[seankenny]

We've been helping the campaign for a public inquiry into the UK's handling of covid:

https://www.theguardian.com/commentisfree/2021/mar/23/london-bus-drivers-covid-ucl-report-public-inquiry

[Falling Down]

That’s a great piece by Lesh Sean. I imagine it was difficult to write but I’m glad she did.

[seankenny]

Thanks. Lesh talked it through with me, I wrote it and she edited it. I was there for all the things mentioned in the piece although it's clearly her take on events not mine. I was surprised how tired I was the day after writing it.

Anyhow, it was definitely worth it and I'm please that people are appreciating it. (Not sure I can use the word "like" in this context, but you know what I mean.)

[tomtom]

👏👏👏

[andy popp]

A wonderfully put together piece Sean, perfectly pitched - thinking of you both.

[Oldmanmatt]

Some interesting perspectives from this man. His credentials seem sound. I will be interested to see what’s dug up on him and how long it will be before he is a broken man. This is one of his longer interviews and the link below is his open letter



https://mcusercontent.com/92561d6dedb66a43fe9a6548f/files/bead7203-0798-4ac8-abe2-076208015556/Public_health_emergency_of_international_concert_Geert_Vanden_Bossche.01.pdf

I see Snopes has zoomed in on Geert. A bit Wakefield, really. “Your vaccine won’t work (because all current vaccines are bad), but mine will”.
https://www.snopes.com/news/2021/03/26/geert-vanden-bossche/?utm_source=agorapulse&utm_campaign=1p&fbclid=IwAR06KQ-nfUO6QWUqDJhKrxcgGThrtrwVO0Aa1WSQuT5gabtVdK3Xy53kfME

[Fultonius]

I know there are some very good statisticians and health researchers etc.

As we're getting closer to low case numbers, with still fairly widespread testing I suspect (and this is what I'm musing over) that that false positives will become more and more influential on public policy.

I read this, no idea if it's all BS as it's not published etc., but it does have a table from the ONS showing the number of "positive cases" considered so from just one gene expression. The WHO recommends counting that as inconclusive until re-tested.  https://arxiv.org/ftp/arxiv/papers/2102/2102.11612.pdf

In Scotland, we not down to very low numbers in hospital, deaths and ICU:



And a very consistently low, and never zero positive rate, not matter the number of tests carried out.



Will it ever go below 2% if we keep testing 20k people per day (many now asymptomatic).

[Oldmanmatt]

I think you’re probably right that testing is moving into the “ not the right thing to watch” category for a variety of reasons, not least the people who will test positive, who have been vaccinated and at very low risk of serious illness.
I imagine the government/SAGE have thought of that.
Maybe.

[Fultonius]

Currently in Scotland they're still basing our lifting of restrictions on case rates per 100k....

[Sidehaas]

As we're getting closer to low case numbers, with still fairly widespread testing I suspect (and this is what I'm musing over) that that false positives will become more and more influential on public policy.

I read this, no idea if it's all BS as it's not published etc., but it does have a table from the ONS showing the number of "positive cases" considered so from just one gene expression. The WHO recommends counting that as inconclusive until re-tested.  https://arxiv.org/ftp/arxiv/papers/2102/2102.11612.pdf

In Scotland, we not down to very low numbers in hospital, deaths and ICU:

I can't comment on the science behind that paper other than to point out that the B1.1.7 (Kent) variant is missing one of the original target genes of PCR tests in most of the UK (not quite all, as some test centres eg in the East of England used a different PCR test, I'm not sure about Scotland), so the best match you can hope in all those areas for is 2 out of 3, rather than 3 out of 3. The target genes weren't changed, at least to begin with, because they found that looking for cases with only 2 genes showing was a very good way of tracking the spread of the variant across the country without having to wait for genome sequencing to be done. You see this tracking technique referred to as S gene target failure (SGTF.) I explain this because obviously if a perfect test only sees 2 target genes, you will have a lot more tests only seeing 1 gene than if a perfect test sees 3, which was originally the case, and the manufacturer's intent. In practice a test now seeing 1 gene has only missed 1, not missed 2 as would originally have had to be the case.

The premise in your post that the occasional false positive becomes more problematic and could affect total case rates significantly at low infection rates is not necessarily true anyway because PCR tests are only used in symptomatic cases, so the true positivity of the population undergoing them is much higher than the true positivity of the general population. They are more significant in LFTs used for mass asymptomatic testing, but a positive LFT is recommended to be confirmed using PCR anyway (except in the first two weeks just gone of school testing) and the chances of someone getting both false positive LFT and false positive PCR are negligible.

Finally, note that case rates last July were a small fraction of case rates now (in Scotland, around 2%), from which you can conclude we are currently way above any rate at which false positives are significant, and rates are no longer dropping quickly, or in some regions at all.

Conclusion equals, in my view there is no real chance of false positives affecting policy, even if the Scottish government continues to use case rates as the driving factor, which I doubt they will long term. Obviously if there are a few of them happening each day then that's a bummer for the people isolating, but it isn't significant to anyone else.

[Sidehaas]

I think you’re probably right that testing is moving into the “ not the right thing to watch” category for a variety of reasons, not least the people who will test positive, who have been vaccinated and at very low risk of serious illness.
I imagine the government/SAGE have thought of that.
Maybe.

I do agree with this though. It has been made clear that rates will be allowed to rise in England as long hospitalisations don't rise too much.

[Sidehaas]

As we're getting closer to low case numbers, with still fairly widespread testing I suspect (and this is what I'm musing over) that that false positives will become more and more influential on public policy.

I read this, no idea if it's all BS as it's not published etc., but it does have a table from the ONS showing the number of "positive cases" considered so from just one gene expression. The WHO recommends counting that as inconclusive until re-tested.  https://arxiv.org/ftp/arxiv/papers/2102/2102.11612.pdf

In Scotland, we not down to very low numbers in hospital, deaths and ICU:

I can't comment on the science behind that paper other than to point out that the B1.1.7 (Kent) variant is missing one of the original target genes of PCR tests in most of the UK (not quite all, as some test centres eg in the East of England used a different PCR test, I'm not sure about Scotland), so the best match you can hope in all those areas for is 2 out of 3, rather than 3 out of 3. The target genes weren't changed, at least to begin with, because they found that looking for cases with only 2 genes showing was a very good way of tracking the spread of the variant across the country without having to wait for genome sequencing to be done. You see this tracking technique referred to as S gene target failure (SGTF.) I explain this because obviously if a perfect test only sees 2 target genes, you will have a lot more tests only seeing 1 gene than if a perfect test sees 3, which was originally the case, and the manufacturer's intent. In practice a test now seeing 1 gene has only missed 1, not missed 2 as would originally have had to be the case.

By the way, I noticed after a more careful read that the author of that paper does refer to this use of SGTF:
"Furthermore in a Public Health England report on variants [11], published January 8th 2021, it
states the goal of using one gene was explicitly to approximate the growth of the new B1.1.7
variant (emphasis mine):
“There has recently been an increase in the percentage of positive cases where only the
ORF1ab- and N-genes were found and a decrease in the percentage of cases with all
three genes. We can use this information to approximate the growth of the new
variant.”"

However the PHE reference he gives is the first in a series of technical briefing papers they published about this (https://www.gov.uk/government/publications/investigation-of-novel-sars-cov-2-variant-variant-of-concern-20201201) and the later ones present data in support of the accuracy of using SGTF to track the variant. It's not credible that this guy wouldn't be aware of those later briefings, so to be honest, the way he referenced the only one of them published before evidence was available and then emphasised (his bold) the word "approximate" makes me smell a rat as to his motivations.

It's also worth noting that everything he writes about single genes is from the ONS surveys, not the pillar 2 testing that form the vast majority of the testing programme. I'm not sure if that's significant.

[Fultonius]

Thanks Sidehaas.

There's a fair amount of asymptomatic PCR testing in Scotland. Struggling to find the exact amount though.

I know in healthcare (care homes etc.) routing PCRs are pretty common, same in oil and gas and my mum is in a government scheme to randomly test people. I can't find any stats on how many OCRs are administered for asymptomatic vs symptomatic cases.

No deaths in Scotland yesterday (often the case on Sundays but hey ho...) good news!   The case rate remains steadfastly above 2.5%....

[SA Chris]

Got AZ at lunchtime, very slick operation. Will see how I feel, but it is looking sunny tomorrow, ooh side effects.

[Stabbsy]

Got AZ at lunchtime, very slick operation. Will see how I feel, but it is looking sunny tomorrow, ooh side effects.

Don't expect too much of yourself, Chris. Felt fine on the day and then barely left the sofa the day after.

[SA Chris]

Aye, I saw your Strava for that day

Seriously, I know it might knock me bad.

[saltbeef]

I had first dose Pfizer in feb, I went skiing for the next week. totally fine (I'm in Canada) I don't know anyone here who has had a bad experience with either Pfizer or moderna or AZ.

[SA Chris]

OK OK, calm down Hercules

[Offwidth]

ONS have assessed the likely scale of long covid. Some frightening numbers...

https://www.theguardian.com/society/2021/apr/01/long-covid-snapshot-poll-finds-million-people-symptoms-uk

[Paul B]

Has anyone else had to have an awkward conversation yet with their Employers about the road map?

We've just had our end of year company review (<10ppl) and there was a big push to get back to normality with the impression given that the Gov. "work from home" message ends Mon 12/04.

I did some digging (as it sounded wrong) and this proved to be incorrect.

[tomtom]

my employer (university) has basically said all remote that can be until 1st June then review. Quite what will happen next (academic) year no-one knows (not even the management probably)... Neighbour who works at Salford said its pretty much the same...

Speaking to a friend over the weekend (IT/Systems management) who said they had a vote as to whether people wanted to come back into the office FT as per before - 5% wanted to.

If I were an employer - and someone working from home 40-100% of the time was working just as well as if they were in the office I would not want to force people in. But some may have different ideas...

I do wonder if there will be a split in some companies - where workers are given the choice -  between those who come in all the time and those who don't....

Anyway, back to your point Paul - I'd assume they have a risk assessment that all staff can see??

[Paul B]

Anyway, back to your point Paul - I'd assume they have a risk assessment that all staff can see??

TBF, having now dug out the actual road map dates and passed it on they just weren't aware (I get frustrated at times but they're a darn good employer). It's a bit awkward talking about measures as I've struggled to convey that 2m social distancing isn't really a silver bullet when you're talking about sitting in an office (converted Victorian terrace building, ventilation is jamming something in the sash windows) for a working day rather than seeing someone for minimal time.

If you look through the Gov. documents, the summaries are poor with "work from home" disappearing as a hit after Monday (including in the simplified pictorial format).

You need to literally go to the full roadmap to get the dates. To save others:
Step 3 (17/05) – WFH is still advised
Step 4 (21/06) – Further advice on WFH will be issued[/li][/list]

Source:
https://www.gov.uk/government/publications/covid-19-response-spring-2021/covid-19-response-spring-2021#roadmap

[mrjonathanr]

Apple and Google decline to update the NHS Covid app due to privacy violations ie uploading of user data to a central location rather than storing on solely on users’ phones.
https://www.theguardian.com/world/2021/apr/12/apple-and-google-block-nhs-covid-app-update-over-privacy-breaches

[tomtom]

Really good article here explaining why the AZ vaccine can cause blood clots in certain people - how it was discovered and how it can be treated.

https://www.theguardian.com/society/2021/apr/13/how-uk-doctor-marie-scully-blood-clotting-link-astrazeneca-covid-jab-university-college-london-hospital?CMP=Share_iOSApp_Other

[slab_happy]

For anyone who might be interested -- the Com-Cov study on mix-and-matching vaccines is expanding:

https://www.theguardian.com/society/2021/apr/14/uk-study-on-mixing-covid-vaccines-between-jabs-to-be-expanded

They're looking for people over 50 who've  already had one shot of a Covid vaccine:

https://comcovstudy.org.uk/

N.B. You're blinded as to which vaccine you get for your second shot but there's no placebo group, so no-one misses out.

IMHO this is one of the most important bits of vaccine research currently underway; if we know for sure that we can mix different vaccines, the increased flexibility would make it far easier to get everyone vaccinated.

And if it turns out -- as people are hoping -- that you get better immune response or increased protection against variants by using different vaccines for the first and second shot, then we've gained a major new weapon.