> 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.
> 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.
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.
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".
>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.
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.
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.
Sweden is a good example, as are state based comparisons across the US. Especially when you look at timing of things like mask mandates in a certain area, where the case trajectory before and after mask mandates in one area looks no different. Especially when compared against differently timed mask mandates in other areas that tracked a near exact case curve.
I've certainly heard those accusations, but it doesn't really stand up on its own. The supply chain disruptions of the restrictions around it will impact it all the same, even among of a population that wasn't forced into lockdowns and other shutdowns.
Also, I want to clearly and strongly reject non-law enforced "change in behavior" as being any defense of government removals of freedom. It does not defend such attacks in ANY way whatsoever.
While in my other reply I express my doubt at "change in behavior" being the driver of any sort of economic impact similarities, say it was. In that case, what it would show is that overbearing government removals of freedoms to the extent that you can't even go out in public are not even needed to have that effect in behavior.
I live in Japan, there was no lockdown and the disease didn't get worst than any other countries that took very harsh measures. Given how restrictive those measures are in comparison to the epsilon effect they have, it's clear it's better to respect people rights instead of crushing them under some heavy-handed wishful thinking.
They let something like 80,000 foreigners into the country for the Olympics. I'd say if there is an anti-lockdown that would be it. The virus surged during this period, and one of the hypothesis floating out there was that the voluntary lockdown suggestions were ignored due to the government holding the Olympics. The case numbers went down when they instituted the state of emergency again.
But that being said I'm not sure we fully understand why the virus didn't hit Japan as hard. The country does have a stronger mask wearing culture (where people actually fully cover their faces) and a homogenous genetic makeup.
To me, lockdown means you tell people they can’t do certain things or they have to do certain things a certain way. And that’s what happened during the Olympics.
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.
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.
Yes, but the public response will be completely different. We're not looking at a virus in a petri dish here, but one that circulates in a human society. That's what tends to lead the virus towards a less lethal evolution.
Another logical fallacy here.
If the society lets the virus spread more once it has become less lethal it has absolutely no effect on the lethality of the virus because the evolution happens in the past.
In the causal world in which we live future actions have absolutely no impact on the present.
> In the causal world in which we live future actions have absolutely no impact on the present.
Of course it doesn't have any impact on the present. Neither did the old apes have any advantage over other animals just because they were gonna evolve into humans in the future. Some of them did however evolve into humans, due to events in the future (none of which were necessarily clear where they happened).
Your argument doesn't make any sense.
We define the success of the virus. We could nuke all humans on the planet right now and get rid of Covid. Or we could impose strict military lockdown measures forever and get rid of Covid. We don't because of the low perceived threat. The virus mutates by itself (call it "in the past" if you will) but human psychology is the main driver of the success of the virus.
Why do you think the virus would all mutate at the same time everywhere? If we let a variant spread, and it mutates in someone there's no system update that will suddenly make the mutation appear in everyone else. It's not a Trojan horse. In reality it would probably just mean that everyone with the earlier less dangerous variant is probably immune or somewhat immune to the new variant if it ever "hops in the opposite direction".
No that logic is completely wrong because covid-19, and especially Delta, transmits during the asymptomatic phase, so logically there is no inherent advantage in becoming less lethal if the lethality is independent from the transmission.
Whoever is asserting that covid-19 WILL become less lethal is simply spreading misinformation.
Plus, if we're still arguing the logic, how exactly does symptomatic/asymptomatic make any kind of difference here? You fail to explain how I'm "completely wrong". Asymptomatic spread is what's made Covid overall so transmissible in the first place, it's not a feature particular to Delta.
The recipe for a successful virus is one that spreads easily. Viruses don't have any particular drive to kill (or even hurt) hosts. The less it hurts us the less we give a shit and the more we allow it to spread.
Just look at Covid now. If it didn't kill people we would never have put up any measures and everyone would've had it many times over already.
But from there if it were to mutate into a variant that starts hurting people, we would start putting measures in place to stop it. Evolution-wise that variant wouldn't do as well as the first one.
It's true that over time the best reproduction strategy for a virus is to becoming incredibly transmissible but invisible to hosts, but the virus evolves via random walk and the local maximum could be more transmissible but lethal after a long delay.
There's no guarantees with randomness, though on a decade-long scale we can probably be sure it will fade into the background.
The evolution might be random, but the environment it evolves in and human behavior in response to it is not random. It was my understanding that the latter function is why we expect the course to result in a more transmissible but less lethal virus.
The more lethal it is, the fewer opportunities it would have to spread.
It is lethal to humans, but not to the animals that typically carry it. Ebola didn't evolve in humans to become highly lethal, it evolved to cross species.
HIV in and of itself does not kill you. It destroys your immune system in a lengthy process that ultimately leads to opportunistic infections that kill you. This process can take several months to several years. Likewise, HIV crossed species to infect humans, it did not evolve it's capabilities directly in humans.
Now that you mention, SarsCovid2 might have originated in either a pangolin, a bat or a bioweapons laboratory, according to early media reports. I can't believe that I am being serious, but it is what it is.
Less lethal or more slowly lethal? HIV is no less lethal now than it was decades ago. It spreads without issues because it kills the host a few years after infection instead of immediately. But HIV is as much of a death sentence today for people who do not seek or do no have access to treatments as it was 30 years ago.
HIV is transmitted pretty slowly - it may take many years to be passed on from one person to the next. Therefore any decrease in lethality might take hundreds of years to happen.
Widespread use of treatments would probably also stop the selection of less lethal strains.
There is no selection pressure for Covid to become less lethal. None whatever.
Furthermore, no human virus has ever evolved to become less lethal.
Unfortunately this myth is often used by those who would like us to let Covid keep on killing, in order to protect their cashflows and for ideological and political reasons.
> There is no selection pressure for Covid to become less lethal.
Isn't there though? Say Covid killed within seconds. Then it couldn't spread. The longer the host lives, the more other people it can infect. I would almost say that the opposite of what you wrote is true.
Length of time until death doesn’t mean a virus is less lethal.
Rabies effectively has a 100% death rate and it can take years for it to kick in. There are cases of people suddenly showing symptoms 5 years after initial exposure, and once that happens, your brain basically rapidly rots and you drop dead.
We have no clue what the long term effects of any covid variants are. We can only speculate.
It’s exactly the opposite of what you are saying.
There is pressure for the virus to NOT become more lethal in less time.
It’s the opposite of saying that there is pressure for the virus to become less lethal in more time.
Yersinia Pestis is a bacterium, not a virus, and it can be killed by antibiotics. It's not gone. It's still around in fleas that live on squirrels and rats. In the mountains near where I live, the squirrels have it, and people get it every couple years.
This is incorrect - there is obvious selection pressure for lower lethality. But it's also absurd and inappropriately politicizing a scientific question to assert that only "those" with a malevolent agenda believe that the virus will ultimately become less dangerous.
It's believed that each one of the other coronaviruses which are now endemic "common colds" began as a more lethal pandemic, the last probably being in 1890.
ACE2 receptors are all over the respiratory tract and the lining of blood vessels[1]
Yes, Covid is primarily dangerous when it manages to get deep in the lungs and cause pneumonia. It takes a week or two of being sick before it gets there. That's why you heard early in the pandemic how people were fine, until about day 7 or day 10 and then suddenly went to the hospital. Other coronaviruses can do the same thing. If you ever get a cold for 10 days, your immune system is probably pretty bad and you very well might get pneumonia. But you don't usually get pneumonia from the cold coronaviruses, because your body knows how to fight them off. When the 1890 coronavirus hit, no one had immunity and it was pretty deadly. But we have good immunity to that virus now (so we call it a common cold). As long as you can ramp up an immune response and kill it off before it gets a foothold deep in your lungs.
This is a myth, or a misunderstanding. SARS-CoV-2 does most of its transmitting before serious symptoms develop. The severity of those symptoms has no bearing on the fitness of the virus. We should not expect SARS-CoV-2 to evolve to be less lethal.
There are other pathogens which we would indeed expect to evolve to become less lethal. On the other hand, there are some which evolve to be more lethal, like Dengue.
I wonder if a viable strategy for a future pandemic outbreak might be to deliberately encourage less lethal mutations to survive by, for example, having lockdowns that apply to contacts, friends and relatives of someone who died only?
On the other hand, we will be fighting less lethal variants much less. Less lockdowns and other hard measures, vaccines will be targeted at the more deadly variants obviously. That will play a role too in the long run. But it could take longer as it's not a direct effect.
No, you can’t say that it will, it’s completely false.
There is no advantage for a virus that has the maximum transmission level in the asymptomatic phase to become less lethal.
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?
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.
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.
As I understand it as well. Catching the virus is more likely from touching surfaces coated with the virus then touching one's face, or something similar.
Interesting (though not surprising) that my question above has been downvoted. This is a touchy topic where political alignment sometimes supersedes even the will to reason.
Apparently there was even a small protective effect from children in the household, though this went away after schools reopened. One of the hypotheses in this paper is cross-immunity with other circulating coronaviruses:
Based on this, I will continue my practice of licking subway handrails instead of religiously “sanitizing” everything like the person preparing to sit next to me just did.
Your immunity is not effective enough (sorry, blame you, your ancestors or your vaccine manufacturer ) or you were infected by a variant with enough differences in its antigens that it counts as a different virus.
If this is true, you are a bit of a “miracle of nature”. Catching it twice is highly unlikely. You’ve had it so many times you can’t remember if it was 4 or 5.
Doubling every 1.2 days, but “Only a single patient on oxygen was fully vaccinated but the reason for the oxygen was Chronic Obstructive Pulmonary Disease”.
Immunity or evasion thereof is never 100%. Natural immunity from prior infection with another variant is certain to provide at least some protection against Omicron but it may be limited.
Hopefully. Those with prior immunity to other coronaviruses actually did worse. The superantigen in SARS-Cov-2 activates the T cells for those viruses. They don’t protect and instead attack the body.
Not without solid evidence that they're actually in competition, to say the least. If it turns out you can easily get both, then spreading the less lethal variant does nothing good.
Need hard data that it's actually less lethal, which means waiting a month or so from the uptick in cases to make sure no hospitalizations or death actually occur. If it is, spread away. If it's not, and has similar mortality to the original strain but with immune escape and better transmissibility, you've screwed us all.
We still don't know how long a person who has recovered from COVID-19 experiences cognitive impairment. If it's never, catching it is not a sacrifice I'd ever want to make. If it's of a reasonable duration after which you return to baseline and it's not lethal, fine.
The loss of taste/smell and risk of cognitive symptoms are really the things that worry me personally about covid. Like many on this site, I’m vaccinated and fairly young, but a world with messed up smells and taste or not being able to do the things I find fulfilling are pretty scary prospects, and there’s very little data that I’ve seen about incidence rates.
Please give me the winning numbers for Euromillions since apparently you can see the future and you absolutely know that everyone is going to get covid.
From the report: “ The best indicator of disease severity is measured by the in-hospital death rate. There were 10 deaths in the SBAH/TDH cohort in the past two weeks, making up 6.6% of the 166 admissions. Four deaths were in adults aged 26 – 36 and five (5) deaths were in adults over 60. One death was in a child in whom the cause of deaths was unrelated to COVID.”
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.
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.
>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.
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.
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.
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"
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.
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.
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.
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[ 2.7 ms ] story [ 56.9 ms ] thread> 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.
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.
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.
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.
Most places have let restrictions ebb and flow accordingly.
While in my other reply I express my doubt at "change in behavior" being the driver of any sort of economic impact similarities, say it was. In that case, what it would show is that overbearing government removals of freedoms to the extent that you can't even go out in public are not even needed to have that effect in behavior.
But that being said I'm not sure we fully understand why the virus didn't hit Japan as hard. The country does have a stronger mask wearing culture (where people actually fully cover their faces) and a homogenous genetic makeup.
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.
I don't speak viruscode
Maybe those of us who the virus kill the fastest die, the rest develops immunity and transmission stops?
All hypothesis
Of course it doesn't have any impact on the present. Neither did the old apes have any advantage over other animals just because they were gonna evolve into humans in the future. Some of them did however evolve into humans, due to events in the future (none of which were necessarily clear where they happened).
Your argument doesn't make any sense.
We define the success of the virus. We could nuke all humans on the planet right now and get rid of Covid. Or we could impose strict military lockdown measures forever and get rid of Covid. We don't because of the low perceived threat. The virus mutates by itself (call it "in the past" if you will) but human psychology is the main driver of the success of the virus.
I keep feeling like what we've had so far is just a preview, and there's going to be some new variant that has a younger target demographic.
> Of course it's not a given though
Plus, if we're still arguing the logic, how exactly does symptomatic/asymptomatic make any kind of difference here? You fail to explain how I'm "completely wrong". Asymptomatic spread is what's made Covid overall so transmissible in the first place, it's not a feature particular to Delta.
The recipe for a successful virus is one that spreads easily. Viruses don't have any particular drive to kill (or even hurt) hosts. The less it hurts us the less we give a shit and the more we allow it to spread.
Just look at Covid now. If it didn't kill people we would never have put up any measures and everyone would've had it many times over already.
But from there if it were to mutate into a variant that starts hurting people, we would start putting measures in place to stop it. Evolution-wise that variant wouldn't do as well as the first one.
There's no guarantees with randomness, though on a decade-long scale we can probably be sure it will fade into the background.
The more lethal it is, the fewer opportunities it would have to spread.
HIV in and of itself does not kill you. It destroys your immune system in a lengthy process that ultimately leads to opportunistic infections that kill you. This process can take several months to several years. Likewise, HIV crossed species to infect humans, it did not evolve it's capabilities directly in humans.
This is also what a couple of heretics have been telling us, but was suppressed in mainstream.
Alpha was just as deadly but more transmissible. While Delta was both more transmissible and more deadly for example.
Widespread use of treatments would probably also stop the selection of less lethal strains.
There is no selection pressure for Covid to become less lethal. None whatever.
Furthermore, no human virus has ever evolved to become less lethal.
Unfortunately this myth is often used by those who would like us to let Covid keep on killing, in order to protect their cashflows and for ideological and political reasons.
Isn't there though? Say Covid killed within seconds. Then it couldn't spread. The longer the host lives, the more other people it can infect. I would almost say that the opposite of what you wrote is true.
Rabies effectively has a 100% death rate and it can take years for it to kick in. There are cases of people suddenly showing symptoms 5 years after initial exposure, and once that happens, your brain basically rapidly rots and you drop dead.
We have no clue what the long term effects of any covid variants are. We can only speculate.
Wikipedia theories are as reliable as usual. (Not reliable)
But that may or may not be what caused the black death in medieval Europe, in my view. There's reason to think it might have been a really nasty hemorhagic virus like Ebola. See: https://history.howstuffworks.com/historical-events/black-de...
There had been several pandemics of black plague, but at some point it didn't come back. Why?
Maybe there was a bacteriophague virus which caused Yersinia Pestis to be lethal? (Hypothesis) But why would it be gone?
https://pubmed.ncbi.nlm.nih.gov/27281573/
It's believed that each one of the other coronaviruses which are now endemic "common colds" began as a more lethal pandemic, the last probably being in 1890.
https://www.theguardian.com/world/2020/may/31/did-a-coronavi...
Yes, Covid is primarily dangerous when it manages to get deep in the lungs and cause pneumonia. It takes a week or two of being sick before it gets there. That's why you heard early in the pandemic how people were fine, until about day 7 or day 10 and then suddenly went to the hospital. Other coronaviruses can do the same thing. If you ever get a cold for 10 days, your immune system is probably pretty bad and you very well might get pneumonia. But you don't usually get pneumonia from the cold coronaviruses, because your body knows how to fight them off. When the 1890 coronavirus hit, no one had immunity and it was pretty deadly. But we have good immunity to that virus now (so we call it a common cold). As long as you can ramp up an immune response and kill it off before it gets a foothold deep in your lungs.
[1] https://www.asbmb.org/asbmb-today/science/051620/what-is-the...
https://twitter.com/BallouxFrancois/status/12768029785826795...
There are other pathogens which we would indeed expect to evolve to become less lethal. On the other hand, there are some which evolve to be more lethal, like Dengue.
(Noting that we don’t know what happened to the Spanish flu)
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?
For example, unmasked attendance to large sporting events, etc?
Microfiber N95 is used for making masks that protect you IF is used properly ( real material, disposable, snug fit)
Interesting (though not surprising) that my question above has been downvoted. This is a touchy topic where political alignment sometimes supersedes even the will to reason.
No. Fomite transmission is extremely unlikely.
https://adc.bmj.com/content/archdischild/early/2021/03/17/ar...
Based on this, I will continue my practice of licking subway handrails instead of religiously “sanitizing” everything like the person preparing to sit next to me just did.
Genuinely curious.
What exactly do you mean by that? Were you left with some permanent symptoms?
https://www.medpagetoday.com/opinion/vinay-prasad/94646
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.
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.
> 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?