projections, so it is time for a review, and this question needs answering for any such a review.

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