Big jump in Covid cases in South Africa

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Brightonian
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Big jump in Covid cases in South Africa

Post by Brightonian » Wed Dec 01, 2021 6:38 pm

From https://twitter.com/BNODesk/status/1466 ... 87650?s=20. As they point out, there's a big increase in testing. However, positivity is also up, so should we be really worried now? (No indication whether it's Omicron or whatever.)
BNO News wrote:South Africa COVID update: Cases surge 571% from last week, testing up 47%

- New cases: 8,561
- Average: 3,797 (+1,041)
- Positivity rate: 16.5% (+6.3)
- In hospital: 2,550 (+136)
- In ICU: 235 (+1)
- New deaths: 28
- Average: 31 (+1)
Edit: this story suggests most of the new cases are indeed Omicron.

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Re: Big jump in Covid cases in South Africa

Post by bob sterman » Wed Dec 01, 2021 8:24 pm

Another 571% increase and they'll have the same number of new daily cases as the UK - which has a similar population size.

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Re: Big jump in Covid cases in South Africa

Post by shpalman » Wed Dec 01, 2021 9:16 pm

having that swing is a necessary but not sufficient condition for it meaning a thing
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Re: Big jump in Covid cases in South Africa

Post by Woodchopper » Wed Dec 01, 2021 9:34 pm

Yes, the trajectory is what matters at the moment.

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Re: Big jump in Covid cases in South Africa

Post by Woodchopper » Wed Dec 01, 2021 9:54 pm

The most important number to watch is hospital admissions. They aren't looking good.

Here's the latest pretty graph from John Burn Murdoch:
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FFjC4OnWYAoYoZp.jpg (407.97 KiB) Viewed 1588 times
Which is from here: https://twitter.com/jburnmurdoch/status ... 76939?s=20

People focus upon the low level of vaccination in South Africa. But I assume that a far higher proportion have antibodies as a result of having caught Covid in the past.

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Re: Big jump in Covid cases in South Africa

Post by jdc » Wed Dec 01, 2021 11:24 pm

Woodchopper wrote:
Wed Dec 01, 2021 9:54 pm

People focus upon the low level of vaccination in South Africa. But I assume that a far higher proportion have antibodies as a result of having caught Covid in the past.
Infection plus vaccination gives excellent immunity but infection alone doesn't have a great antibody response:
https://www.medrxiv.org/content/10.1101/2021.09.30.21264363v1 wrote:Here, we characterized the magnitude and specificity of SARS-CoV-2 spike-reactive antibodies from 10 acutely infected health care workers and 23 participants who received mRNA-based SARS-CoV-2 vaccines. We found that infection and primary mRNA vaccination elicited S1 and S2-reactive antibodies, while secondary vaccination boosted mostly S1 antibodies. Using magnetic bead-based absorption assays, we found that SARS-CoV-2 infections elicited a large proportion of original antigenic sin-like antibodies that bound efficiently to common seasonal human coronaviruses but poorly to SARS-CoV-2. In converse, vaccination only modestly boosted antibodies reactive to common seasonal human coronaviruses and these antibodies bound efficiently to SARS-CoV-2

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Re: Big jump in Covid cases in South Africa

Post by Woodchopper » Thu Dec 02, 2021 6:12 am

jdc wrote:
Wed Dec 01, 2021 11:24 pm
Woodchopper wrote:
Wed Dec 01, 2021 9:54 pm

People focus upon the low level of vaccination in South Africa. But I assume that a far higher proportion have antibodies as a result of having caught Covid in the past.
Infection plus vaccination gives excellent immunity but infection alone doesn't have a great antibody response:
https://www.medrxiv.org/content/10.1101/2021.09.30.21264363v1 wrote:Here, we characterized the magnitude and specificity of SARS-CoV-2 spike-reactive antibodies from 10 acutely infected health care workers and 23 participants who received mRNA-based SARS-CoV-2 vaccines. We found that infection and primary mRNA vaccination elicited S1 and S2-reactive antibodies, while secondary vaccination boosted mostly S1 antibodies. Using magnetic bead-based absorption assays, we found that SARS-CoV-2 infections elicited a large proportion of original antigenic sin-like antibodies that bound efficiently to common seasonal human coronaviruses but poorly to SARS-CoV-2. In converse, vaccination only modestly boosted antibodies reactive to common seasonal human coronaviruses and these antibodies bound efficiently to SARS-CoV-2

Interesting, that’s not what was found in this paper: viewtopic.php?t=747&start=6075

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Re: Big jump in Covid cases in South Africa

Post by jdc » Thu Dec 02, 2021 1:26 pm

Woodchopper wrote:
Thu Dec 02, 2021 6:12 am
jdc wrote:
Wed Dec 01, 2021 11:24 pm
Woodchopper wrote:
Wed Dec 01, 2021 9:54 pm

People focus upon the low level of vaccination in South Africa. But I assume that a far higher proportion have antibodies as a result of having caught Covid in the past.
Infection plus vaccination gives excellent immunity but infection alone doesn't have a great antibody response:
https://www.medrxiv.org/content/10.1101/2021.09.30.21264363v1 wrote:Here, we characterized the magnitude and specificity of SARS-CoV-2 spike-reactive antibodies from 10 acutely infected health care workers and 23 participants who received mRNA-based SARS-CoV-2 vaccines. We found that infection and primary mRNA vaccination elicited S1 and S2-reactive antibodies, while secondary vaccination boosted mostly S1 antibodies. Using magnetic bead-based absorption assays, we found that SARS-CoV-2 infections elicited a large proportion of original antigenic sin-like antibodies that bound efficiently to common seasonal human coronaviruses but poorly to SARS-CoV-2. In converse, vaccination only modestly boosted antibodies reactive to common seasonal human coronaviruses and these antibodies bound efficiently to SARS-CoV-2

Interesting, that’s not what was found in this paper: viewtopic.php?t=747&start=6075
I think you've linked to a thread rather than a post.

Was your paper looking at infection rather than measuring antibodies? That could point to an explanation for the apparent discrepancy (i.e. mine's only looking at antibodies while yours is looking at the whole immune system). Or there could be some other factor. Or one of our preprints could just be wrong.

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Re: Big jump in Covid cases in South Africa

Post by Woodchopper » Thu Dec 02, 2021 3:31 pm

jdc wrote:
Thu Dec 02, 2021 1:26 pm
Woodchopper wrote:
Thu Dec 02, 2021 6:12 am
jdc wrote:
Wed Dec 01, 2021 11:24 pm

Infection plus vaccination gives excellent immunity but infection alone doesn't have a great antibody response:

Interesting, that’s not what was found in this paper: viewtopic.php?t=747&start=6075
I think you've linked to a thread rather than a post.

Was your paper looking at infection rather than measuring antibodies? That could point to an explanation for the apparent discrepancy (i.e. mine's only looking at antibodies while yours is looking at the whole immune system). Or there could be some other factor. Or one of our preprints could just be wrong.
Sorry, here's a link to the paper: https://www.medrxiv.org/content/10.1101 ... 21262415v1

Its a comparison between outcomes of infection, symptoms and death between cohorts that have been vaccinated, had a prior infection and neither. It concludes that:
This study demonstrated that natural immunity confers longer lasting and stronger protection against infection, symptomatic disease and hospitalization caused by the Delta variant of SARS-CoV-2, compared to the BNT162b2 two-dose vaccine-induced immunity. Individuals who were both previously infected with SARS-CoV-2 and given a single dose of the vaccine gained additional protection against the Delta variant.
I think you're right that the above paper would cover much more than the presence of antibodies.

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Re: Big jump in Covid cases in South Africa

Post by jdc » Thu Dec 02, 2021 6:39 pm

Well, infection data > biomarkers in the medrx version of rock-paper-scissors so I'm going with Chops' paper.

Mine only measured antibodies to the spike protein so factors that might explain the apparent discrepancy would include broader immunity in the infected - e.g. T cells and antibodies to the nucleocapsid protein. That felt likeliest of the things that occurred to me.

Other possibles include things like vaccination schedule - if the paper I linked to had subjects vaccinated with a significantly longer gap than the 3 weeks in Israel (see the report of the Finzi paper in the booster thread viewtopic.php?p=105511#p105511).

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Re: Big jump in Covid cases in South Africa

Post by Woodchopper » Fri Dec 03, 2021 7:20 am

jdc wrote:
Thu Dec 02, 2021 6:39 pm
Well, infection data > biomarkers in the medrx version of rock-paper-scissors so I'm going with Chops' paper.

Mine only measured antibodies to the spike protein so factors that might explain the apparent discrepancy would include broader immunity in the infected - e.g. T cells and antibodies to the nucleocapsid protein. That felt likeliest of the things that occurred to me.
Yes, indeed, and also as far as I remember infection is better at inducing mucosal antibodies whose purpose is to block the virus in the upper reparatory tract.
jdc wrote:
Thu Dec 02, 2021 6:39 pm
Other possibles include things like vaccination schedule - if the paper I linked to had subjects vaccinated with a significantly longer gap than the 3 weeks in Israel (see the report of the Finzi paper in the booster thread viewtopic.php?p=105511#p105511).
I agree, there's still a lot of variables. More research is needed.

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Re: Big jump in Covid cases in South Africa

Post by Woodchopper » Mon Dec 06, 2021 10:50 pm


Some South Africa hospital wards are jammed with patients infected with the omicron coronavirus variant as President Cyril Ramaphosa urged South Africans on Monday to get vaccinated.

[…]

“Unfortunately, we’re seeing a more than doubling of hospital admissions each day,” said Ian Sanne, an infectious diseases specialist who serves on South Africa’s COVID-19 presidential advisory committee.

Sanne is advising hospitals to prepare for “significant surges” of patients in the coming weeks and months, and to make sure they have plenty of oxygen.

Dr. Fareed Abdullah, who heads the South African Medical Research Council, says the surges are already happening in Johannesburg and Tshwane.

Hospitals in South Africa’s Gauteng province, which contains two of the country’s biggest cities, are packed with people infected with the omicron variant. Doctors say most of the patients haven’t been vaccinated, and an alarming number of them are children under the age of five-years-old.

“There’s been a rather rapid rise in hospital admissions with patients who have COVID, whether they’re presenting with COVID pneumonia or severe COVID disease," Dr. Abdullah said.

"All of the hospitals in Tshwane are seeing an upsurge, and the COVID bed occupancy is increasing 30% to 40% per day, over the last few days,” he said.

[…]

“At this time, we think about 75% to 80% of hospitalizations are unvaccinated," he said. "It could be as large as 40% of the population that has not yet either been vaccinated or had a previous infection with coronavirus up until now,” he noted. “So, we have a large pool of people who can still present with overwhelming infection and severe disease,” he said.

Since detection of the variant was first announced in southern Africa last month, scientists have been hoping that most cases would be mild.

Health authorities say omicron is re-infecting some people who have been vaccinated, but mostly their symptoms are not severe.

One of the country’s top epidemiologists, Salim Abdool Karim, told VOA that current vaccines should provide “good protection” against omicron.
https://www.voanews.com/a/south-africa- ... 40912.html

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Re: Big jump in Covid cases in South Africa

Post by jdc » Tue Dec 07, 2021 3:29 pm

"It could be as large as 40% of the population that has not yet either been vaccinated or had a previous infection with coronavirus up until now,” he noted. “So, we have a large pool of people who can still present with overwhelming infection and severe disease,” he said.
Between this and the high HIV prevalence, things aren't looking great for SA right now.

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Re: Big jump in Covid cases in South Africa

Post by Woodchopper » Wed Dec 08, 2021 11:18 pm


South African excess deaths, a measure of mortality above a historical average, almost doubled in the week ending Nov. 28 from the preceding seven-day period as a new coronavirus variant spread across the country.

During the period 2,076 more people died than would normally be expected, the South African Medical Research Council said in a report on Wednesday. That compares with 1,091 the week earlier.

The rise, while only reflecting a week of data, contrasts with hospitalization numbers that show that most admissions have mild forms of the coronavirus, spurring hope that the omicron variant is more benign than earlier strains.

Excess deaths are seen as a more accurate measure of the impact of Covid-19 than official deaths. While South Africa’s official coronavirus death toll is just over 90,000 the number of excess deaths during the pandemic is 275,000. During the week to Nov. 28 just 174 deaths were officially attributed to the respiratory disease.
https://www.bloomberg.com/news/articles ... icron-wave

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