Question for those in the know

How much does a virus have to mutate before it’s classed as a new virus in its own right rather than a variant of what went before?

Or does that never really happen?

and if it does happen how far away from being classed as a new virus in its own right is omicron?

as i regularly find myself in disagreement with kelvin, i thought this was worth a quote/repeat

There are plenty of other interesting and useful posts and contributors, I’m not suggesting TiRed’s posts are the only ones worth reading. The signal to noise ratio isn’t great right now though.

but im having to think of it as the noise to signal ration currently, just sits better in my head that way round

It’s a little technical but you want pango
https://en.wikipedia.org/wiki/Phylogenetic_Assignment_of_Named_Global_Outbreak_Lineages

The rules for a new lineage are here:

Statement of Nomenclature Rules

Basically, you align the amino acid sequences for samples and look to see how similar what you have tested is to previous reference strains. If it looks “mostly similar” and has similar epidemiological features, it’s a substrain. If it doesn’t align (some drop out acids), has lots of mutations and has different clinical features, it’s a new strain.

A single mutation could be a new strain. The first was D614 mutating to G. That increased transmission and the new strain replaced the Wuhan reference almost immediately. UK variant (Alpha) dropped some acids at position 67/70 and changed at N501 to Y. It’s part science and part art.

Influenza has two surface antigens and these can undergo huge changes on an annual basis (H and N proteins – hence “H1N1 strain”). Coronaviruses do not change their coats to the same extent. Instead they mutate at individual points on the surface spikes.

Your best post.
Don’t forget to close door on your way out.

Poor show @frankconway

How much does a virus have to mutate before it’s classed as a new virus in its own right rather than a variant of what went before?

I’d also wondered this. And related, why it’s generally assumed that a new variant will tend to displace the existing, or not spread. What is stopping both co-existing ?

It’s a little technical but you want pango
https://en.wikipedia.org/wiki/Phylogenetic_Assignment_of_Named_Global_Outbreak_Lineages

Thanks – that deals with whether a virus is a substrain or a new strain of sars-cov-2 , but what I was getting at in my original question is, is it possible for a virus to mutate so much that its no longer classed as a sars-cov-2 virus?

and if that is possible , how far is omicron from being a new virus?

Apologies If I’m using the wrong terminology above.

What is stopping both co-existing ?

Darwin

Fittest will outcompete. But local pockets (e.g., regions or even countries) can harbour independent strains without competition. When you get an introduced new fitter strain, it tends to outcompete the others. There have been three such events in the UK; D614G, Alpha (November 2020) and Delta (April 2021). Omicron _may_ be not as fit as Delta, but we shall see. It took off in South Africa when Delta was very low. Whether it can push aside UK Delta and substrings is unknown.

New variants may not displace others, but of course, you detect cases and type them. Countries do not do this uniformly (UK is the world leader here). So we might be missing strains that are not outcompeting but pop up and down. You see this in the UK with Beta and a few others.

A very very mild but very transmissible strain would be good news if it keeps out a severe but less transmissible strain. It might still be bad news for the elderly/immunocompromised, but this is a form of vaccination using Live Attenuated Virus. Current COVID LAVs have not been impressive.

https://www.gavi.org/vaccineswork/what-are-whole-virus-vaccines-and-how-could-they-be-used-against-covid-19

how far is omicron from being a new virus?

A very long way. SARS-COV-1 has 30k nucleotides and is about 67% similar to SARS-COV-1, It forms a different strain of the “sarbecovirus” family. MERS is further away still but still a coronavirus. This paper is worth a quick read for taxonomy of SARS viruses and influenza.

Although the media says it has a LOT of mutations, this is relative and I am most definitely not a Taxonomist!

A very long way. SARS-COV-1 has 30k nucleotides and is about 67% similar to SARS-COV-1, It forms a different strain of the “sarbecovirus” family. MERS is further away still but still a coronavirus. This paper is worth a quick read for taxonomy of SARS viruses and influenza.

Although the media says it has a LOT of mutations, this is relative and I am most definitely not a Taxonomist!

thanks – appreciate your info on this.

Don’t forget to close door on your way out.

Doors don’t do anything, you can still open them to get through. I refuse to use them as they do nothing.

Not wanting to be the harbinger of doom, but I wouldn’t be surprised if there was a lockdown in the New Year, Omicron or not.

Not wanting to be the harbinger of doom, but I wouldn’t be surprised if there was a lockdown in the New Year, Omicron or not.

Don’t worry, you’re only a mild familiar of doom-lite; people on this thread have been predicting another lock down since the summer televised Euro football.

From the top of my head:
Lockdown by end of august
Lockdown to coincide with schools going back
Lockdown by end of september
2 week half term circuit breaker
Lockdown by end of november

In the same way that someone usually wins the lottery, someone probably will be right at some point.

You’re listing occasions where a “lock down” could have helped avoid our health service being overstretched. It’s clear that the government (well, our PM really) won’t take such preventative steps now. That doesn’t mean that a future “lock down” can be ruled out… at some point it stops being a preventative tool to prevent the health service failing to treat critical cases, and becomes a response to the health service failing to treat critical cases. This government is “responsive” to public pressure, if nothing else. People dying in large numbers of Covid without access to hospital treatment would result in plenty of public pressure. Hopefully it won’t come to that in January. I’m hopeful that it won’t. My expectation is that it won’t. But the confidence to rule it out outright doesn’t seem well founded to me. A two week closure of pubs, clubs and restaurants etc (or curfew or other reduction in physical contacts) during the January slow down needs to be a possible tool for the government to use if it’s needed.

Everything coming out of our Govt scientists is that “Get a booster – the high levels of antibody will offset the lowered effectiveness of vaccines”

My Booster was nearly 6 months ago under the CovBoost trial. Do I need to be concerned about my waning antibodies after 6 months post boost? How will having caught Delta in August affect this?

No communication from your trial? Some people are getting a fourth dose.

wow – so did you have 2xvaccs, then a booster in May and then CV19(Delta) in August.

i assume the booster was early, but even so that four ‘doses’ in under a year, potentially five if you get a ‘standard’ booster….. does that make you “covid proof” or “full of covid”

We have decided to err on caution at work – we work daily in multiple schools, with staff moving between them each week. We are winding back in-school and in-nursery delivery work, with a stopping of most delivery in a week. We are also ceasing our office use – it was limited, but we are now all working properly from home with office only to collect or drop off resources needed for delivery.

It is not panic, we are keen to a) not see staff enter Christmas holidays with CV19 or seasonal flu (etc) caused by being expected in school, and b) loosing a week or two delivery now ‘buys’ a month with our usual Christmas full closure.

Hard to make that call, but it is on balance the right thing.

We have managed to work right through the pandemic, in fact grow as an organisation, and avoided any issues that our work could have caused for staff and customers despite being in multiple schools and nurseries daily. This in itself is a near miracle.

The level of antibodies needed for protection for vaccines, which make a polyclonal response, isn’t really known. Their persistence in the body halves every two months as the cells that make them wane. Down to low levels levels. For super potent monoclonal antibodies the levels are known from prophylaxis studies. Although these may be higher with the new strain. It’s all too early for doomongering

Delta spread through vaccinated populations, but for the same number of cases as alpha, hospitalisations were only a quarter. I think omicron looks more like alpha, but there were no vaccines then – hence the concern.

Like any chronic therapeutic, repeat administration will eventually be balanced by elimination. Boosters raise antibody levels more than first doses. I’ve not seen data on fourth doses, but would expect the same. Infections will add even more.

Kelvin – not a lot as its all blinded.

Ive emailed for some details and apparently something is being published in the Lancet Friday.

As I understand it, 4th jabs are for those immunosuppressed, whose 3rd wasn’t officially called a booster, just that their treatment was 3 jabs.

The other issue for me is that my booster doesn’t show on my Covid Passport, as its still a trial and blinded. It won’t be long until I need to show my boosted status o travel to certain countries for work. They did agree a few months back to unblind all placebo trialists, and offer them a booster, but we still don’t know what booster we had.

EDIT: Thanks TiRed – that ties in with what I had previously understood.

4yo daughter woke in the night with a constant cough so no school and we’ve just been for a ‘tickle test’ as we call it. Test centre busiest I’ve seen it by a margin. All mum’s with Little’uns. School cold and cough season in full swing I guess!

https://www.bbc.co.uk/news/business-59426353

Moderna reckon less effective vaccine. Just guess work at this stage?

No, Covid is rife in primary schools at the moment. All thanks to Mr “Covid Secure” Williamson.

neilnevill
Free Member
https://www.bbc.co.uk/news/business-59426353

Moderna reckon less effective vaccine. Just guess work at this stage?

The vaccines are a little less effective against Delta too so it’s really all about how much less effective. I get the impression no one knows that yet.

Fingers crossed on that one.

Well I’m currently down near Exeter and at the two deliveries I’ve had to make, the petrol station and the shop I got my lunch from have all had near-100% mask wearing. A complete change from when I was down here last week where it was down to roughly 40%. Everyone giving each other plenty of space too so it seems that the message gas got through to most people at the moment.

Moderna reckon less effective vaccine. Just guess work at this stage?

I know we all need to exercise caution, stay chilled, and just be patient at this early stage… but the different noises coming out of Moderna and Oxford does seem odd. It is about the different vaccine technology used, or simply extra caution required for a vaccine supplier (rather than research body)?

I’m not sure why the moderna thing is news, I thought it was considered fairly much a given that vaccine effectiveness would be lower for this mutation…?

It is about the different vaccine technology used, or simply extra caution required for a vaccine supplier (rather than research body)?

I think the problem is that everyone is hanging on the data for this one (and theres a lot of partisanship regards covid) so anything said gets blown up way out of significance

Omicron evident in Dutch samples earlier than 1st official recognition in SA https://www.bbc.co.uk/news/world-europe-59473131

be interesting to see what S-gene drop out looks like across countries over the last month

4yo daughter woke in the night with a constant cough so no school and we’ve just been for a ‘tickle test’ as we call it. Test centre busiest I’ve seen it by a margin. All mum’s with Little’uns. School cold and cough season in full swing I guess!

Was busy when we went yesterday morning – all those Sunday night pre-school/work LFT tests kicking in.

The press conference on Saturday said that it was only in younger children that rates were currently rising, and daughter said they were missing some Rainbows Thursday night, and some of the younger gymnasts she coaches on Friday due to Covid. I wonder where she picked it up from to test positive on Sunday night?

MrsMC and I have both had our negative PCR results through from yesterday’s tests, nothing yet to confirm daughters result – wondered if it had gone for further omicron testing first?

reluctantjumper

Well I’m currently down near Exeter and at the two deliveries I’ve had to make, the petrol station and the shop I got my lunch from have all had near-100% mask wearing. A complete change from when I was down here last week where it was down to roughly 40%. Everyone giving each other plenty of space too so it seems that the message gas got through to most people at the moment.

A message that has not yet got through back here in the City of London.
Commute in this morning from the darklands of Essex, and I’d estimate the mask wearers accounting for about 1 in 5. Lunchtime stroll, passing through a few shops and it seems similar, if not worse.

In the bank today, someone was offered a mask by a member of staff, to which the response was “no thanks, I don’t do masks”.

wow – so did you have 2xvaccs, then a booster in May and then CV19(Delta) in August.

Sandwich Jr managed to contract COVID for the second time around the time he had his flu and booster jabs in Bristol. We managed to avoid catching it from him but Mrs S was pinged at the weekend for a trip to Stratford Westfield during her lunch hour last week on her one day in the office. We are awaiting her PCR result.

So here we are again. Bojo is stepping up to the Mic to sort all this out for us.

I’ve zero sympathy for him, at every stage of this I think he’s failed to accept hard facts until it’s too late, and don’t suspect this will be any different.

But… I wouldn’t want to be in his shoes right now.

Omicron is here, little pockets of it all over the UK, as ever, you never find out about new strains until it’s too late.

The WHO are telling us not to panic, don’t punish the Southern African Countries for spotting it first, wait and see.

The Boss of Moderna has said a material drop in vaccine efficacy is a certainty.

Prof Karl Luterbach who wants to be the next German health minister say it could be a Christmas Gift, a less lethal, but more contagious variant that out-competes Delta. Backed up slightly by data coming out of SAfrica that it’s seems so far to be milder.

A Tory minster said we shouldn’t mix un-necessarily at Christmas, but Boris shut her down saying, “no we’re all going to have a great Christmas”.

So… does he do the hard thing, impose restrictions until we know more, or bottle it, wait and see, by which time, if it is indeed more contagious, it’ll be way on it’s way to becoming the dominate strain in the UK and World, but does that matter? If it is, it will anyway.

Flu season officially starts tomorrow, yay!

A Tory minster said we shouldn’t mix un-necessarily at Christmas,

It was actually Dr Jenny Harries, a senior public health official. But I guess we’ve had enough of experts.

You have to remember it’s Christmas party season for Boris, too, why should he miss out?

The Boss of Moderna has said a material drop in vaccine efficacy is a certainty.

That is not what he said. He said he though it was highly likely there would be a significant drop in effectiveness. Lets stick to what we know & what was said – otherwise we end up in Chinese whispers (no pun intended). Bancel may turn out to be right, but so far all he’s said is “I think…”

“There is no world, I think, where [the effectiveness] is the same level . . . we had with [the] Delta [variant],” Bancel told the Financial Times in an interview at the company’s headquarters in Cambridge, Massachusetts.

He added: “I think it’s going to be a material drop. I just don’t know how much because we need to wait for the data. But all the scientists I’ve talked to . . . are like, ‘This is not going to be good’.”

https://www.bbc.co.uk/news/business-59426353
https://www.ft.com/content/27def1b9-b9c8-47a5-8e06-72e432e0838f

Forget Covid (for a second) has TiRed been undercover brainwashing other Elites into working for his Great Reset overlords?

We need to know.

https://www.ft.com/content/f159ffc9-65d8-4206-bf81-41b42689228b

For the record, I don’t work on Vaccines 😀 . I was wondering this morning when the Sanofi/GSK Phase 3 results were coming. I have however spent the day looking at 1) omicron materials from lots of sources (no data, but LOTS and lots of speculation), and 2) Molnupiravir FDA Ad Comm (no efficacy in second half of the trial – they don’t know why).

Prof Karl Luterbach who wants to be the next German health minister say it could be a Christmas Gift, a less lethal, but more contagious variant that out-competes Delta. Backed up slightly by data coming out of SAfrica that it’s seems so far to be milder.

I like this a lot, but the age distribution is younger in SAfrica, and of course it is summer for a likely seasonal respiratory virus, so we don’t know about pathogenicity (or much else) really.

And now I am off for the Tuesday club ride. That’s progress for me.

We need to know.

Indeed, those of us who don’t subscribe to the FT need to know what the article says…

The thing that annoyed me the most in this evening’s announcement was “increasing the per-jab payment to pharmacists from £10 to 15, or £20 on Sunday’s. All the vaccinators in my local pharmacy clinics are retired nurses/pharmacists doing it as VOLUNTEERS! The bosses are trousering these payments whilst volunteers do all the work.

So… does he do the hard thing, impose restrictions until we know more, or bottle it, wait and see, by which time, if it is indeed more contagious, it’ll be way on it’s way to becoming the dominate strain in the UK and World, but does that matter? If it is, it will anyway.

We’ve had the least effective but least disruptive intervention so far. Anything else will have significant cost. It’s already here, we can only hope to slow it’s spread rather than eradicate it so nothing else will de done unless the healthcare system appears to be on the verge of collapse.

@Murray,

Lol, sorry, neither do I. Turns out I also don’t check links before I paste them too.

Don’t worry though, was just a little frivolity.

dantsw13
All the vaccinators in my local pharmacy clinics are retired nurses/pharmacists doing it as VOLUNTEERS! The bosses are trousering these payments whilst volunteers do all the work.

Sleaze from the top down is the real new, normal. I expect those bosses will buy them a box of Quality Street when they are on offer.

Indeed, those of us who don’t subscribe to the FT need to know what the article says…

If you copy and paste the FT headline into a general Google search it should throw up a result which you can click and open. The FT rarely makes it impossible to circumvent their paywall…. they’re not that mean!

^^ Didn’t know that.👍