South African Doctor Angelique Coetze

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Stranger Mouse
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South African Doctor Angelique Coetze

Post by Stranger Mouse » Sun Dec 12, 2021 12:26 pm

My alarm bells are ringing. She is so absolutely certain that Omicron will be mild in all cases (including 80 year olds etc) that it sounds like confirmation bias to me. If she said “probably mild” I wouldn’t feel this way. Or maybe it’s my own confirmation bias. Thoughts ?

https://twitter.com/lbc/status/1469998211863621636?s=21
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Re: South African Doctor Angelique Coetze

Post by sTeamTraen » Sun Dec 12, 2021 7:08 pm

Stranger Mouse wrote:
Sun Dec 12, 2021 12:26 pm
My alarm bells are ringing. She is so absolutely certain that Omicron will be mild in all cases (including 80 year olds etc) that it sounds like confirmation bias to me. If she said “probably mild” I wouldn’t feel this way. Or maybe it’s my own confirmation bias. Thoughts ?

https://twitter.com/lbc/status/1469998211863621636?s=21
At one point she says "Yes, you will get people that will get sick, but it will be the minority". But across all the age groups that's probably already the case. What we need are estimates of, for example, the % of people whose O2sat will drop below 93% for Omicron versus Delta. So I find her claims rather unconvincing. If she turns out to be an epidemiologist who is just trying to simplify the story for the media then perhaps fair enough, but if she is just a random medical doctor with the minimal understanding of effect sizes, etc, that typifies that profession, then I'm not going to set too much store by what she's saying.
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Re: South African Doctor Angelique Coetze

Post by Stranger Mouse » Sun Dec 12, 2021 7:18 pm

sTeamTraen wrote:
Sun Dec 12, 2021 7:08 pm
Stranger Mouse wrote:
Sun Dec 12, 2021 12:26 pm
My alarm bells are ringing. She is so absolutely certain that Omicron will be mild in all cases (including 80 year olds etc) that it sounds like confirmation bias to me. If she said “probably mild” I wouldn’t feel this way. Or maybe it’s my own confirmation bias. Thoughts ?

https://twitter.com/lbc/status/1469998211863621636?s=21
At one point she says "Yes, you will get people that will get sick, but it will be the minority". But across all the age groups that's probably already the case. What we need are estimates of, for example, the % of people whose O2sat will drop below 93% for Omicron versus Delta. So I find her claims rather unconvincing. If she turns out to be an epidemiologist who is just trying to simplify the story for the media then perhaps fair enough, but if she is just a random medical doctor with the minimal understanding of effect sizes, etc, that typifies that profession, then I'm not going to set too much store by what she's saying.
She isn’t an epidemiologist- in the interview I listened to (not sure if it is all in the clip above) she says she is is not a scientist. She makes a big deal of the patients being treated in the front line but as far as I can tell from this article she is referring to a couple of dozen people. She’s head of the South African Medical Association but I’m not sure how prominent they are.

https://www.telegraph.co.uk/global-heal ... -symptoms/

She’s getting a lot of publicity for this but my b.llsh.t alarm is going apeshit.

Although I would love her to be right
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Re: South African Doctor Angelique Coetze

Post by Millennie Al » Mon Dec 13, 2021 2:33 am

One of the things that this pandemic has shown is the extent to which people completely fail to understand exponential growth.

Suppose we have two variants. One spreads twice as fast (i.e. new cases double in time T) as the other (i.e. new cases double in time 2T). Suppose the fast variant is 1% as serious as the slow one, meaning that only 1% of cases result in hospital admissions. The power of exponential growth means that the fast variant will cause more admissions than the slow and that will happen fairly quickly. Here is a graph showing this effect:
lin.png
lin.png (5.82 KiB) Viewed 1206 times
After only 7 doublings the fast but mild variant has already exceeded the number of hospitalisations of the slow and severe variant.


Or, switching to a log scale:
log.png
log.png (6.58 KiB) Viewed 1206 times
In the real world things are much worse because the slow variant has almost been brought to a standstill, so we'll see the exponential growth only for the fast variant. Due to the lag between cases and admissions, and the large fixed number of cases from slow variants, it will take some time before we can see the effects of the fast variant (i.e. Omicron) and by the time we see any effects, it will be too late to stop it - just as was the case at the beginning of the pandemic where the government did nothing useful while watching cases start to grow exponentially.

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Re: South African Doctor Angelique Coetze

Post by Woodchopper » Mon Dec 13, 2021 8:08 am

There are a few red flags.

Coetzee is head of the board of the South Africa Medical Association: https://www.samedical.org/about-us/board

But it’s a professional association or trade union rather than a scientific body. Prior to November 2021 she was mentioned in South African media reports in that role rather than as a scientific authority.

Coetzee is often described in UK media as being the doctor who discovered Omicron. But this detailed South African newspaper about the discovery doesn’t mention her. Instead it describes the discovery as follows (I’m quoting a lot as it’s interesting).

One afternoon in early November, junior scientist Alicia Vermeulen, who works at a Lancet Laboratories facility in Pretoria, glanced at data from a batch of coronavirus tests and noticed something strange.

She was not aware at the time that her observation would set in motion a chain of events that would eventually lead to the discovery that the Omicron coronavirus variant was present and circulating in South Africa, news of which has led to global fears and travel bans targeted at southern African countries.

The existence of the B1.1.529 variant - named Omicron on Friday - was first officially confirmed by South African scientist Professor Tulio de Oliveira on 25 November, however, the first samples were sequenced by the Botswana-Harvard AIDS Institute Partnership in Botswana, and in Hong Kong as early as 11 and 13 November.

[…]

on the afternoon of 4 November, Vermeulen had spotted an anomaly in one positive test result in the roughly 300 tests the lab had processed that day. It was something she had seen before earlier this year.

The test had not picked up a specific gene that is looked for to confirm whether the SARS-Cov-2 virus is present in a sample, the S-gene - which creates the spike protein.

[…]

Only one specific type of PCR assay reacts this way - the ThermoFisher TaqPath assay - which is not used widely by all laboratories.

Vermeulen, who holds a master's degree in medical virology, said it made her instantly curious.

"It piqued my curiosity. We wanted know what was causing the S-gene fallout, because early on we had seen something similar happen with the Alpha variant," Vermeulen told News24 on Sunday.

After noticing the anomaly, she notified the head of the lab and her manager. The next day, she found another one. The following week, she said, there were more. And the number of positives with this S- gene fallout grew rapidly, she explained.

During the peaks of coronavirus waves, Vermeulen could be found inside the lab, processing "batch after batch" of samples, once up to 3 000 a day.

During lulls, such as South Africa has found itself in over the past month or more, she is roped in to analyse test results and disseminate them for wider reporting - as she had been doing that day.

Vermeulen said:

At first we thought it might be Alpha again, but we decided to keep an eye on it, because if it was something else, we needed to know, so we could raise the alarm.

Alpha, a variant of concern first discovered in the UK in November 2020, caused a similar S-gene fallout, but fizzled out quickly in samples processed at the Pretoria lab.

"Then we started seeing more positive results with the same S-gene fallout the next week. By Thursday [11 November] between the HOD, the manager and myself, we decided to email Dr Glass, to ask if she was seeing the same thing anywhere else."

Dr Allison Glass, who serves on the Ministerial Advisory Committee on Covid-19, is a clinical virologist and the head of molecular pathology for Lancet Laboratories.

She receives a few hundred emails daily, but noticed the email from Vermeulen and her team and sprang into action.

[…]

Glass reviewed the results from the Lancet Laboratories in Johannesburg and arranged for positive samples to be transported from the Pretoria lab.

She also alerted Professor Anne von Gottberg, who is a principal pathologist at the National Institute for Communicable Diseases (NICD). News24 understands the NICD also then started looking at data from National Health Laboratory Service testing, some of which use the same type of PCR test that first picked up the missing S-gene.

"We had seen that [S-gene fallout] with Alpha, but with Delta which replaced everything, we hadn't seen it for a few months. She [Vermeulen] said to me that we are seeing a lot of it and I was like, 'oh it's only one or two positives in a batch, so you know, is that a lot'?" Glass said.

She explained:

So, I sort of looked at it and we gave it a day or two to see because at that stage there weren't a lot of positives, but we were seeing a slight increase. We gave it the weekend, and then reviewed the data at our Johannesburg lab, and realised it was a trend we were seeing and that more and more of the positives were coming up like that, and we were seeing a rise in the positivity rate.

Glass said they asked the Pretoria lab to send their positive samples to Johannesburg, and because there were so few positive samples, it took a few days to build up enough samples to send a "decent sized" batch to the NICD.

"We did send those off to the NICD, but we have a sequencing machine at our lab which is much faster, it can sequence the samples in a day where other machines take two days or so. So, I said to my senior scientist, please take a few samples and sequence them."

Dr Raquel Viana, who holds a PhD in molecular pathology, was asked by Glass to run the sequencing.

By the evening of Friday, 19 November, Viana had confirmed from an initial check of the data, that something had changed. Over that weekend, Viana and scientists from the NICD undertook more extensive analysis.

On Monday, 22 November, Viana sequenced more samples. By the next day, the NICD uploaded the data and confirmed the news.

There was a new variant of SARS-Cov-2.

The findings were shared with the NICD and the scientists who form part of the Network for Genomic Sequencing South Africa (NGS-SA), which encompasses De Oliveira's KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP).

The NGS-SA is a series of laboratories around the country that look at positive test samples regularly to detect these variants.

Glass said the ability of Lancet Laboratories to communicate their observations quickly and with confidence to the NICD and these scientists was a sign that collaboration and a good working relationship, which is important to the company, had prevailed.

"From the start of Covid-19 it has been very important for us to have a good relationship with the NICD and we have a very professionally courteous relationship, and we talk to each other to make sure we are all on the same page."
https://www.news24.com/news24/southafri ... l-20211128

Finally, Coetzee is quoted a lot in the UK and US media about Omicron, but very little in South Africa or elsewhere in articles about the variant.

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Re: South African Doctor Angelique Coetze

Post by shpalman » Tue Dec 14, 2021 10:38 am

She's telling MPs that Omicron has not led to intensive care units being 'overwhelmed' in South Africa
She said Omicron was at least as transmissible as the Delta variant.

She said it generally produced a mild disease.

It was different for people in hospital, she said. Most people in hospital were unvaccinated, she said. She told the MPs that they did not do genomic sequencing for most patients, so the hospital statistics did not differentiate between Delta patients and Omicron patients. But she said intensive care units were “not overwhelmed” with Covid cases.
The Daily Mail has her reckoning that the UK government is over-reacting, if that's the sort of thing which tells you anything.
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