Omicron - a dive into the data

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SternAAlbifrons
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Omicron - a dive into the data

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Finally.. the mists are starting to clear

Omicron: a deep dive into the data

SMH By Liam Mannix
Jan 18, 2022


Scientists had long warned the world not to get too comfortable: the next COVID-19 variant was always only just around the corner.
However, few predicted Omicron, a variant that seems both more contagious and less deadly, and that has changed the pandemic in several important ways.

Since Omicron reared its head in late November, scientists around the world have published reams of data, much of it contradictory. Now, almost two months down the line, the dust – and the science – has started to settle.
So, what does the highest-quality data say about Omicron’s infectiousness, mortality and vaccine evasiveness? Let’s dive in.

What is an Omicron, anyway?
First spotted in South Africa and Botswana in November, Omicron has quickly become the dominant variant in many countries, outstripping Delta.

An important note: data suggests that for every five cases Australian scientists sequence, one is Delta. Omicron may be dominant, but make no mistake, Delta is not finished yet.

Omicron has about 50 mutations, many in the spike protein, some of which had cropped up in previous variants and some of which are unique. However, more mutations do not always mean a fitter virus. It’s how those mutations combine that seems to be important and, unfortunately for us, Omicron’s combination appears particularly powerful.

There is some lab evidence that Omicron’s mutations allow it to bind more effectively to human cells and evade antibodies – a significant advantage for new variants. But this study may be the most interesting: it suggests Omicron really is behaving differently to previous variants.

Omicron replicates much more effectively in human upper airway cells. However, it is much less infectious than Delta in the deeper lung.

This is known as viral tropism (new science term!), which is a way of describing the part of the body a virus likes to live in.

Scientists speculate that this could make the variant more contagious but less lethal. More virus in the upper airways means it is easier to cough and sneeze and spray around, while less virus deep in the lungs means it is less likely to kill.

Associate Professor Stuart Turville’s team of variant hunters at the Kirby Institute in NSW have taken a look at the first Omicron virus detected in Australia – extracted from a traveller on November 27.

“The change in tropism could be lowering disease severity,” he said. “[But] we still don’t know [enough] about Omicron to say it is ‘mild’. Clinical manifestations of viral infections may be short term and also long term. This is not to make people anxious, but to say many of us simply do not know what this virus is up to. We are catching up to it in real time.”

How infectious is it?

The obvious marker here is raw case counts. The US is experiencing its largest surge in infections since the pandemic began, averaging more than 800,000 new cases a day. Australia’s spike in infections in recent weeks has been so pronounced that, looking at a cumulative case graph, it appears as if COVID-19 did not exist here until a few weeks ago.

So yeah, it’s pretty infectious, but can we put a real number on it?

A Danish study of 11,937 households estimated Omicron’s secondary attack rate – the chances of an infected person passing on the virus to someone at home – was 31 per cent, compared to 21 per cent with Delta. UK data puts that rate at about 15 per cent, compared to 10 per cent with Delta.

South Africa’s Omicron cases now appear to have peaked and are dropping sharply, as are cases in several neighbouring countries.

However, these sharp turnarounds are likely the result of those countries slamming on restrictions as their health systems become overwhelmed, rather than anything intrinsic about the variant, says Professor James Trauer, head of epidemiological modelling at Monash University’s School of Public Health. The restrictions won’t stop it, though. “It’s impossible to get a reff [effective transmission number] below one for Omicron,” he said.

When you get it, what are the chances Omicron will make you really sick?

Compare South Africa’s weekly death toll, which remains well below the peaks seen in mid-2021, with its daily new cases. Unlike with other variants, where each surge in cases was followed by a rise in deaths; we’re not seeing that same strong relationship now. The Omicron surge appears much less deadly.

“We’re clearly seeing much lower mortality than with previous waves,” says University of NSW infectious diseases modeller Associate Professor James Wood. “My guesstimate is about 20-times lower fatality rate in this wave than in the NSW Delta wave. It’s pretty obvious just from the standard reporting curves for each country that mortality is generally well down.”

This clever South African study gives us a clearer picture of what’s really going on. Rather than looking only at hospital admissions, researchers tracked individuals from when they caught Omicron, and recorded if they ended up in hospital. The findings are encouraging: compared to Delta, people infected with Omicron had a 70 per cent lower chance of getting severely ill.

UK data, using a sample of more than 1 million cases, suggests the risk of going to hospital with an Omicron infection is about half that of Delta.

What about my vaccine - how well does that work?

Australia is at the forefront of answering these questions. A Kirby Institute team led by Miles Davenport and Deborah Cromer uploaded a preprint meta-analysis in mid-December, pulling together early studies of Omicron’s response to vaccines.

Here are the key numbers by vaccine (more-recent UK real-world vaccine effectiveness data comes to similar conclusions).

Effectiveness against symptomatic infection, six months after second dose:
AstraZeneca: 7.5 per cent
Pfizer: 28.1 per cent
Moderna: 40.4 per cent

Other variants, most notably Delta, have also reduced the effectiveness of vaccines against symptomatic infection, but protection against severe illness, the data point we really care about, has held up.

But according to the Kirby analysis, that is not the case with Omicron.

Effectiveness against severe infection, six months after second dose
AstraZeneca: 36.7 per cent
Pfizer: 70.9 per cent
Moderna: 81.1 per cent

These numbers represent a significant drop considering vaccines previously offered close to 100 per cent protection against severe disease.

The confidence intervals are very wide on these numbers, as there is less data available: for example, AstraZeneca ranges from 7 per cent to 73 per cent. The lower overall fatality rate of Omicron also messes with the data, so take it with a pinch of salt.

Even so, while vaccines may offer lower protection against severe illness with Omicron, it’s important to remember that the data so far suggests the variant causes less severe disease in the first place.

Nevertheless, as someone who has been double-dosed with AstraZeneca … those numbers are scary.

Personally, I had been mulling over declining a booster, as the evidence suggested it did not really offer additional protection against severe illness when coming up against Delta – and because we really should be sending more doses to the developing world. No longer. I’m booked in for my booster this week.

The Kirby Institute has good news on boosters, too:

MRNA booster, effectiveness against symptomatic infection
86.2 per cent

MRNA booster, effectiveness against severe infection
98.2 per cent

“We should all go get a booster straight away, if we are eligible. As you can see, boosting provides increased protection against disease in general,” says Dr Cromer.

“From a public health point of view, the stuff that is coming out is positive. But I’m a very cautious person. I still don’t feel like we’re out of the woods.”

https://www.smh.com.au/national/omicron ... 59p7r.html
i posted this in full because the SMH is getting harder to reach without a sub.
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Re: Omicron - a dive into the data

Post by violet »

Thank you!!!
Despite what angsta states, it’s clear from reading through his posts that angsta supports the free FreePalestine movement.
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Re: Omicron - a dive into the data

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More data on Omicron. This suggests it isn't just the flu.. Caveat: see my bolding.

Nevertheless, this might explain to some extent why some countries are reluctant to fully open despite high vax rates in the population.

Omicron 40 per cent deadlier than seasonal flu: Japanese study

Japan: The Omicron strain of COVID-19 is at least 40 per cent more lethal than seasonal flu, according Japanese scientists, underscoring the potential danger of lifting pandemic curbs too quickly and underestimating the virus’s ongoing health risks.

The case fatality rate of Omicron in Japan, based on cumulative excess deaths and the number of infections since January, was about 0.13 per cent, according to an analysis by scientists who advise the country’s health minister. While that is significantly lower than the 4.25 per cent case fatality rate from earlier in the outbreak, it’s still higher than the 0.006 per cent to 0.09 per cent seen with seasonal flu, they said.

Countries around the world have been relaxing mitigation measures, from mask mandates to testing requirements, and pushing for a return to normal life. The public has grown tired of restrictions and the reduced severity of Omicron has reassured many that the rules are no longer essential.

While Japan hasn’t formally downgraded the condition, it is easing border restrictions and quarantine periods for travellers, essential workers and close contacts of positive cases to keep the economy going.

The decline in mortality with Omicron could reflect both the reduced virulence of the strain, particularly in comparison to the Delta variant, and the benefits of vaccination, the researcher said. The findings show the importance of putting control measures in place before vaccines are fully distributed, they said.

More research is needed to determine the impact of the easing once all the restrictions are lifted, Takaji Wakita, chair of the health ministry’s advisory board, said at a briefing. The current information was obtained when most of the pandemic curbs were still in place, he said.

The study, which hasn’t been peer-reviewed or published in a medical journal, has several limitations, including differences in the way the data was collected that makes cross-comparisons difficult, Wakita said.


“Still, there’s a considerable difference in mortality,” though the arrival of Omicron has narrowed the gap between COVID and influenza, he said.

https://www.brisbanetimes.com.au/world/ ... 5a1km.html
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Re: Omicron - a dive into the data

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Omicron 40 per cent deadlier than seasonal flu


As seasonal flu kills very few people that weren't already at deaths door. I don't see that headline as 40% more deadly, but rather 40% more than f**k all, is still f**k all.

Sorry, but I just ain't buying this anymore. I just had Covid and it symptoms were virtually non-existent. An insult to any self-respecting cold virus.
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Re: Omicron - a dive into the data

Post by Jerry Atrick »

Doc67 wrote: Fri Mar 04, 2022 3:25 pm
Omicron 40 per cent deadlier than seasonal flu


As seasonal flu kills very few people that weren't already at deaths door. I don't see that headline as 40% more deadly, but rather 40% more than f**k all, is still f**k all.

Sorry, but I just ain't buying this anymore. I just had Covid and it symptoms were virtually non-existent. An insult to any self-respecting cold virus.
I think that it's possible that the flu is a co-morbidity in many deaths but doesn't get the full credit as the deceased were already fucked medically/going to die in any case

As opposed to the opposite phenomenon we saw with the covid, particularly in 2020, where it was blamed for almost all deaths in western countries regardless of the rather significant com-morbities present in most cases
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