13 ms·

Tshwane District Omicron Variant Patient Profile – Early Features

82 points by pama 5y ago

rasengan 5y ago
> Though the NICD has confirmed that almost all cases of SARS-C0V-2 in Tshwane are due to the new variant, we have not been able to establish that in every instance the variant is Omicron as the PCR machine in use at the SBAH laboratory does not screen for the S-gene. A reasonable assumption is being made that the cases described here represent infection with the new variant. > The main observation that we have made over the last two weeks is that the majority of patients in the COVID wards have not been oxygen dependent. SARS-CoV-2 has been an incidental finding in patients that were admitted to the hospital for another medical, surgical or obstetric reason. Basically the facts that are being reported aren’t facts. Nothing new. This is how free speech ends.
- slimbods 5y ago
  Looks pretty factual. They've been quite clear that it's a 'reasonable assumption'
rubyist5eva 5y ago
It's a cold.
pezzana 5y ago
> Though the NICD has confirmed that almost all cases of SARS-C0V-2 in Tshwane are due to the new variant, we have not been able to establish that in every instance the variant is Omicron as the PCR machine in use at the SBAH laboratory does not screen for the S-gene. A reasonable assumption is being made that the cases described here represent infection with the new variant. Translation(?): It's omicron all right, but we didn't test for it because we don't have the equipment. Still, it's reasonable to assume we're dealing with omicron. This statement alone throws into question, at a minimum, the competence of the author and likely all of the report's data and conclusions.
- bhouston 5y ago
  I think that their reasoning is solid though. Omicron is the majority of SA cases now. It is early days and it is great to get any information like this out into the world, even if it is imperfect.
  - encryptluks2 5y ago
    Unless it favors unvaccinated people, then it should definitely be censored. Sarcasm but not.
- mmastrac 5y ago
  It's in your quote: "NICD has confirmed that almost all cases of SARS-C0V-2 in Tshwane are due to the new variant". They have confirmed almost all of them. That's a far cry from "we didn't test for it because we don't have the equipment".
- matthewdgreen 5y ago
  >This statement alone throws into question, at a minimum, the competence of the author and likely all of the report's data and conclusions. This is an emerging situation where all data may be useful. At present, the authors have access to some imperfect data due to circumstances beyond their control, and are clearly reporting the data -- complete with appropriate caveats about the limitations of their measurement equipment. This is exactly what competent practitioners should be doing, and to impugn their competence is completely inappropriate.
- shkkmo 5y ago
  The NICD has (presumably) been doing sample sequencing of local positive covid cases. This is how the NICD knows that almost all new covid cases in Tshwana are omicron. The SBAH lab is using PCR tests to confirm cases. Some PCR tests detect the "s gene", which omicron lacks. Thus a positive PCR test that lacks the s-gene is quite probably a case of omicron. The SBAH lab's PCR tests doesn't check for the "s gene" so can't be a direct indicator that the particular strain of covid is omicron. However, because the NICD sequencing has shown that almost all covid cases in the area are omicron, it is pretty safe to assume that almost all the cases at SBAH are omicron (as long as you trust NICD's data.) The responsible thing as a scientist is make such assumptions explicit, even when those assumptions are pretty safe. This statement should increase your confidence in the credibility of the scientist issuing it, not call it into question. Edit: If you don't think the assumption is safe, do you think it is less safe than relying on the lack of an "s gene" to indicate omicron without doing the sequencing? Both are assumptions whose reasonableness depend entirely on assumptions about the current local genetic pool of variations.
snowwrestler 5y ago
It’s a positive-sounding report but appropriately qualified with caveats that another ~2 weeks are needed to clarify whether the appearance of milder disease persists, or reflects a difference in how the disease progresses.
- mwint 5y ago
  Oh sweet, we get to Wait Two Weeks again!
  - ethanbond 5y ago
    Yes, the world is in flux.
    - deleted 5y ago
      [deleted]
  - encryptluks2 5y ago
    The best part about 2 weeks to flatten the curve is the first 2 years.
    - bavxo 5y ago
      “Day 500 of 15 days to flatten the curve. I remain perfectly still as a U.N. anal swab drone hovers overhead.”
    - ceejayoz 5y ago
      We did flatten the curve. Look at any graph of COVID cases, hospitalizations, and deaths, and this becomes readily apparent. Most places have let restrictions ebb and flow accordingly.
      - dude187 5y ago
        Nobody "flattened" anything. Places without restrictions had those exact ebbs and flows of "cases".
deleted 5y ago
[deleted]
jacob019 5y ago
It matches what we've been told all along, that the virus will become more transmissable and less lethal.
- sjg007 5y ago
  Your logic is faulty.
  - spurgu 5y ago
    No it's not. The more a virus spreads, the more it mutates. The more it mutates towards more transmissible and less lethal, the more it spreads. Thus it's a positive feedback loop. Of course it's not a given though (there could be a more dangerous and more transmissible mutation), but the logic is clear.
    - jhardy54 5y ago
      The global maxima is high transmission and high duration, not necessarily low morbidity. A virus that makes you contagious for two weeks and then kills you is just as transmissible as a virus that makes you contagious for two weeks and then you get better.
      - derbOac 5y ago
        ... assuming no reinfection and that the population of infected individuals is always small compared to a reservoir of susceptible individuals.
        tgv 5y ago
        And assuming no counter measures. The deadlier the virus, the more measures we take. So it's in the virus' interest to become relatively benign.
        spurgu 5y ago
legitster 5y ago
It's early, but there have still been no reported Omicron deaths. If this is that less lethal variant that we have all been waiting for, what's the call here? Should we be intentionally helping spread it to edge out Delta?
- phkahler 5y ago
  A non-lethal, highly contagious version of the virus is a sort of natural vaccine. I wouldn't try to spread it, but I could see people trying to catch it. I've had Covid (maybe twice) and that was quite enough for me.
  - newbamboo 5y ago
    Odd, I’ve had it 4 or 5 times maybe and only the first was like the real flu. But the long COVID is an annoyance. I did get the vaxxx do maybe that’s why the later rounds were so mild.
    - GGfpc 5y ago
      Did you get tests to confirm that all of those cases were covid?
    - bredren 5y ago
      Would you share the general lifestyle you’ve lived where you’ve been exposed and taken even mildly ill from covid four or five times? For example, unmasked attendance to large sporting events, etc?
      - hereforphone 5y ago
        Are masks supposed to protect you, or protect others from you?
        catlikesshrimp 5y ago
        All masks are for protecting others from your virus. Microfiber N95 is used for making masks that protect you IF is used properly ( real material, disposable, snug fit)
NoblePublius 5y ago
I think this says that mortality appears to be lower for Omicron, and that the need for oxygen treatment is lower in severe Omicron cases. Looking forward to Fauci not talking about this ever.
- encryptluks2 5y ago
  Just like he talks about how gain of function research wasn't really gain of function.
emerged 5y ago
Omicron is the coolest variant so far. But I’ve been holding off catching COVID until we get a variant with extra perks like increased vo2max or loss of pain sensitivity. I’m confident at global scale we will get there eventually.
- cbfrench 5y ago
  I’m holding out for the patch with liver restore and eyesight enhance.
- ChuckNorris89 5y ago
  >But I’ve been holding off catching COVID until we get a variant with extra perks Once the supply chains loosen up and they solve that spike protein shortage, Covid can finally open preorders for their Zeta Pro Max variant, provided enough people haven't ordered the vaccine instead until then.
prof-dr-ir 5y ago
I would caution against getting your hopes up. A milder variant might be nice, and on the longer term help resolve the pandemic. On the short term, however, increased infectiousness may easily outweigh this. It is not hard to see the number of hospitalizations and deaths increasing, simply because of the larger total number of cases. Humanity will then generally try to mitigate this by stricter measures, and altogether we might end up with a rather nasty winter... again.
- tasogare 5y ago
  It's been two years the media are saying "the hospital capabilities will be overflowed if this or that". It never happened. Each "wave" is small than the precedent and the disease is now somewhat known. The situation even seems fine enough in some countries that they fired a part of their health workers.
  - swiley 5y ago
    The admins have had two years to fix staffing/equipment shortages. If they're still struggling it's not the public that should suffer.
dsizzle 5y ago
> we have seen a sharp rise in [hospital] admissions > SARS-CoV-2 has been an incidental finding in patients that were admitted to the hospital for another medical, surgical or obstetric reason It seems either the rise in admissions is purely coincidental, or Omicron is causing atypical symptoms?
- Imnimo 5y ago
  I read it as "lots of people have Omnicron now whereas previously Delta had passed, so we're picking it up a lot on routine testing, even for asymptomatic peopel"
  - dsizzle 5y ago
    Yeah, except there is also an increase in hospital admission, so the question is what's causing that if it's not omicron?
    - Imnimo 5y ago
      Oh, to be clear, I'm not saying Omicron isn't causing the increase - it definitely is. I just meant that when Omicron is running wild, you'll also start finding it among the baseline admissions.
panabee 5y ago
if not all tests can identify omicron, how do we know where the epicenter is or even where omicrom is most concentrated right now?
- occamrazor 5y ago
  It appears that almost all rapid tests identify omicron quite well.
  - adrianN 5y ago
    Rapid tests don't distinguish between variants.
    - occamrazor 5y ago
      You’re right. What I mean is that rapid tests are positive for omicron-infected cases, just as for other variants. They don’t distinguish between omicron and other variants.
tomjuggler 5y ago
Well, here in South Africa we are feeling extremely hopeful and positive at the moment. The SA govt has so far refrained from imposing any further restrictions, despite the "massive rise in infections", unlike what they did in previous waves.

82 points by pama 5y ago

> Though the NICD has confirmed that almost all cases of SARS-C0V-2 in Tshwane are due to the new variant, we have not been able to establish that in every instance the variant is Omicron as the PCR machine in use at the SBAH laboratory does not screen for the S-gene. A reasonable assumption is being made that the cases described here represent infection with the new variant. > The main observation that we have made over the last two weeks is that the majority of patients in the COVID wards have not been oxygen dependent. SARS-CoV-2 has been an incidental finding in patients that were admitted to the hospital for another medical, surgical or obstetric reason. Basically the facts that are being reported aren’t facts. Nothing new. This is how free speech ends.

slimbods 5y ago
Looks pretty factual. They've been quite clear that it's a 'reasonable assumption'

rubyist5eva 5y ago

It's a cold.

pezzana 5y ago

> Though the NICD has confirmed that almost all cases of SARS-C0V-2 in Tshwane are due to the new variant, we have not been able to establish that in every instance the variant is Omicron as the PCR machine in use at the SBAH laboratory does not screen for the S-gene. A reasonable assumption is being made that the cases described here represent infection with the new variant. Translation(?): It's omicron all right, but we didn't test for it because we don't have the equipment. Still, it's reasonable to assume we're dealing with omicron. This statement alone throws into question, at a minimum, the competence of the author and likely all of the report's data and conclusions.

bhouston 5y ago
I think that their reasoning is solid though. Omicron is the majority of SA cases now. It is early days and it is great to get any information like this out into the world, even if it is imperfect.
- encryptluks2 5y ago
  Unless it favors unvaccinated people, then it should definitely be censored. Sarcasm but not.
mmastrac 5y ago
It's in your quote: "NICD has confirmed that almost all cases of SARS-C0V-2 in Tshwane are due to the new variant". They have confirmed almost all of them. That's a far cry from "we didn't test for it because we don't have the equipment".
matthewdgreen 5y ago
>This statement alone throws into question, at a minimum, the competence of the author and likely all of the report's data and conclusions. This is an emerging situation where all data may be useful. At present, the authors have access to some imperfect data due to circumstances beyond their control, and are clearly reporting the data -- complete with appropriate caveats about the limitations of their measurement equipment. This is exactly what competent practitioners should be doing, and to impugn their competence is completely inappropriate.
shkkmo 5y ago
The NICD has (presumably) been doing sample sequencing of local positive covid cases. This is how the NICD knows that almost all new covid cases in Tshwana are omicron. The SBAH lab is using PCR tests to confirm cases. Some PCR tests detect the "s gene", which omicron lacks. Thus a positive PCR test that lacks the s-gene is quite probably a case of omicron. The SBAH lab's PCR tests doesn't check for the "s gene" so can't be a direct indicator that the particular strain of covid is omicron. However, because the NICD sequencing has shown that almost all covid cases in the area are omicron, it is pretty safe to assume that almost all the cases at SBAH are omicron (as long as you trust NICD's data.) The responsible thing as a scientist is make such assumptions explicit, even when those assumptions are pretty safe. This statement should increase your confidence in the credibility of the scientist issuing it, not call it into question. Edit: If you don't think the assumption is safe, do you think it is less safe than relying on the lack of an "s gene" to indicate omicron without doing the sequencing? Both are assumptions whose reasonableness depend entirely on assumptions about the current local genetic pool of variations.

snowwrestler 5y ago

It’s a positive-sounding report but appropriately qualified with caveats that another ~2 weeks are needed to clarify whether the appearance of milder disease persists, or reflects a difference in how the disease progresses.

mwint 5y ago
Oh sweet, we get to Wait Two Weeks again!
- ethanbond 5y ago
  Yes, the world is in flux.
  - deleted 5y ago
    [deleted]
- encryptluks2 5y ago
  The best part about 2 weeks to flatten the curve is the first 2 years.
  - bavxo 5y ago
    “Day 500 of 15 days to flatten the curve. I remain perfectly still as a U.N. anal swab drone hovers overhead.”
  - ceejayoz 5y ago
    We did flatten the curve. Look at any graph of COVID cases, hospitalizations, and deaths, and this becomes readily apparent. Most places have let restrictions ebb and flow accordingly.
    - dude187 5y ago
      Nobody "flattened" anything. Places without restrictions had those exact ebbs and flows of "cases".

deleted 5y ago

[deleted]

jacob019 5y ago

It matches what we've been told all along, that the virus will become more transmissable and less lethal.

sjg007 5y ago
Your logic is faulty.
- spurgu 5y ago
  No it's not. The more a virus spreads, the more it mutates. The more it mutates towards more transmissible and less lethal, the more it spreads. Thus it's a positive feedback loop. Of course it's not a given though (there could be a more dangerous and more transmissible mutation), but the logic is clear.
  - jhardy54 5y ago
    The global maxima is high transmission and high duration, not necessarily low morbidity. A virus that makes you contagious for two weeks and then kills you is just as transmissible as a virus that makes you contagious for two weeks and then you get better.
    - derbOac 5y ago
      ... assuming no reinfection and that the population of infected individuals is always small compared to a reservoir of susceptible individuals.
      - tgv 5y ago
        And assuming no counter measures. The deadlier the virus, the more measures we take. So it's in the virus' interest to become relatively benign.
        spurgu 5y ago

legitster 5y ago

It's early, but there have still been no reported Omicron deaths. If this is that less lethal variant that we have all been waiting for, what's the call here? Should we be intentionally helping spread it to edge out Delta?

phkahler 5y ago
A non-lethal, highly contagious version of the virus is a sort of natural vaccine. I wouldn't try to spread it, but I could see people trying to catch it. I've had Covid (maybe twice) and that was quite enough for me.
- newbamboo 5y ago
  Odd, I’ve had it 4 or 5 times maybe and only the first was like the real flu. But the long COVID is an annoyance. I did get the vaxxx do maybe that’s why the later rounds were so mild.
  - GGfpc 5y ago
    Did you get tests to confirm that all of those cases were covid?
  - bredren 5y ago
    Would you share the general lifestyle you’ve lived where you’ve been exposed and taken even mildly ill from covid four or five times? For example, unmasked attendance to large sporting events, etc?
    - hereforphone 5y ago
      Are masks supposed to protect you, or protect others from you?
      - catlikesshrimp 5y ago
        All masks are for protecting others from your virus. Microfiber N95 is used for making masks that protect you IF is used properly ( real material, disposable, snug fit)

NoblePublius 5y ago

I think this says that mortality appears to be lower for Omicron, and that the need for oxygen treatment is lower in severe Omicron cases. Looking forward to Fauci not talking about this ever.

encryptluks2 5y ago
Just like he talks about how gain of function research wasn't really gain of function.

emerged 5y ago

Omicron is the coolest variant so far. But I’ve been holding off catching COVID until we get a variant with extra perks like increased vo2max or loss of pain sensitivity. I’m confident at global scale we will get there eventually.

cbfrench 5y ago
I’m holding out for the patch with liver restore and eyesight enhance.
ChuckNorris89 5y ago
>But I’ve been holding off catching COVID until we get a variant with extra perks Once the supply chains loosen up and they solve that spike protein shortage, Covid can finally open preorders for their Zeta Pro Max variant, provided enough people haven't ordered the vaccine instead until then.

prof-dr-ir 5y ago

I would caution against getting your hopes up. A milder variant might be nice, and on the longer term help resolve the pandemic. On the short term, however, increased infectiousness may easily outweigh this. It is not hard to see the number of hospitalizations and deaths increasing, simply because of the larger total number of cases. Humanity will then generally try to mitigate this by stricter measures, and altogether we might end up with a rather nasty winter... again.

tasogare 5y ago
It's been two years the media are saying "the hospital capabilities will be overflowed if this or that". It never happened. Each "wave" is small than the precedent and the disease is now somewhat known. The situation even seems fine enough in some countries that they fired a part of their health workers.
- swiley 5y ago
  The admins have had two years to fix staffing/equipment shortages. If they're still struggling it's not the public that should suffer.

dsizzle 5y ago

> we have seen a sharp rise in [hospital] admissions > SARS-CoV-2 has been an incidental finding in patients that were admitted to the hospital for another medical, surgical or obstetric reason It seems either the rise in admissions is purely coincidental, or Omicron is causing atypical symptoms?

Imnimo 5y ago
I read it as "lots of people have Omnicron now whereas previously Delta had passed, so we're picking it up a lot on routine testing, even for asymptomatic peopel"
- dsizzle 5y ago
  Yeah, except there is also an increase in hospital admission, so the question is what's causing that if it's not omicron?
  - Imnimo 5y ago
    Oh, to be clear, I'm not saying Omicron isn't causing the increase - it definitely is. I just meant that when Omicron is running wild, you'll also start finding it among the baseline admissions.

panabee 5y ago

if not all tests can identify omicron, how do we know where the epicenter is or even where omicrom is most concentrated right now?

occamrazor 5y ago
It appears that almost all rapid tests identify omicron quite well.
- adrianN 5y ago
  Rapid tests don't distinguish between variants.
  - occamrazor 5y ago
    You’re right. What I mean is that rapid tests are positive for omicron-infected cases, just as for other variants. They don’t distinguish between omicron and other variants.

tomjuggler 5y ago

Well, here in South Africa we are feeling extremely hopeful and positive at the moment. The SA govt has so far refrained from imposing any further restrictions, despite the "massive rise in infections", unlike what they did in previous waves.