SARS-CoV-2 testing

Covid-19 discussion, bring your own statistics
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shpalman
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Re: SARS-CoV-2 testing

Post by shpalman » Sun Nov 29, 2020 9:47 am

shpalman wrote:
Mon Nov 16, 2020 10:59 am
Out of their 959 subjects, there was generally more IgM+ than IgG+, but from September to February there isn't an obvious trend. If anything there was a slightly higher prevalence in September to November, decreasing a bit in December, almost gone in January, and then back quite a lot in February.

It was scattered all over Italy in a way which may or may not correlate with official covid prevalence in the period up until 10th March.

Could there have been a different coronavirus around in the second half of 2019 which induces similar antibodies?

I'm not reading the full text, just looking at the pictures.
Reports of Covid circulating in Italy in autumn 2019, based on samples from a cancer unit, seem “weak”, said Prof Jonathan Stoye, a virologist at the Francis Crick Institute in London. “The serological data [from Italy] can most likely be explained by cross-reactive antibodies directed against other coronaviruses.” In other words, antibodies found in the cases in Italy had been triggered in individuals who had been infected by different coronaviruses, not those responsible for Covid-19.
molto tricky

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Re: SARS-CoV-2 testing

Post by shpalman » Sat Dec 05, 2020 12:25 pm

Government figures from the mass testing programme in Liverpool showed that the tests missed half of all positive cases detected by the standard coronavirus tests, and missed 30% of those with a high viral load
“They are a low-tech test, they can’t detect low levels of the virus. The World Health Organization has said: ‘Don’t use it for this purpose’, the manufacturer said: ‘Don’t use it for this purpose’”
molto tricky

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Re: SARS-CoV-2 testing

Post by jdc » Sat Dec 05, 2020 3:49 pm

shpalman wrote:
Sat Dec 05, 2020 12:25 pm
Government figures from the mass testing programme in Liverpool showed that the tests missed half of all positive cases detected by the standard coronavirus tests, and missed 30% of those with a high viral load
“They are a low-tech test, they can’t detect low levels of the virus. The World Health Organization has said: ‘Don’t use it for this purpose’, the manufacturer said: ‘Don’t use it for this purpose’”
Dr Susan Hopkins, the chief medical adviser to NHS test and trace, defended the use of the tests, saying they had picked up many cases of infection which would otherwise have been missed.

“What we are doing here is case detection. We are not saying people do not have the disease if their test is negative,”
I read this in the BMJ yesterday: https://www.bmj.com/content/371/bmj.m4690
Pollock believes that the harms of testing have not been adequately considered. “Some people are getting false reassurance as the tests are not very accurate,” she said. “People were being told on the radio that if they got a negative test they could go about their business.” She added that, since she raised concerns, the FAQ page on the Liverpool council website has been updated to include information on false negatives, and it now says that a negative lateral flow test result does not constitute a “green pass.”
The following quote looks to me like it's suggesting that this initial stage shouldn't have involved telling people to crack on once they got a negative test but that future stages would:
Buchan said that Liverpool was pursuing “SMART” testing: systematic, meaningful asymptomatic repeated testing. This has three components: test to protect (where testing is accessible to the whole community but can focus on people at highest risk, such as care home visitors), test to release (to enable people to exit quarantine earlier), and test to enable (to allow a return to activities).

Buchan said they were just completing the pilot’s first phase, which was about making testing accessible to all members of the community. They are about to enter phase 2, which is about targeting areas of high need, such as care home visiting, and release from lockdown.
Some fairly damning quotes from Pollock and Peto in the BMJ piece too:
“The whole thing seems extraordinarily rushed and poorly thought through. It appears they are making it up as they go along, and they have marginalised experts who could have offered help, such as the National Screening Committee.”
An advocate of mass testing, Julian Peto, professor of epidemiology at the London School of Hygiene and Tropical Medicine, told The BMJ, “The pilot scheme in Liverpool has been ridiculous and an absurd way to go about mass testing. It’s missing those in the areas that are most affected.” He added, “They have been inundated with the worried well, and those in the most deprived areas are not coming forward.”

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Re: SARS-CoV-2 testing

Post by shpalman » Mon Dec 07, 2020 6:00 pm

molto tricky

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Re: SARS-CoV-2 testing

Post by shpalman » Mon Dec 07, 2020 7:45 pm

shpalman wrote:
Fri Oct 30, 2020 7:12 pm
Slovakia to test all citizens over age of 10 for coronavirus

That would be 4 million people, to be tested over three weeks, using one of those tests which gives a result in half an hour.
Mass testing for Covid brought down the infection rate in Slovakia by about 60% in one week, say UK researchers – but in combination with tough quarantine rules and other measures that are not being implemented in Liverpool or elsewhere in the UK.

Also, they used a rapid test which worked, and did it properly.
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Re: SARS-CoV-2 testing

Post by badger » Tue Dec 08, 2020 2:12 pm

What's with the lack of privately available antigen testing in UK?

Boots announced in October imminent rollout, followed by some regulatory grumblings, then silence.

If you're going to allow for mixed households at Christmas, then at least get a cheap test out on the high street. In Germany (and Spain? And probably everywhere else?) you can get one for ~20 euro.

Yes, it's not a "green pass", but it can help families with their decision-making.

For families who are going to mix anyway, a cheap, quick test is surely a good idea as it will pick up some (but not all) of the positives, which is more than the none if no test was available (or took too long & too expensive)?

Even better, then, for those who are isolating for a week or so before mixing (between schools breaking up and Xmas mixer) who can test just before.

What am I missing? Why the f.ck allow for mixing/temporary list of restrictions but deny that population cheap testing?

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Re: SARS-CoV-2 testing

Post by shpalman » Tue Dec 08, 2020 2:25 pm

The private clinic that I went to yesterday for a swab says it doesn't offer the rapid tests because it doesn't consider them trustworthy enough.

But then there appear to be private clinics doing covid testing around here in Lombardy, such that I could walk to one. This doesn't seem to be the case in the UK unless you happen to live in the right part of London, or you pretend to have symptoms such that you can get a Serco test.

The €87 I paid was considerably less than it generally costs in the UK to get a swab kit which you're supposed to do yourself at home and then post back - especially if you need it to actually be processed within a finite time window - which is what I did before I came back to Italy. Italy won't even consider DIY swab kits like this to be valid for the purposes of the inter-region travel rules though.
molto tricky

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Re: SARS-CoV-2 testing

Post by badger » Tue Dec 08, 2020 2:46 pm

PCR I think is needed for "fit to fly" here in UK, and private ones widely available around the 130 quid mark (including Boots).

Antigen not trustworthy in some instances, for sure, but useful in others. That is, if you're clear about level of trust and can communicate risk accordingly.

Am not suggesting they replace PCR for "fit to fly", or for when people with symptoms need testing, to be clear!

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Re: SARS-CoV-2 testing

Post by Bird on a Fire » Tue Dec 08, 2020 2:50 pm

The new rules for international arrivals start on 15 December, wherein you no longer have to isolate if you pass a test 5 days after arrival. Tests are apparently going to be €65-120 https://www.bbc.com/news/uk-55052381 which is quite a bit more than in Portugal, where they've been available on the high street since the summer.

Though checking the government website it sounds like tests have to be booked in advance of travel via the government website, so still not available to the general public. https://www.gov.uk/guidance/coronavirus ... nal-travel

I also note that you can't use an NHS test and trace test to end isolation early, so either they're not considered reliable enough or they're trying to make extra money (or both).

It's weird - these tests are definitely available and affordable, so how come the vibrant UK private sector isn't offering them?
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Re: SARS-CoV-2 testing

Post by shpalman » Tue Dec 08, 2020 2:53 pm

Sure, the point was that I couldn't even find rapid tests to buy online.

I think there was only this one which you need to go to one of their testing sites to do and costs £99 anyway.
molto tricky

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Re: SARS-CoV-2 testing

Post by shpalman » Wed Dec 09, 2020 5:40 pm

A CDC report
... identified severe acute respiratory syndrome coronavirus 2 RNA in an oropharyngeal swab specimen collected from a child with suspected measles in early December 2019, ≈3 months before the first identified coronavirus disease case in Italy. This finding expands our knowledge on timing and mapping of novel coronavirus transmission pathways.
As participants in Italy’s Measles and Rubella Network, a sensitive case-based surveillance system, we observed in Milan during late autumn 2019 cases of suspected measles in patients who eventually tested negative for measles. We therefore retrospectively explored a possible etiologic involvement of SARS-CoV-2 in these non–measles-linked rash cases.
One oropharyngeal swab specimen tested positive. The amplicon was sequenced by using Sanger technology, resulting in a sequence of 409 bp. Sequence analysis performed by using BLAST showed 100% identity to the reference sequence Wuhan-HU-1 (GenBank accession no. NC_045512.2) as well as to sequences of other SARS-CoV-2 strains circulating worldwide at a later stage; therefore, accurately determining the origin of the identified strain was not possible. The specimen was confirmed as positive by repeated amplification and sequencing, and all other specimens were repeatedly negative. The sequence (SARS-CoV-2_Milan_Dec2019 [GenBank accession no. MW303957]) was identified in a specimen collected from a 4-year-old boy who lived in the surrounding area of Milan and had no reported travel history. On November 21, the child had cough and rhinitis; about a week later (November 30), he was taken to the emergency department with respiratory symptoms and vomiting. On December 1, he had onset of a measles-like rash; on December 5 (14 days after symptom onset), the oropharyngeal swab specimen was obtained for clinical diagnosis of suspected measles. This patient’s clinical course, which included late skin manifestations, resembles what has been reported by other authors; maculopapular lesions have been among the most prevalent cutaneous manifestations observed during the COVID-19 pandemic, and several studies have noticed a later onset in younger patients (7).
molto tricky

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Re: SARS-CoV-2 testing

Post by jimbob » Sun Dec 13, 2020 12:32 am

Have you considered stupidity as an explanation

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Re: SARS-CoV-2 testing

Post by jimbob » Sun Dec 13, 2020 9:04 pm

On the "Oh but the rise in cases is driven by false positives" narrative

Image

If that were the case, then the positivity rate for symptomatic and asymptomatic cases in England would be in tandem - data from the week 50 report for England here:

https://www.gov.uk/government/statistic ... ce-reports
Have you considered stupidity as an explanation

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Re: SARS-CoV-2 testing

Post by badger » Tue Dec 15, 2020 7:53 am

A thread on Test to Fly (which starts today) problems.

https://mobile.twitter.com/RajeshThind/ ... 8109430784

Worth reading to see a surprising name crop up as one of the govt contracted companies.

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Re: SARS-CoV-2 testing

Post by sTeamTraen » Tue Dec 15, 2020 12:28 pm

badger wrote:
Tue Dec 15, 2020 7:53 am
Worth reading to see a surprising name crop up as one of the govt contracted companies.
Sorry, I give up. Can you Spoiler it or something?
Something something hammer something something nail

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Re: SARS-CoV-2 testing

Post by badger » Tue Dec 15, 2020 12:45 pm

sTeamTraen wrote:
Tue Dec 15, 2020 12:28 pm
badger wrote:
Tue Dec 15, 2020 7:53 am
Worth reading to see a surprising name crop up as one of the govt contracted companies.
Sorry, I give up. Can you Spoiler it or something?
Oh, sh.t sorry. Short twitter thread becomes massive mess.

Yes: Dr Lawrence Gerlis, @samedaydoctor one of the nut jobs in the Julia HB and Clare Craig Cabal. Reckons Covid deaths stopped in spring, etc. etc.

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Re: SARS-CoV-2 testing

Post by sTeamTraen » Tue Dec 15, 2020 1:40 pm

badger wrote:
Tue Dec 15, 2020 12:45 pm
sTeamTraen wrote:
Tue Dec 15, 2020 12:28 pm
badger wrote:
Tue Dec 15, 2020 7:53 am
Worth reading to see a surprising name crop up as one of the govt contracted companies.
Sorry, I give up. Can you Spoiler it or something?
Oh, sh.t sorry. Short twitter thread becomes massive mess.

Yes: Dr Lawrence Gerlis, @samedaydoctor one of the nut jobs in the Julia HB and Clare Craig Cabal. Reckons Covid deaths stopped in spring, etc. etc.
So if I wanted a negative test, he might be the person to call. :lol:

Relatedly: On some of the sites in the list I see they have tests you can do at home. Do those count for the 5-day release? If so, isn't there (another) incentive not to push the stick too far up your nose? The only point I can see to a test you do at home is if you really want to know if you're positive, which most people who have been made to quarantine probably have at least some degree of motivated reasoning about.
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Re: SARS-CoV-2 testing

Post by badger » Tue Dec 15, 2020 2:11 pm

sTeamTraen wrote:
Tue Dec 15, 2020 1:40 pm
badger wrote:
Tue Dec 15, 2020 12:45 pm
sTeamTraen wrote:
Tue Dec 15, 2020 12:28 pm


Sorry, I give up. Can you Spoiler it or something?
Oh, sh.t sorry. Short twitter thread becomes massive mess.

Yes: Dr Lawrence Gerlis, @samedaydoctor one of the nut jobs in the Julia HB and Clare Craig Cabal. Reckons Covid deaths stopped in spring, etc. etc.
So if I wanted a negative test, he might be the person to call. :lol:

Relatedly: On some of the sites in the list I see they have tests you can do at home. Do those count for the 5-day release? If so, isn't there (another) incentive not to push the stick too far up your nose? The only point I can see to a test you do at home is if you really want to know if you're positive, which most people who have been made to quarantine probably have at least some degree of motivated reasoning about.
:lol:
I don't know re home test for Test & Release, but yes, it's a worry. It's part of a bigger worry for me having been through the testing process a few times for me and small kids, just how hard it is to follow the nose and throat swabbing procedure to the letter. Though in this case no one can get a test from the companies that have been mandated to provide a certificate...

With the Boots antigen test that they announced but PHE seem to have stopped and/or delayed at least there would be trained staff taking the swabs.

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Re: SARS-CoV-2 testing

Post by shpalman » Tue Dec 15, 2020 9:40 pm

molto tricky

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Re: SARS-CoV-2 testing

Post by jimbob » Tue Dec 22, 2020 4:22 pm

https://www.theguardian.com/world/2020/ ... racy-fears

No surprise there:
The government has shelved plans to open rapid-turnaround coronavirus test centres across England over Christmas amid concerns from public health experts about the accuracy of their results, the Guardian has learned.
Have you considered stupidity as an explanation

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Re: SARS-CoV-2 testing

Post by shpalman » Fri Dec 25, 2020 5:26 am

molto tricky

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Re: SARS-CoV-2 testing

Post by shpalman » Mon Jan 11, 2021 7:04 pm

COVID‐19 related dermatosis in November 2019. Could this case be Italy’s patient zero?

https://doi.org/10.1111/bjd.19804
In November 2019, a 25-year-old woman presented with urticarial plaque-like dermatosis on the arms (Fig. A). The only systemic symptom she complained was a mild sore throat. A punch biopsy showed a dense perivascular and periglandular infiltration. We suspected “lupus erythematosus tumidus”. PCR swab not performed.
Don't they know it's never lupus?

With something called RNA-FISH analysis, they claim to have detected viral RNA; RT-PCR didn't work.
molto tricky

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Re: SARS-CoV-2 testing

Post by Woodchopper » Mon Jan 11, 2021 8:41 pm

shpalman wrote:
Mon Jan 11, 2021 7:04 pm
COVID‐19 related dermatosis in November 2019. Could this case be Italy’s patient zero?

https://doi.org/10.1111/bjd.19804
In November 2019, a 25-year-old woman presented with urticarial plaque-like dermatosis on the arms (Fig. A). The only systemic symptom she complained was a mild sore throat. A punch biopsy showed a dense perivascular and periglandular infiltration. We suspected “lupus erythematosus tumidus”. PCR swab not performed.
Don't they know it's never lupus?

With something called RNA-FISH analysis, they claim to have detected viral RNA; RT-PCR didn't work.
I call a false positive like all the other early European cases.

This extensive research in Wuhan found that symptoms in the first known case began on 1 December 2019.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159299/

We can also trace the evolution of the virus from its beginning in Wuhan and its spread to Europe.

There wasn’t an Italian outbreak in December 2019.

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Re: SARS-CoV-2 testing

Post by Gfamily » Fri Feb 05, 2021 4:44 pm

Has anyone had a PCR Home testing kit recently?
How much of the 'liquid' was in the sample receiving tube?

At the start of the week I reported a slight ringing in my ears on the Covid Zoe app. Next day I got an email suggesting that although this isn't a 'red flag symptom' for Covid, they would like to invite me to take a PCR home test as part of their study.

This is the second time I've had one of these, the first being back in May (negative result).

The first time, I recall there being no more than about a cm of the liquid in the bottom of the tube; whereas this time the tube was about half full.

What's it been for others?
My avatar was a scientific result that was later found to be 'mistaken' - I rarely claim to be 100% correct
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Meta? I'd say so!

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Re: SARS-CoV-2 testing

Post by shpalman » Mon Feb 08, 2021 11:51 am

molto tricky

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