Covid-19 Outbreak of new SARS-like coronavirus (Covid-19)

[novaveritas]

It's bs anyway. A 99.97% survival rate isn't a 99.97% recovery rate.

can you walk through the logic of that? on a long enough time line there is 0% recovery rate 0% survival rate.

 

[Jabberwocky]

anyway lets discuss the question posed which is your field, your claimed area of expertise.

Viral genetics

viral genomics. i've repeated it a million times and genomics and genetics have been separated a long way for a long while now. if you can't get one word correct i don't see why i should be expected to believe any 'facts' you state.

now as it happens i have heard of the variant you mention and it peturbs me greatly because you are actually right about its level of variance, in my job we use a mutation rate of one base per 10 kb for rna viruses and obviously this is much higher. but i just analyse data its not my job to speculate as to causes.

to be fair i didn't do an undergrad in biology so only know the bits directly relevant to my job but that's enough for this discussion. i haven't refused to read any primary literature i've actively read quite a lot over the course of this discussion but will not be wasting my time again because when i quote papers grimez links to contradict what he says they say, he ignores me, and i suspect you would do the same.

 

[Jabberwocky]

so thinking about it some more- a lot of this could be to do with the COG methodology. clearly they aren't sequencing every COVID positive patient, and i don't know what percentage they are- how likely is it that they just missed the progenitors? what sequencing technology were they using? illumina vs nanopore would give massive differences. you'd need illumina for this, but that is way more expensive so you will have less data and more of a chance of missing the progenitors. what assembly software did they use? viral assembly is a fucking dumpster fire- de bruijn graph approaches can't really cope very well so we can't really leverage the massive advances made in human and crop genomics, alignment based methods are too slow for analysing large amounts of data. so presumably because they analyse large amounts of data, they went for a DBG-based assembler, and i would guess reference based- this will give a strong bias towards the existing reference (so progenitors could be miscalled and lost).

to see if it really spontaneously appeared in milton keynes, we would need to rerun sequencing- likely impossible. and reanalyse a hell of a lot of data, which is probable unfeasible.

edit- obviously if they did alignment based assembly that could be reference based too. now i'm thinking about it more i hope they have applied a de novo approach but, assuming they use a DBG with a low k value so it runs with reasonable memory requirements, it would still be biased towards being highly conservative.

so, i don't know anything about genetics and never claimed i did. but i think i can give a reasonable explanation for what i assume @novaveritas thinks is a conspiracy.

 

[novaveritas]

viral genomics. i've repeated it a million times and genomics and genetics have been separated a long way for a long while now. if you can't get one word correct i don't see why i should be expected to believe any 'facts' you state.

now as it happens i have heard of the variant you mention and it peturbs me greatly because you are actually right about its level of variance, in my job we use a mutation rate of one base per 10 kb for rna viruses and obviously this is much higher. but i just analyse data its not my job to speculate as to causes.

to be fair i didn't do an undergrad in biology so only know the bits directly relevant to my job but that's enough for this discussion. i haven't refused to read any primary literature i've actively read quite a lot over the course of this discussion but will not be wasting my time again because when i quote papers grimez links to contradict what he says they say, he ignores me, and i suspect you would do the same

try me. You are being evasive. According to you viral genomics so far from viral genetics that you couldn't possibly use your 'expertise'. What is it that the data you are processing represents and how did it arise?

I asked you to read the Oxford AZ paper an original source that directly refutes your assertion that vaccines prevent infection, you refused. You have appealed to authority, your authority and when challenged you evade.

that is what it looks like.

 

[ions]

No doubt corona virus are real. It’s there to distract you from the fact that your govt went belly up bankrupt. Keep fueling the fire.

 

[Jabberwocky]

look again @novaveritas

 

[Jabberwocky]

so thinking about it some more- a lot of this could be to do with the COG methodology. clearly they aren't sequencing every COVID positive patient, and i don't know what percentage they are- how likely is it that they just missed the progenitors? what sequencing technology were they using? illumina vs nanopore would give massive differences. you'd need illumina for this, but that is way more expensive so you will have less data and more of a chance of missing the progenitors. what assembly software did they use? viral assembly is a fucking dumpster fire- de bruijn graph approaches can't really cope very well so we can't really leverage the massive advances made in human and crop genomics, alignment based methods are too slow for analysing large amounts of data. so presumably because they analyse large amounts of data, they went for a DBG-based assembler, and i would guess reference based- this will give a strong bias towards the existing reference (so progenitors could be miscalled and lost).

to see if it really spontaneously appeared in milton keynes, we would need to rerun sequencing- likely impossible. and reanalyse a hell of a lot of data, which is probable unfeasible.

edit- obviously if they did alignment based assembly that could be reference based too. now i'm thinking about it more i hope they have applied a de novo approach but, assuming they use a DBG with a low k value so it runs with reasonable memory requirements, it would still be biased towards being highly conservative.

so, i don't know anything about genetics and never claimed i did. but i think i can give a reasonable explanation for what i assume @novaveritas thinks is a conspiracy.

just in case you missed it

So you are just a number cruncher a sequence aligner a computer programmer? Great, you wouldn't know one end of a Gilson from the other.

you're right i don't do wet lab stuff. do you have any idea where algorithms come from? you don't start from a blank sheet, you have to have a genuine understanding of the processes that generate the data you are analysing. and to write bioinformatics algorithms you need to be shit hot at theoretical computer science and software engineering due to the inherent complexities and sizes of the datasets. straight biologists can't do my job and i can't do theirs. big deal.

 

[novaveritas]

so thinking about it some more- a lot of this could be to do with the COG methodology. clearly they aren't sequencing every COVID positive patient, and i don't know what percentage they are- how likely is it that they just missed the progenitors? what sequencing technology were they using? illumina vs nanopore would give massive differences. you'd need illumina for this, but that is way more expensive so you will have less data and more of a chance of missing the progenitors. what assembly software did they use? viral assembly is a fucking dumpster fire- de bruijn graph approaches can't really cope very well so we can't really leverage the massive advances made in human and crop genomics, alignment based methods are too slow for analysing large amounts of data. so presumably because they analyse large amounts of data, they went for a DBG-based assembler, and i would guess reference based- this will give a strong bias towards the existing reference (so progenitors could be miscalled and lost).

to see if it really spontaneously appeared in milton keynes, we would need to rerun sequencing- likely impossible. and reanalyse a hell of a lot of data, which is probable unfeasible.

edit- obviously if they did alignment based assembly that could be reference based too. now i'm thinking about it more i hope they have applied a de novo approach but, assuming they use a DBG with a low k value so it runs with reasonable memory requirements, it would still be biased towards being highly conservative.

so, i don't know anything about genetics and never claimed i did. but i think i can give a reasonable explanation for what i assume @novaveritas thinks is a conspiracy.

assume makes an ass out of U and Me

so back to the VUI 2020, you are being presumptive as to what appeared in the Milton Keynes Lab means. It simply means that the variant was found in a positive that was subsequently sequenced. The sequence is correct and the differences are large. There is enough sequencing of positive patients to be able to generate lineages with very few gaps for all vairiants in the UK. The progenitors would have been in other sequenced samples from before the 21st September as the patient that supplied the new variant sample must have gotten the coronoavirus from somewhere. Where was it? and how did it develop so many differences in such a short period of time. There is no suggestion that this is a conspiracy indeed you were the only one that suggested it might be.

I agree this is really not your field and you indeed are too hyper-specialized and narrow focused to contribute much to a discussion on a topic that is so closely related to your field, it is a great shame you do not have a broader knowledge base.

thank you.

 

[JGrimez]

Much as I generally love the bill of rights, I'm also quite fond of living in a country where I can go out and not worry about giving my older relatives a potentially lethal disease.

You can't even leave the country (without asking Daddy Government for permission and proving you have an "acceptable" reason). Australia has reverted once again to a penal colony.
Also did you forget about influenza? You could always go out and give older people a potentially-lethal virus.

but will not be wasting my time again because when i quote papers grimez links to contradict what he says they say, he ignores me, and i suspect you would do the same.

You mean I read them and attempt to dissect them while you blatantly ignore a scientific consensus.

When you read a study about the safety of a vaccine, and you find out that the data used to decide that the vaccine is safe comes from the vaccine manufacturer who is, essentially, selling a product and has been provided with immunity for any injury claims, how confident should you be that the claim is legit?


Why Most Published Research Findings Are False
"The greater the financial and other interests and prejudices in a scientific field, the less likely the research findings are to be true."

 

[Jabberwocky]

I agree this is really not your field and you indeed are too hyper-specialized and narrow focused to contribute much to a discussion on a topic that is so closely related to your field, it is a great shame you do not have a broader knowledge base.

you are totally ignoring half my post. how are these lineages created? which algorithms are used? they never give a 100% picture. how many times have the results been replicated using different pipelines?

i know what 'appeared in a Milton Keynes lab' means and was merely parroting your own terminology:

appearing out of nowhere on the 21st September at the Milton Keynes Pillar 2 lab

if you had any understanding of how biological data is analysed then you would know how easy it is to have missed something. we are talking about 17 bases out of 30kb in an RNA virus (they have their own foibles when it comes to sequencing, and then there's sequencers general foibles for specific bits of code) in an inherently biased sequencing methodology followed by an inherently biased analytical pipeline. i doubt any progress will have been made over christmas but i would be very surprised if the mystery hadn't been cleared up in a few months following a reanalysis of the data using different methods.

what i'm saying, is that the progenitors are probably there. but the methods used by COG were unable to find them. this may be because the sequence coverage was so low that these were thrown away as errors, in which case we could find them running the same software with different parameters- but we'd likely introduce a whole load of bollocks in too. i'd hope they sequenced with sufficient coverage but sequencing is really expensive so i highly doubt read depth is sufficient to capture every variant out of every patient. i do however suspect that a more nuanced analysis could get more insight from existing data.

without knowing what the COG methodology is, i can't really comment, and you didn't answer any of my questions about that.

you say they were able to generate lineages- how? tell me the names of the algorithms you put your faith in and then i'll have a better chance of explaining to you how they can have cocked this up.

 

[Jabberwocky]

You mean I read them and attempt to dissect them while you blatantly ignore a scientific consensus.

oh the irony! i have enjoyed our chats today.

When you read a study about the safety of a vaccine, and you find out that the data used to decide that the vaccine is safe comes from the vaccine manufacturer who is, essentially, selling a product and has been provided with immunity for any injury claims, how confident should you be that the claim is legit?

do you take any medication ever? i have some news to break to you about how its efficacy was tested that you might need to sit down for. (even in the case of non vaccines, where immunity is not granted, in practise its there- seroxat and the US opioid crisis bear testament to that)

 

[JessFR]

You can't even leave the country (without asking Daddy Government for permission and proving you have an "acceptable" reason). Australia has reverted once again to a penal colony.
Also did you forget about influenza? You could always go out and give older people a potentially-lethal virus.

Influenza is significantly less lethal and there are effective vaccines for influenza.

But it's completely redundant because the same measures that have kept Australians safe from covid have meant there is almost no influenza around this year anyway. So the odds of me giving that are also extremely low.

 

[F.U.B.A.R.]

Influenza is significantly less lethal and there are effective vaccines for influenza.

But it's completely redundant because the same measures that have kept Australians safe from covid have meant there is almost no influenza around this year anyway. So the odds of me giving that are also extremely low.

Tbh, I found Covid-19 to be a walk in the park compared to some doses of influenza I've had. It was the longevity that dragged me down. I guess I was just one of the lucky ones...

 

[JessFR]

Tbh, I found Covid-19 to be a walk in the park compared to some doses of influenza I've had. It was the longevity that dragged me down. I guess I was just one of the lucky ones...

Some people haven't realized they had it at all.

That's the problem. It's so lethal for some people and benign for others. Making it almost impossible to keep contained.

 

[JessFR]

No doubt corona virus are real. It’s there to distract you from the fact that your govt went belly up bankrupt. Keep fueling the fire.

How can a government that only owes money in a currency it controls and can limitlessly print more of ever go bankrupt?

Answer: it can't, not unless it chooses to default on purpose.

 

[AutoTripper]

Guys and girls. Very short post here. (Edit- NOT in the end lol). Firstly, very interesting and dare I say considerably more productive discussion I am still reading through.

And I feel we (you all) are actually working together more now. Two heads are always better right?

Im pleased that a good number of actually intelligent, educated people are chiming in.

It's clear to me now that I have been a naive fool offering my own dumb and limitted subjective offerings. This is not my fortitude, and I concede in humbleness..

Just to be clear again though, I am not a covid denier at all. It's real. But I support the In my view, very wise words and perspective put forward by @JGrimez and @finitelifeform whose basic throurough expose I already have strongly built into my view, understsnding, belief etc. Many others here too.

Including @novaveritas who clearly has lots of knowledge and factually researched data to supoort his arguments, where I lack pittifully myslef.

I feel it was my own riducullable outlandish comments here of late which I am not qualified with skills to substantiate, to say least here days ago, which has partly fuelled this escalating fiery debate here.

I feel humbled in realisation of my sheer unqualification to debate this with you on the strength and merit of grounds you all are now.

But I am pleased to see some apparent progress and togetherness, hence my pitiful attempt to diffuse snd encourage peace and civility last night..
I am a peacekesper, a comedian,,a philosopher and one hell of a true psyconaut, whiit a massivle imparied autistic set of congnitive faculties from excessive MDMA and Lyme desrtoyed brain fucntion on tops.

I am no scientist. I can offer no more of value. Others less damaged and more intellectual have taken up the reigns.

I must focus on my priorities now, survival essentially.

One thing I absolutlely cannot ever afford to do is become immoblie for the sake of managing my life threatening allergies and infections every day, and being admitted to hospital would be almost certsin death to me, honestly. A longly held terrifying thought of mine.

I can only eat exclusively home cooked, mega restricted food. And my daily survivial depends on being able to manage my severe allergies and dangerous (non- Covid) respiratory infecfions.

I would not be able to do this one iota in a in-hospital stay. My conditions from Lyme are extremely unusual, I can only manage them myself,,at home, with my mum's constant assistance, practical and emotionsl support.

Standard hospital food would surely kill me no exagerration, so restricted is my specisl diet and severe allergies.

Also, I have a heavy Etizolam dependance. I cannot afford to risk cold turkey WD.

Etizolam is illegal in UK.

Im extremely allergic to valium pills, lorazepam, etc, basicsally all prescription medicines. I would not be able to stay in hospitsl, say- i will WD dangerously from benzos, and my only hope would be benzodiazepine injection, if thst would even be an option? I have no idea there.

I say this now because last night saw me seriously damage my left knee in a fresk toppling accident in the bathroom. I have never been in anywhere near as much pain. I cannot put the slightest weight on my left knee.

I'm sure I either tore cartillage, ligaments or tendons, or maybe dislocated my knee as well. I can only crawl slowly on hands and knees. I can't stand up at all or even get on my feet. The pain in my left knee is the worst psin I felt in 40 years.

I really need to visit hopital, but my lungs are full of mucus and I need to do my esential oil steam inhalation first which is near impossible in my immobile condition.

I can't est any food until I have done this first, on daily basis, and needs repeating after every meal to prevent allergy mucus suffocation. Not something I could do in hospital either.

I honetly see a hospital stay as huge threat to my abnormal life and condition.

So I am pretty scared. Just praying the acute pain level will level off gradually before deciding on a course of action.

In the meanitme, I feel I should leave this ongping debate to the far more intelligent, non-handicapped members here from now.

If anybody has any insight to possibly offer, should I have no option but a hospital stay and potentially knee operation for all I know now, regarding specifically my very high benzo dependenca on etiz, which I would not legally be allowed into hospital (I use oilve oil dissolved powder, I could smuggle a large pot of capsules in with me, or I have few hindered- albeit marked, blotters), and if there is a chance they would be able to offer me injectibible Benzo subststites, It could be very helpful.

Sorry I know this trailed OFF T but this is the hardest challenge to my survivial ever right now.

You guys, this place, has kept me through hard times. Hence this post here now.

Otherwise I admit I am out of my pond here but do keep up the well meaning constructive discussion here folks, and as @cduggles rightly says, please let's try and be civil.

Wish me luck and any insight into potential hoslital in-stay protocol, in regards to my above concern, would be very welcomed.

My mum would not even ne allowed to visit me in hospital for vital emotiinal support, bring me foods I can eat, and in the ideal world, etizolam to keep WD's at bay.

The fact I do have actuall legit proper Flu right now also means Im virtually guaranteed a false Covid daiagnosis from PCR test I absolutly do not want, is just an aside.

And @negrogesic no worries for your passion, I know you speak from heart and mean well. And sorry if I riled you.

All that matters to me right now is surviving this ditch Im in, first and foremost.

 

[ions]

How can a government that only owes money in a currency it controls and can limitlessly print more of ever go bankrupt?

Answer: it can't, not unless it chooses to default on purpose.

Really it’s the spending power of the dollar that changes. The dollar will collapse. Other countries will stop buying our bonds. No country that has left the gold standard has ever been successful. How’s that?

I should also mention that it relates to corona as what will come soon because of a) what’s been going on feudal b)corona mandates.

 

[novaveritas]

you are totally ignoring half my post. how are these lineages created? which algorithms are used? they never give a 100% picture. how many times have the results been replicated using different pipelines?

i know what 'appeared in a Milton Keynes lab' means and was merely parroting your own terminology:


if you had any understanding of how biological data is analysed then you would know how easy it is to have missed something. we are talking about 17 bases out of 30kb in an RNA virus (they have their own foibles when it comes to sequencing, and then there's sequencers general foibles for specific bits of code) in an inherently biased sequencing methodology followed by an inherently biased analytical pipeline. i doubt any progress will have been made over christmas but i would be very surprised if the mystery hadn't been cleared up in a few months following a reanalysis of the data using different methods.

what i'm saying, is that the progenitors are probably there. but the methods used by COG were unable to find them. this may be because the sequence coverage was so low that these were thrown away as errors, in which case we could find them running the same software with different parameters- but we'd likely introduce a whole load of bollocks in too. i'd hope they sequenced with sufficient coverage but sequencing is really expensive so i highly doubt read depth is sufficient to capture every variant out of every patient. i do however suspect that a more nuanced analysis could get more insight from existing data.

without knowing what the COG methodology is, i can't really comment, and you didn't answer any of my questions about that.

you say they were able to generate lineages- how? tell me the names of the algorithms you put your faith in and then i'll have a better chance of explaining to you how they can have cocked this up.

I know the principles, smash it all into peices sequence the bits then overlay the peices using processor power. Kind of like a jigsaw. if there is too much sky in the jigsaw it gets more difficult, and if two similar jigsaws get mixed it gets much more complex.

I am not ignoring your points about the sequencing methodology merely properly considering the implications of what you are saying given the emergence of this VUI 2020 variant has had serious repercussions on policy. Tell me if I misunderstood you, from a given pile of raw data out of a sequencer you can derive different sequences depending on the parameters of the algorithm used to rebuild the sequence?

I put no absolute faith in anything, but I would be very surprised that CoG actually Wellcome Sanger I think, screwed this up badly. I think the variant sequence differences is real and correct and the genetic distance is large which then requires an explanation.

Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations

Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations Report written by: Andrew Rambaut1, Nick Loman2, Oliver Pybus3, Wendy Barclay4, Jeff Barrett5, Alesandro Carabelli6, Tom Connor7, Tom Peacock4, David L Robertson8, Erik...

virological.org

As I see it the VUI variant is 27 bases from Wuhan so about right 52 weeks one change every 2 weeks... but 10 from the nearest circulating sequenced virus in September. so that would imply a split away roughly 20 weeks before some time in March.... so its progenitors would have to be missed to sequencing for almost 5 months but roughly 10% of positives are sequenced and in the summer lull the proportion was higher.

this is where a hypothesis that this was passaged through a non human host fits rather well, otherwise it requires some magic or unusual conditions. For example antibody therapy but where there was no testing for weeks or months.

 

[novaveritas]

Really it’s the spending power of the dollar that changes. The dollar will collapse. Other countries will stop buying our bonds. No country that has left the gold standard has ever been successful. How’s that?

I should also mention that it relates to corona as what will come soon because of a) what’s been going on feudal b)corona mandates.

Two ways out of un-repayable debt, pay back the debt at cents on the dollar haircutting the creditors or repay the whole nominal with dollars worth cents, haircutting everyone. They both are defaults in real terms.

 

[ions]

@novaveritas washington has to audit the fed, reestablish gold standard, end the drug war. Debt spending is no good