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COVID SNAPS: vaccination gaps, Omicron, reasons for optimism, a shout-out to health workers – and some catchy tunes

Introduction by Croakey: The need for coordinated, community-led action to address COVID vaccination gaps for Aboriginal and Torres Strait Islander people was one of the calls to action from the OzSAGE network of experts this week.

During a briefing on 29 November, Dr Kalinda Griffiths, an epidemiologist and Yawuru woman, provided this update, and reiterated calls for states and territories to open up only after 95 percent of all Aboriginal and Torres Strait Islander people over the age of five are double vaccinated.

The group recommended that the surveillance of Aboriginal and Torres Strait Islander vaccination and booster rates and COVID hospitalisations be presented by state and territory Local Government Areas, as appropriate, and that this information be released more often.

“If there are population groups and regions that have lower vaccination rates than other areas, then it is critical to direct information, resources and workforce to better support vaccine uptake,” Griffiths said.

“The gaps between the vaccination rates of Aboriginal and Torres Strait Islander people and the rest of the Australian population requires a spotlight. It is clear that despite being a priority population, Aboriginal and Torres Strait Islander people have been left behind.

“There is also a pressing need to further support the community controlled sector to ensure the timely delivery of health services including the delivery of vaccines. This includes ensuring people are also able to source and get booster shots.”

Meanwhile, in her final column for this year, Professor Kathy Eagar, Director of the Australian Health Services Research Institute at the University of Wollongong, gives an update on the new coronavirus variant Omicron, does some crystal ball gazing and shares some encouraging reflections – as well as various catchy COVID tunes.

And she presents the ‘2021 COVID Vaccination Honours Award for most improved’.


Kathy Eagar writes:

Welcome to the 2021 Christmas edition of my COVID update. 🔔🎉🎅🎁🎄

This is my final edition for 2021 and I had expected it might be my final edition for 2022 and beyond as well. But COVID may have other plans.

Quote of the week:

“The 1918 has gone: a year momentous as the termination of the most cruel war in the annals of the human race; a year which marked, the end at least for a time, of man’s destruction of man; unfortunately a year in which developed a most fatal infectious disease causing the death of hundreds of thousands of human beings. Medical science for four and one-half years devoted itself to putting men on the firing line and keeping them there. Now it must turn with its whole might to combating the greatest enemy of all – infectious disease.”

Journal of the American Medical Association final edition of 1918 (28/12/1918).

Word of the week: Omicron

Australian COVID at a glance

Here is a summary of the COVID state of the nation. Case numbers continue to fluctuate around 1,200 most days. The good news is that de-coupling is still going well. Thanks covid19data.com.au for this daily update.

Reff round up

The Effective Reproduction number or the Reff or the RO tells you how quickly the virus is spreading. When the Reff is greater than 1.0, cases are increasing. When the Reff is less than 1.0, cases are decreasing. Thanks Professor Adrian Esterman for his daily calculation of the Reff.

NSW: 271 cases and no deaths yesterday. The 7-day moving average is 215 (215 last week), Reff 0.98 (0.95 last week) – the Reff continues to hover around 1.00 and case numbers look like being stuck at this level right through to Christmas and beyond. The two unknowns are the speed by which Omicron spreads and the impact of international borders when they eventually re-open.

Victoria: 1,419 cases and 10 deaths yesterday. The 7-day moving average is 1,164 (1,001 last week) and the Reff is 1.03 (0.95 last week) – as with NSW, the Reff continues to hover around 1.00. Victorian case numbers continue to hover in the 800-1,200 a day range. As with NSW, I’m expecting Victoria to go into the Christmas period with cases remaining at a similar level.

I have been asked several times why case numbers in Victoria remain so much higher than case numbers in NSW. Victoria opened up with case numbers at a much higher level than NSW. Since then, the Reff has hovered around 1.00 in both states, meaning that both states have effectively been stuck at the level they were when they eased restrictions.

There is a key lesson in this for next time. The goal should always be to get cases as low as possible before opening up. Once restrictions are eased, the best we can do is maintain case numbers, not decrease them.

A trickle of cases are now being reported in other jurisdictions with WA now the only state to be totally COVID-free. The good news is that the Northern Territory has done a great job and appears to have contained its recent outbreak.

Vaccination round up

Here is a table showing vaccination rates by jurisdiction. The highest levels of vaccination are still in the ACT, NSW and Victoria.

But the good news is that other jurisdictions are catching up. I am expecting to see only marginal improvements from this point in ACT, NSW and Victoria.

But I am still hopeful that NT, WA, Queensland and SA will keep improving and progressively close the vaccine equity gap. That said, there is also significant inequity within states and territories, and addressing this must remain a national and jurisdictional priority.

Magic double vaccination rates

Here is how we are ending 2021 in terms of vaccination rates for NSW statistical areas.

In total, 14 of the 28 areas are now above 95 percent (up from seven last week). All but five of the 28 areas now have more than 90 percent of the eligible population vaccinated.

Sydney City and Inner South is still below 80 percent and remains the outlier. Interestingly the Richmond-Tweed is well on its way to achieving 95 percent with 93 percent of the community having had one dose. This is quite an achievement that challenges the ‘anti-vax’ reputation of the NSW north coast.

The 2021 COVID Vaccination Honours Award for most improved goes to the Coffs Harbour-Grafton region. It has increased double vaccination coverage by a massive 43.6 percent in just eight weeks and is now at greater than 95 percent.

The top five regions are:

Looking at the data on all of the population over 16, the vaccination rate in NSW is now almost stagnant.

In total, 79.9 percent of the whole NSW population (including children) has now had one dose (up from 79.7 percent last week) and 78.0 percent has had two (up from 77.2 percent last week).

We remain about 15 percent below the level necessary to achieve any level of herd immunity. There is no likelihood of achieving that until such time as vaccination is approved for babies and children.

What’s in a name? SARS-CoV-2 variants

The World Health Organization (WHO) is responsible for tracking coronavirus variants as they develop.

The highest level of classification is a ‘Variant of Concern’ (VOC). Virus variants typically start off being classified by WHO as a Variant under Monitoring (VUM). If they look like becoming a problem they get reclassified and the next level up is Variant of Interest (VOI). The top level is Variant of Concern (VOC).

Omicron is a VOC. It skipped being a VOI and went straight to the top of the class within one week.

Omicron is the 5th VOC – Alpha, Beta, Gamma, Delta and now Omicron.

A VOC is a VOI that has one or more of the following changes at a “degree of global public health significance”:

  • Increase in transmissibility OR
  • Increase in illness severity OR
  • Decrease in effectiveness of public health and social measures or available diagnostics, vaccines, therapeutics.

WHO has two coronavirus Variants of Interest (VOI) under constant review:

There are also seven Variants under Monitoring. VUMS don’t get a Greek Alphabet name.

These lists are constantly under review with variants being added and removed as the situation changes. For example, Kappa, Iota and Eta were previously VOIs but have been downgraded when they were overtaken by other variants. You can follow developments here.

A fascinating website for nerds is www.nextstrain.org. A massive team of contributors keep this up to date by contributing genomic material from all around the world. Be patient when you open it. It is slow as it updates each time.

Here is the latest global picture of coronavirus strains. In jargon terms, you are looking at a graphical representation of the “genomic epidemiology of novel coronavirus”.

Remember this phrase and impress your family on Christmas Day:

“So, what’s new with you?” “Not much, I’ve been busy keeping up to date with the genomic epidemiology of the novel coronavirus.”

The red line and dots in the graph above is Omicron. You can see that Omicron is not a variant of Delta (the top green section). Omicron has actually being hanging around undetected for a long time until now.

Here is the genomic epidemiology for Australia.

Being an island with our borders shut, we have actually skipped a few COVID variants.

Can you see Iota and Lambda?

They are clearly seen in orange in the global picture above.

But you can’t see them in the Australian sequence because we managed to keep almost all of it out. You also can’t see any visible evidence of Omicron red dots yet. But it is only a matter of time.

Omicron

The Omicron strain was first detected in South Africa but probably didn’t originate there. We should all be grateful to South Africa. It is not a wealthy country but, at the beginning of the pandemic, South Africa made a decision to invest in sophisticated genomic testing capacity.  If it wasn’t for that, we probably wouldn’t even know about Omicron at this point.

Omicron has arrived with quite a splash. There are already signs that Omicron may be triggering a new wave in South Africa as can be seen in this graph from the Financial Times.

The laboratory evidence is that, compared to previous variants, it has 32 changes to its spike protein. It is spreading much faster than Delta. Delta spread twice as fast as Alpha and now Omicron is spreading faster again.

The rate of spread can be clearly seen in this graph It has taken less than three weeks for Omicron to represent 90 percent of all COVID cases in South Africa. This is about four times faster than the spread of Delta in South Africa. Spread is usually a measure of how infectious a disease is.

But spread can also be the result of ‘immune escape’ (in which viruses evade your immune system, similar to how some bacteria are now resistant to antibiotics).

Scientists are now racing to identify whether the Omicron variant has developed any potential to evade the immunity engendered by vaccination and/or previous COVID infection. If so, it will require some changes to the makeup of current vaccines.

Here is a table showing the first reports of cases. Omicron is now in several continents in just a few days. Around the world in 80 days.

But the good news is that there is a big difference between speed and disease severity.

There is no evidence as yet that Omicron is harder to treat or that it results in more several illness or that it is more deadly. And there is no evidence as yet that it is better at evading public health measures or is more complex to diagnose.

But it is early days. In just a week Omicron has spread to more than a dozen countries so it won’t be long until we know more. The three key questions we can’t answer definitely at this point are:

·       Does it cause more severe illness (is it more deadly)?

·       Does it respond to vaccines in the same way as other variants?

·       Is it powerful enough to knock off other variants of concern especially Delta?

I am expecting that we will have enough evidence to answer all three questions within the next two weeks. In the meantime, common sense (remember that?) dictates that we should act with an abundance of caution until we know more.

It is not surprising that this variant originated in southern Africa. Southern Africa has such a high endemic rate of untreated HIV that it has always been a time bomb. People with untreated HIV and other chronic diseases are so immunocompromised that the virus has a field day invading their bodies and mutating without resistance.

If we were really smart as well as really ethical, we would not only be really helping low income countries with COVID-19 vaccine. We would also be really helping them to reduce the rate of endemic diseases which allow COVID-19 to thrive. PNG on our doorstep is a disaster waiting to happen and only a canoe ride away from North Queensland.

Omicron and the crystal ball

I wouldn’t normally speculate on what might happen next. But, as this is my last COVID update for 2021, I thought I should mention that there are a range of possibilities about what will happen next.

Best case scenario: the goodies win

The best case scenario is that Omicron is very infectious, causes only mild disease and is more powerful than Delta.  The genomic epidemiology graph becomes a sea of red as Omicron spreads around the world. Everyone becomes immune to COVID either because they are vaccinated or develop natural immunity after being infected with Omicron. Delta has nowhere left to spread and withers away. Omicron, the goody, defeats Delta, the baddie. We all live happily ever after, albeit with occasional mild infections (similar to the common cold) caused by Omicron.

Worst case scenario: the baddies win

The worst case scenario is that Omicron causes more severe illness than it appears at the moment. Omicron and Delta join forces and mutate into yet another variant that contains the worst of both of them.

A reality check: somewhere in the middle

My guess is that the future lies somewhere in between. As we approach the end of 2021, we need to be realistic that COVID isn’t finished with us yet. Omicron will hopefully reduce the spread of Delta but the virus will keep evolving and mutating. Vaccine technology will continue to improve, public health measures will continue to be effective and treatment for severe illness will become much more effective.

Life in 2022 will settle into a new normal that includes living with COVID for the foreseeable future.

Reasons for optimism: what a difference a year makes

Thinking back over 2021, there have been remarkable improvements in the prevention and treatment of COVID. These really are a cause for celebration.

Here are some of them:

We went into 2021 knowing what works at the general population level. In 2021 we got used to living with them – masks, QR codes, social distancing and so on.

For the at-risk population (which is pretty much all of us), 2022 saw some significant scientific developments. Expect to see smarter vaccine technology (such as nose sprays and patches) and the next generation of vaccines in the foreseeable future.

Two big developments occurred in 2021 in relation to diagnosis and early treatment.

Rapid antigen tests (RATS) are becoming increasingly accurate and have become routine. Also in 2021, the first treatments were approved that are designed to be taken as soon as a person is diagnosed. The goal is to prevent the person becoming severely ill. Paxlovid by Pfizer is one of these, as is Molnupiravir (Merck) and Evusheld (AstraZeneca).

These are potentially a game changer as they come in tablet form. I think it’s realistic to expect that they will be approved for GP prescription before too long. Pack some in your suitcase when heading overseas.

The risk of course is that some people will think taking a pill is easier than preventing COVID in the first place. If everyone elects a pill rather than vaccine, it would only make things worse in the long run.

We need to minimise the spread of the virus so that it cannot keep mutating. If we don’t, it won’t take long before a variant comes along that is resistant to these new treatments. And then the whole process would start again. Prevention is always better than cure.

The range of drugs for treating severe COVID in hospital is improving (see this table, published in The Conversation on 12 November, which summarises some of them).

The other major improvements relate to best practice care.  As one simple example, we now know that COVID patients with breathing difficulties do better when they lie on their front and not their back.  In health jargon, prone not supine.  Prone positioning is already being attributed to saving literally hundreds of lives.

The one aspect where we have made relatively little progress this year is in the recognition and treatment of long COVID.

While all of the focus has been on prevention, diagnosis and acute treatment for COVID, we have paid too little attention to what comes next. As my colleagues in rehabilitation remind us:

Acute care saves lives

Rehabilitation makes the saved life worth living

A major research and development strategy for long COVID remains as unfinished business as we go into 2022.

The month ahead

2021 is almost over. Yippee!

Summer reading

The Conversation: We shouldn’t lift all COVID public health measures until kids are vaccinated. Here’s why.

It is extraordinary that, as we go into the Christmas season, vaccination for 5-11 year olds in Australia has still not be approved or procured. The Commonwealth failed by being too slow with its adult vaccination strategy and now the same is happening again. If vaccine is safe for children in the USA, Canada, Hong Kong, Israel and a growing number of other countries, it’s safe for Aussie kids too.

CDC: Myths and Facts about COVID-19 Vaccines for Children

The New Daily: Greece to fine unvaccinated people over 60

Residents in Greece over the age of 60 will be fined €100 a month if they fail to get vaccinated against the coronavirus. The money will go to hospitals.

Washington Post: As the omicron variant arrives in the West, wealthy countries are reaping what they sowed

Variants are one deadly side effect of vaccine inequality — and a global system that has allowed wealthy nations, and large developing ones, to corral jabs for themselves, leaving poorer and less powerful countries to subsist on vaccine crumbs.

The Conversation: Wealthy nations starved the developing world of vaccines. Omicron shows the cost of this greed

Unless governments take urgent action to correct these inequities, we risk the emergence of further variants, some of which may evade vaccines

New York Times: Omicron carries scary mutations. That doesn’t mean they work well together

Medical Republic: Is Omicron more contagious than Delta?

Nature: Heavily mutated Omicron variant puts scientists on alert

NPR: How vaccine-makers plan to address the new COVID-19 omicron variant

Stanford: The Influenza Pandemic of 1918.

This is a fascinating read about the influenza pandemic that killed more people than World War I. At somewhere between 20 and 40 million people, the Spanish flu killed at least four times more people than COVID-19 so far.

I had a little bird,

Its name was Enza.

I opened the window,

And in-flu-enza.

The Conversation: COVID death data can be shared to make it look like vaccines don’t work, or worse – but that’s not the whole picture

The Conversation: Pfizer’s pill is the latest COVID treatment to show promise. Here are some more

Thinking of the perfect home-made gift for that special person in your life? Try this embroidery gift idea.

Big shout out to health workers everywhere

The Royal Melbourne Hospital Scrub Choir joined up with more than 900 healthcare workers from Australia, the UK, Ireland, Norway and Japan to bring joy this holiday season with Scrub Choir Plus.

Watching this made me shed a tear or two. A big shout of thanks to health workers everywhere. What a hell of a year you have had.

 

Christmas listening for the whole family

For those who loved The Sound of Music last week:

 

I hope you have a wonderful Christmas day celebrating with family and friends. Don’t turn your day into a superspreader event as grandmother and grandfather are doing in today’s attachment. 🎄💃🎅🎶👏 👩💳🎁✨🟡 👦📝📨🎅 🤚✨🎄🟡⭐


Croakey thanks and acknowledges Professor Kathy Eagar for this column, which is based upon a regular COVID update that she emails her networks, combining a mixture of evidence, observation and pithy humour. On Twitter, follow @k_eagar

Bookmark this link to follow the series.

 

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