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OK. For what it's worth I'm going to try and explain why genomics is important in a ssRNA virus epidemic. No doubt it will end up being recited badly at a briefing, but, well, whatever. You read it he

Rachel has tried every which way to re-offer her services. This last tweet wasn't the first time she's reached out. Government has made it very clear they do not want her to be involved. I want h

I think you'll find most so called anti-government rhetoric is focused on government-stupidity and government-selfishness. In recent times - under Brown, Bell and now Quayle - all too many govern

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Initial 3 weeks was an open ended political safe bet. Long enough to recognise the virus characteristics and potentially get the spread under control but short enough not to riot the populace, albeit there's been enough bleating already.

Still open ended though - tacking one week on at a time now means people grumble but accept it by and large. Throw another 3 weeks at them in one block and some of them will flip.

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I have millions of questions.

Wrighty the other day (week?) said something along the lines of 'nowhere has been able to say they put the restrictions in too early' and that's a fair point. Everywhere has done it too late. Can we say that we did? Or is everyone happy that the gov took strong early action? What happens next time, when this happens again next month? Another 3 weeks off? What is the plan? Is there even one, and if there is, will they bother to stick to it?

There is much uncertainty, I doubt they have even the slightest clue how it affects people. This is hugely damaging, they've got to sort it out.

 

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13 minutes ago, Non-Believer said:

Initial 3 weeks was an open ended political safe bet. Long enough to recognise the virus characteristics and potentially get the spread under control but short enough not to riot the populace, albeit there's been enough bleating already.

Still open ended though - tacking one week on at a time now means people grumble but accept it by and large. Throw another 3 weeks at them in one block and some of them will flip.

Well if builders , windows cleaners etc go back Thursday that will take some pressure off and save a few £m

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9 minutes ago, TheTeapot said:

I have millions of questions.

Wrighty the other day (week?) said something along the lines of 'nowhere has been able to say they put the restrictions in too early' and that's a fair point. Everywhere has done it too late. Can we say that we did? Or is everyone happy that the gov took strong early action? What happens next time, when this happens again next month? Another 3 weeks off? What is the plan? Is there even one, and if there is, will they bother to stick to it?

There is much uncertainty, I doubt they have even the slightest clue how it affects people. This is hugely damaging, they've got to sort it out.

 

Suppose that really is the question: what is the plan for the future and what weapons do we have to deploy?

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49 minutes ago, Max Power said:

 1 2 3 4 5 6

 

40 minutes ago, WTF said:

thanks, you can have 10% when they come in for me.

Wouldn’t be much. Apparently several thousand people pick 1 2 3 4 5 6 in the belief that nobody else would do so, and they’d get the jackpot on their own if they came up, which they’re as likely to do as any other combination. 

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10 minutes ago, Gladys said:

Suppose that really is the question: what is the plan for the future and what weapons do we have to deploy?

I've bought a new lightweight snood for when it gets a little warmer.

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OK. For what it's worth I'm going to try and explain why genomics is important in a ssRNA virus epidemic. No doubt it will end up being recited badly at a briefing, but, well, whatever. You read it here first.

The COVID19 viral genome is a little under 30,000 letters long and is made of single stranded (ss)RNA, not DNA. One of the aspects of ssRNA viruses is that they mutate faster than DNA viruses, because they don't have a proof-reading capability when they make copies of their RNA to make more of themselves.

This is a double-edged sword. It can be advantageous to the virus as it may accumulate mutations that increase transmissibility. It can also be a disadvantage to the virus if those mutations kill the host too quickly (e.g. Ebola) as if the host dies quickly then there isn't much opportunity to transmit the virus to a new host. These mutations are a huge advantage to the scientists though as they accumulate within transmission chains.

With COVID19, extended transmission chains are called "lineages". Each lineage has a unique pattern of mutations along those 30,000 letters (we're starting to call these "constellations" now to add more terminology) which make the lineage identifiable if you have a case you want to classify. As the transmission chain continues within the lineage and more mutations are accumulated, the lineage might be split by scientists based on the new mutations. For example, the "UK variant" is lineage B.1.1.7. However, three months ago, there was just B.1.1 and three months before that, there was just B.1. If you want to read more then this paper should be of interest: https://www.nature.com/articles/s41564-020-0770-5

However, a lineage is a blunt tool. Mutations can accumulate within one infectious person, and then more mutations can accumulate in the person they transmit the virus to. Relatively, COVID19 is a bit slow at accumulating mutations compared to other ssRNA viruses. In most of the ssRNA viruses I've studied in my career we tend to say they exist as "quasispecies" because it's basically a cloud of virus variants which infect a single host. However, COVID19 does mutate fast enough to accumulate very distinct mutations in transmission chains and the work I did on the first week of the Isle of Man outbreak showed that it is possible to see the exact human-to-human transmission chain from the mutations alone. Many of those human-to-human transmission chains had unique mutations but were all classified as the same lineage.

So when they said at the briefing today that all the cases were identical they were only looking at the lineage, not the individual genome sequences. That's where I get frustrated because analysing and clustering the viral genome sequences is a highly specialised thing that not even most major NHS labs try their hand at (which is why https://www.cogconsortium.uk/ exists). Most major hospitals don't try to do this themselves, they leave it up to people like me who know what they're doing. 

To conclude, the lineage is just the virological city name. The genome sequence and specific mutations unique to each case are the postcode and house number that can be used to show all the addresses that the virus visited in that city. Probably a bad analogy but hopefully you get the gist of broad/specific analyses.

 

 

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34 minutes ago, TheTeapot said:

What happens next time, when this happens again next month? Another 3 weeks off? What is the plan? Is there even one, and if there is, will they bother to stick to it.

 

Well, there was a plan...but as someone said, the plan is the first casualty of any battle.

https://covid19.gov.im/outbreak-management-plan/outbreak-plan/

 

 

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3 hours ago, John Wright said:

Not really. You don’t know whether Man 1 got from Man 2 or vice versa. And your tracing for both is forward for both from their contact. Genotyping doesn’t help, at all.

You're wrong to assume that the direction of transmission in not detectable, in the early days at least, or looking at a single transmission line.

If A and B have the same variant and A has not left the Island but B is a recent arrival, then it is obvious that the line is B to A.

This has to be detected early before cross contamination within the Island corrupts the early data. Hence the need for speed in the virus identification. 1-2 days rather than 5-8 days.

That is the backwards identification that you say is not possible?

In simple terms there could be said to be a Blackburn variant and a Formby variant and people arriving on the Island by Sea or Air could have one or the other! Unfortunately, the cross contamination in England would mean that would only apply when the variants are first forming.

It still remains that forward and backwards identification can be greatly enhanced by knowing which variants are here and early identification.

Of course, Lockdown should negate any need for tracing, what we have got here is under the control of lockdown  and if it is working, it will fizzle out!!!

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7 minutes ago, Kopek said:

You're wrong to assume that the direction of transmission in not detectable, in the early days at least, or looking at a single transmission line.

If A and B have the same variant and A has not left the Island but B is a recent arrival, then it is obvious that the line is B to A.

This has to be detected early before cross contamination within the Island corrupts the early data. Hence the need for speed in the virus identification. 1-2 days rather than 5-8 days.

That is the backwards identification that you say is not possible?

In simple terms there could be said to be a Blackburn variant and a Formby variant and people arriving on the Island by Sea or Air could have one or the other! Unfortunately, the cross contamination in England would mean that would only apply when the variants are first forming.

It still remains that forward and backwards identification can be greatly enhanced by knowing which variants are here and early identification.

Of course, Lockdown should negate any need for tracing, what we have got here is under the control of lockdown  and if it is working, it will fizzle out!!!

Attribution?

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1 hour ago, Banker said:

Well if builders , windows cleaners etc go back Thursday that will take some pressure off and save a few £m

Sounds like the CoC have been lobbying HRH The Chief Minister and Ashy. The clinicians will be most unhappy.

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