SARS CoV-2 coronavirus / Covid-19 (No tin foil hat silliness please)

[Shakesy]

It did we just didn't know as much at first. The European variant that caused most of the first wave has only small differences to the Wuhan original, but it was different. Alpha and beta emerged in the following 6 months.

Do you think it's strange that two of the four biggest mutations originated in SA? Or is it just bad luck?

 

[Withnail]

Well he didn’t have to mention symptoms if he just wanted to worry people.

Maybe he didn't do it on purpose and you're right he didn't have to put the caveat in if he was just on a wind up but going in heavy on the twice vaccinated + boosters and still caught it vibe when we know this is possible anyway and we've no idea if these people are sick was a little sensationalist.

 

[Shakesy]

" A South African patient with uncontrolled HIV could not clear the virus that caused Covid-19 from her body for 216 days, researchers have found. Over that time the virus, SARS-CoV-2, mutated a lot. " - July 2021

Being immunocompromised, as many South Africans are, spells trouble for everyone. Especially since those who are compromised generally come from countries with low vaccination rates.

 

[11101]

If that's the case then why didn't the virus mutate more in the first wave when no-one was vaccinated?

Lots of immunocompromised people (HIV & poverty), low vaccine rate, lots who were vaccinated got a sub-optimal vaccine, incompetent government. It all adds up. Plus, South Africa variant is unlikely to be South Africa variant. It will probably be Africa variant that was first picked up in South Africa.

I feel like we have been here before though. We don't know if it evades vaccines, we don't know if its more deadly, we don't know if its more transmissible. Let's find out before the whole world shits itself.

 

[jojojo]

Do you think it's strange that two of the four biggest mutations originated in SA? Or is it just bad luck?

SA is strong on sequencing and information sharing. It's quite possible they're effectively the lens through which we see large parts of Africa. Low vaccination rates make the whole of Africa vulnerable.

There's also a wild card in the SA story which comes from the high HIV+ rates in the adult population. There's a view that variants showing multiple simultaneous mutations occur in single individuals who are struggling to fight off the disease effectively ending up with multiple reinfections. That could mean someone severely immune compromised (on a HIV drug regime that isn't working for example) or someone going through multiple failed treatments in hospital or elsewhere.

 

[Pogue Mahone]

" A South African patient with uncontrolled HIV could not clear the virus that caused Covid-19 from her body for 216 days, researchers have found. Over that time the virus, SARS-CoV-2, mutated a lot. " - July 2021

Being immunocompromised, as many South Africans are, spells trouble for everyone. Especially since those who are compromised generally come from countries with low vaccination rates.

I’m not sure that last bit necessarily true. Certainly wealthy countries are better able to keep severely immune compromised patients alive for a very long time, after they catch covid. Which can generate loads of mutations in the virus. The use of expensive monoclonal antibodies as treatments (not available in underfunded health services) is supposed to accelerate this process. Which is thought to be how the alpha variant came about, in the UK.

 

[Sparky Rhiwabon]

We go again

 

[Pogue Mahone]

It is just worth noting that we really don't know how worried to be. There are massive causes for concern because of the quantity and the nature of the mutations but not all mutations work out as destructive as they look.

The UK for example has been monitoring a delta mutation AY42 which looks to have a transmission advantage over the original delta, that is to say: the proportion of delta cases with mutation is growing. However the React-1 study that tracks cases in more detail is seeing more cases with mild symptoms and fewer severe/hospitalised cases. That's also still seen as early data, despite the fact that tens of thousands of cases are involved - because you need a lot of cases to see real patterns in hospitalisations, particularly among younger age groups.

It's right to be concerned, it's wrong to assume worst case. I'm particularly worried that assuming the worst will become another reason for vaccine hesitancy, or delaying boosters because people get trapped in a mindset of "none of them work" or talk about "waiting for a better one". That kind of thinking could kill hundreds of thousands this winter for no gain at all.

I’m still clinging to the possibility that we get a variant soon (possibly this one?) which is a lot more transmissible than delta but causes much less severe disease. That could de-fang the virus even more effectively than vaccinations.

 

[Pickle85]

We are supposed to be flying to Mexico on Tuesday, for a holiday that's been deferred from 2019. Obviously there are WAY bigger things at stake here than me and my desire for sun and drinks with tiny umbrellas and tequila in them, but I'm already preparing myself for the inevitable travel lockdown gutpunch. Probably on Tuesday morning.

 

[jojojo]

Genuinely fascinating and encouraging commentary on why we shouldn't panic just yet and in particular why a PCR test on a vaccinated individual showing that they're infected shouldn't scare the rest of us into thinking that the vaccines have stopped working.

One for people who would like a bit of hope along with the doom and gloom.

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[Shakesy]

I’m not sure that last bit necessarily true. Certainly wealthy countries are better able to keep severely immune compromised patients alive for a very long time, after they catch covid. Which can generate loads of mutations in the virus. The use of expensive monoclonal antibodies as treatments (not available in underfunded health services) is supposed to accelerate this process. Which is thought to be how the alpha variant came about, in the UK.

South Africa has a low vaccination rate and is home to 20% of ALL HIV cases in the world. So, the virus ought to have more time to mutate.

Are you sure about that bolded part? SA has fairly decent healthcare.

* In fact, let me edit my response: The virus can mutate in asymptomatic cases, as you know. So, keeping immunocompromised patients alive longer in a hospital is surely irrelevant.

 

[berbatrick]

Tell you what would have been a novel idea, spend some of those utter insane lockdown costs that have ran into the hundreds of billions and the past two years on actually improving hospitals, building new ones, training new nurses and hugely increasing pay in the health sector.

A lockdown can be imposed in a day. Hospitals take time to build, even more time to equip, and potentially years to staff. It's not a 1-1 tradeoff.

 

[Buster15]

We go again

That is what viruses do. Mutate and the strongest survive.

 

[berbatrick]

Probably is everywhere already.

A report I read from South Africa stated that it's very easily detectable in routine, unmodified PCR screens (because it is slightly shorter than other variants, and that shows up as a slightly differently sized band). So, unless nobody is looking too closely at PCR results outside SA, it wouldn't have gone undetected.

 

[Pogue Mahone]

South Africa has a low vaccination rate and is home to 20% of ALL HIV cases in the world. So, the virus ought to have more time to mutate.

Are you sure about that bolded part? SA has fairly decent healthcare.

* In fact, let me edit my response: The virus can mutate in asymptomatic cases, as you know. So, keeping immunocompromised patients alive longer in a hospital is surely irrelevant.

The point is that if you’re severely immune compromised and you catch covid you’re probably going to die very quickly. Which is also the end of the virus.

In terms of generating variants the worst case scenario is a severely ill immune compromised patient being kept alive in ICU by administering a bunch of very expensive and not very widely available medicines such as monoclonal antibodies over a long period of time. So the virus is continually replicating for months and months in a scenario where there is a constant selective pressure on it to evolve to evade these antibodies.

Now, obviously, South Africa is a diverse country. With some extremely well equipped hospitals. But I don’t think the scenario I describe above will happen in much greater numbers there than in other more wealthy countries. Even though the AIDS epidemic creates a lot of immune suppressed people (predominantly amongst the poorer members of South African society)

In more general terms, the more people catch covid the more likely a variant. So countries with the biggest surges are the most likely to produce them. Hence Brazil, South Africa and India have produced three VOC’s already (arguably same applies to the UK and alpha).

 

[Shakesy]

The point is that if you’re severely immune compromised and you catch covid you’re probably going to die very quickly. Which is also the end of the virus.

In terms of generating variants the worst case scenario is a severely ill immune compromised patient being kept alive in ICU by administering a bunch of very expensive and not very widely available medicines such as monoclonal antibodies over a long period of time. So the virus is continually replicating for months and months in a scenario where there is a constant selective pressure on it to evolve to evade these antibodies.

Now, obviously, South Africa is a diverse country. With some extremely well equipped hospitals. But I don’t think the scenario I describe above will happen in much greater numbers there than in other more wealthy countries. Even though the AIDS epidemic creates a lot of immune suppressed people (predominantly amongst the poorer members of South African society)

In more general terms, the more people catch covid the more likely a variant. So countries with the biggest surges are the most likely to produce them. Hence Brazil, South Africa and India have produced three VOC’s already (arguably same applies to the UK and alpha).

For sure, severe immune compromised people will die faster from Covid in developing countries.

The problem arises when those who are not *severely compromised become incubators for the virus. The woman in the linked article tested positive 216 times, for goodness sake. SA is a hotbed for mutations.

* Are all HIV patients "severely compromised"? I don't know. But my point stands.

 

[DavidDeSchmikes]

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[Penna]

Italy's stopping the opportunity for unvaccinated people to get a temporary Green Pass by having a negative test.

A government decree that comes into force from December 6th will require a ‘super green pass’ health certificate to access most venues and services across the country, in a bid to contain Italy’s rising infection rate and ensure Christmas celebrations can go ahead as planned.

The ‘super green pass’ can be obtained only by those who are vaccinated against or have recovered from Covid-19.

It supersedes the basic ‘green pass’, which was also available to those who had recently tested negative for the virus; though the basic green pass will still be valid for use on public transport and to access workplaces.

https://www.thelocal.it/20211125/it...new_covid_strain_detected&utm_term=2021-11-26

 

[OleBoiii]

The new strain has a name: Omicron

Easily the most scary-sounding so far.

 

[Pogue Mahone]

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[Suv666]

On a scale of one to ten how stressed out should I be right now?

 

[V.O.]

On a scale of one to ten how stressed out should I be right now?

A solid Persei 8.

 

[jojojo]

On a scale of one to ten how stressed out should I be right now?

You shouldn't get stressed out. You should try and make sure that you, your family, your friends and anyone else you can influence are fully vaccinated and get the booster if they're eligible.

 

[Ferguson’s Hairdryer]

The new strain has a name: Omicron

Easily the most scary-sounding so far.

Does sound like a villain from transformers

 

[WI_Red]

A solid Persei 8.

Well done.

 

[Ferguson’s Hairdryer]

On a scale of one to ten how stressed out should I be right now?

From a psychological view this will cause more stress and fear amongst some people because of how quickly it’s escalated… identified yesterday, flights banned, present in Europe, named by WHO all within 24 hours or so. In contrast with previous variants where the same process has been much slower.

Could look at it in a positive. Governments are acting quicker, research is better so we’re better prepared. But of course scientists know very little about this new variant, so best thing is to wait for the scientific view on how infectious and deadly Vs other variants and if vaccines work on it.

 

[Ferguson’s Hairdryer]

That is what viruses do. Mutate and the strongest survive.

Not an expert. But I read that it’s usually in a virus’ interest to mutate and become more infectious but less deadly. The Dr stated that 10000 years ago or do it was likely that the when the common cold first around it was very deadly… a very good more recent example is the flu. When it first came it killed millions of healthy young adult but nowadays most won’t die from it. A mixture of natural immunity and the way its mutated.

 

[jojojo]

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First notes from Belgium including details on their first case of confirmed Omicron there.
"The patient infected with B.1.1.529 is a young adult woman who developed symptoms 11 days after travelling to Egypt via Turkey. The patient had a high viral load at the time of diagnosis (Cq of 14,2) The patient did not report any link with South Africa or other Southern African countries. This patient had not previously been vaccinated and had not yet been infected. She developed flu-like symptoms, but does not present at this stage signs of severe disease.

The patient did not report high risk contacts outside her household. None of her household members have developed symptoms, but have nevertheless been referred for testing. An extended investigation will be launched."

Based on PCR tests (that are now being sequenced) they've been seeing what they now view as potential cases rising for the past couple of weeks.

 

[Revan]

Did they skip Nu, so then they also skip Xi (for obvious political reasons) and thus it looks less obvious?

 

[RoadTrip]

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First notes from Belgium including details on their first case of confirmed Omicron there.
"The patient infected with B.1.1.529 is a young adult woman who developed symptoms 11 days after travelling to Egypt via Turkey. The patient had a high viral load at the time of diagnosis (Cq of 14,2) The patient did not report any link with South Africa or other Southern African countries. This patient had not previously been vaccinated and had not yet been infected. She developed flu-like symptoms, but does not present at this stage signs of severe disease.

The patient did not report high risk contacts outside her household. None of her household members have developed symptoms, but have nevertheless been referred for testing. An extended investigation will be launched."

Based on PCR tests (that are now being sequenced) they've been seeing what they now view as potential cases rising for the past couple of weeks.

I guess the most alarming thing about this is that it has no link at all to the areas where the variant was first released.

What is the likelihood that this is the variant causing a spike in Europe? I imagine slim if at all, as at this rate of infection it would have been picked up?

 

[massi83]

I guess the most alarming thing about this is that it has no link at all to the areas where the variant was first released.

What is the likelihood that this is the variant causing a spike in Europe? I imagine slim if at all, as at this rate of infection it would have been picked up?

Zero.

 

[Rektsanwalt]

Not an expert. But I read that it’s usually in a virus’ interest to mutate and become more infectious but less deadly. The Dr stated that 10000 years ago or do it was likely that the when the common cold first around it was very deadly… a very good more recent example is the flu. When it first came it killed millions of healthy young adult but nowadays most won’t die from it. A mixture of natural immunity and the way its mutated.

you are right. Viruses want to survive and reproduce. Killing its host is detrimental to that, as it can‘t be spread afterwards and dies with the host.

 

[Revan]

you are right. Viruses want to survive and reproduce. Killing its host is detrimental to that, as it can‘t be spread afterwards and dies with the host.

Not necessarily. If it can spread for several days, killing the host, won't matter.

Viruses do not want anything, they just spread. If they can efficiently spread, then the mutations that will make them lethal, likely won't provide any advantage for it to become dominant.

 

[Pogue Mahone]

Genuinely fascinating and encouraging commentary on why we shouldn't panic just yet and in particular why a PCR test on a vaccinated individual showing that they're infected shouldn't scare the rest of us into thinking that the vaccines have stopped working.

One for people who would like a bit of hope along with the doom and gloom.

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Thanks for this. Is a good read indeed. Thoroughly recommended for anyone feeling a bit down in the dumps about this omicron twat of a variant.

 

[Rektsanwalt]

Not necessarily. If it can spread for several days, killing the host, won't matter.

Viruses do not want anything, they just spread. If they can efficiently spread, then the mutations that will make them lethal, likely won't provide any advantage for it to become dominant.

I‘m aware they don‘t have a will in that kind of sense, I meant what their evolutionary determination might be. For the other part, you are right - efficient spread is key to persist, not necessarily surviving. What I meant is that a reduction of pathogenicity of pathogenes is connected with a higher reproduction rate. Many herpes viruses are living the viral dream by spreading to around 90% yet persisting a whole life of a human.
but you are right, my words were chosen poorly as efficient spread is key which doesn’t necessarily mean survival

 

[Champ]

Well i hope that he beats it soon and fully. Poor little fella.

I got word from my sons school today that a kid in his pod is covid positive and his parents had sent him in whilst knowing he was positive. Disgusting! We actually got our son tested on Monday this week as he had a bad cough but it was negative. Thankfully it’s almost gone

That's ridiculous! I can't comprehend why the parents would even consider doing that!

Fingers crossed your son remains Covid free.

 

[Rektsanwalt]

Well i hope that he beats it soon and fully. Poor little fella.

I got word from my sons school today that a kid in his pod is covid positive and his parents had sent him in whilst knowing he was positive. Disgusting! We actually got our son tested on Monday this week as he had a bad cough but it was negative. Thankfully it’s almost gone

I feel like these people should be reported to the police, honestly. I know no one likes to shit where they eat, but they should be punished accordingly. It‘s criminal assault. Disgusting, almost unbelievable.

 

[Suv666]

You shouldn't get stressed out. You should try and make sure that you, your family, your friends and anyone else you can influence are fully vaccinated and get the booster if they're eligible.

Too late I've already started stockpiling toilet paper.

Everyone I know is fully vaxxed.

 

[Suv666]

From a psychological view this will cause more stress and fear amongst some people because of how quickly it’s escalated… identified yesterday, flights banned, present in Europe, named by WHO all within 24 hours or so. In contrast with previous variants where the same process has been much slower.

Could look at it in a positive. Governments are acting quicker, research is better so we’re better prepared. But of course scientists know very little about this new variant, so best thing is to wait for the scientific view on how infectious and deadly Vs other variants and if vaccines work on it.

Yeah I guess we'll see how it works out.
When are we going to find out if this cnut is vaccine resistant or not?

 

[Phurry]

On a scale of one to ten how stressed out should I be right now?

Well, from my point of view, I’m not stressed about it. For context, I landed at Heathrow at 0730 yesterday morning having been on holiday in South Africa since 30th October. We’ve done a lateral flow test which was negative, and the Test & Trace service actually sent me a text message earlier today saying that they were sending us a couple of PCR test kits they’d like us to complete.