How do they discover new variants

[Jenasaurus]

I was just thinking about this and wondering how they discover new variants, do they test everyone that goes to hospital to see whether its an exsisting variant or a new one?

They do something called sequencing on PCR tests. I think they do it randomly as a routine then once they find a variant of concern they increase sequencing in that region.

@Wildewoodz

They do something called sequencing on PCR tests. I think they do it randomly as a routine then once they find a variant of concern they increase sequencing in that region.

Ahh, thank you for this.

www.cogconsortium.uk/

For most of the pandemic ~10% of all positive PCR tests were sent to the COG for full sequencing .

The standard PCR you do just amplifies up specific regions of the viral genome. You can think of these as markers or a COVID signature and it gives you a “yes” or “no”.

The full sequencing (also using PCR) tells you the whole genome code. It tells you the genetic code which makes amino acids which make proteins which are the building blocks of the virus.

It is more low throughput than the standard test.

Now, I believe they have expanded their capabilities across the country and are covering a much higher percentage of the daily tests.

All of this information is used to pick up individual changes in code called mutations, that sometimes can lead to changes in the proteins and only sometimes are meaningful and termed variants.

It is truly world leading. TheUK also provide sequencing for other parts of the world and are by far the biggest contributor of sequences in the whole world. We’d be screwed without them!

I heard a scientist on the Today programme a couple of months ago saying that the UK contributed almost half of all the sequencing tests to the WHO. On Devex.com it shows (cumulative?) at March 2021 the UK at 41%, US 22%, Denmark 8%, Australia 3%

@everythingthelighttouches

For most of the pandemic ~10% of all positive PCR tests were sent to the COG for full sequencing .

The standard PCR you do just amplifies up specific regions of the viral genome. You can think of these as markers or a COVID signature and it gives you a “yes” or “no”.

The full sequencing (also using PCR) tells you the whole genome code. It tells you the genetic code which makes amino acids which make proteins which are the building blocks of the virus.

It is more low throughput than the standard test.

Now, I believe they have expanded their capabilities across the country and are covering a much higher percentage of the daily tests.

All of this information is used to pick up individual changes in code called mutations, that sometimes can lead to changes in the proteins and only sometimes are meaningful and termed variants.

It is truly world leading. TheUK also provide sequencing for other parts of the world and are by far the biggest contributor of sequences in the whole world. We’d be screwed without them!

Thats really useful, thank you for taking the time to write that out for me.

So, if they discover a new variant, do they back track to the infected person/people with the new variant to see how the virus reacts/symptoms/severity/deaths/response to vaccine, I am assuming the sequencing although random wouldnt be annonymous or you wouldnt know how it had mutated, if that makes sense.

My son seems to think AZ is less effective against Delta than Pfizer after reading a report from the states. I am guessing this is something discovered by studying the number of people vaccinated with AZ and comparing to the ones with PFizer who caught it or had worse infections/consequences.

Thank you again, I am still getting my head around this but I am genuinely interested in the virus variants and how/why it mutates.

They sequence a random sample but they also aim to sequence all/most of the samples where the person has been hospitalised, vaccinated or reinfected. They'll also sequence more samples from areas where cases are rising rapidly. If any particular variant is over represented in any of these samples versus the random sampling then it becomes a variant of interest or variant of concern. They'll then do more in depth analysis of that variant including looking more closely at the mutations that virus has, predicting how they might affect things like receptor binding and if they affect surface antigens on the virus particle (i.e. the bits of the virus that the immune system can see). They'll also do labs studies to see how well antibodies from people who've been vaccinated or who've previously had covid bid to the virus.

*bind to the virus

Yes the person who has a different variant to the dominant one circulating will have additional questions asked to see if they can work out if it is linked to another case of the same variant or travel etc.
Each country will have a dominant variant so our dominant variant could be one not seen elsewhere

The scientist and lab people working on this are amazing if you ask me