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 » Fri Jun 19, 2020 12:11 pm

The first was the presense of viral RNA in waste water indicates that the virus might have been circulating in Milan and Turin back in December: https://medicalxpress.com/news/2020-06- ... ember.html

The second, from the director of the Mario Negri Pharmacological Institute, Giuseppe Remuzzi, is that it's being noted that more PCR cycles are necessary in order to detect the virus from some of the latest swabs, such that they are suggesting that these subjects are not even contagious so could probably be classified as negative.

Something in not-very-well-written English: https://www.web24.news/u/2020/06/the-ne ... gious.html
“there are now cases of positivity with a very low, non-contagious viral load. They call them contagions, but they are buffer positive people.

“We conducted a study on 133 Mario Negri researchers and 298 Brembo employees. In all, forty positive buffer cases – explains Remuzzi in an interview with Corriere della Sera – But the positivity of these buffers emerged only with very amplification cycles high, between 34 and 38 cycles, which correspond to less than ten thousand copies of viral RNA. Commenting on the data that is provided every day is useless, because it deals with positivity that has no effect in real life.”
molto tricky

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Re: SARS-CoV-2 testing

Post by Woodchopper » Wed Jun 24, 2020 7:45 pm

It looks like there’s been an age shift in US positive US tests. Average age has decreased. Which would explain why the increasing numbers of cases hasn’t been followed increasing deaths.

See here https://twitter.com/dkthomp/status/1275 ... 15968?s=21

https://twitter.com/nataliexdean/status ... 06274?s=21

Looks like there has been an increase in hospital admissions in some states:

https://twitter.com/jburnmurdoch/status ... 49953?s=21

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Re: SARS-CoV-2 testing

Post by FlammableFlower » Wed Jun 24, 2020 8:07 pm

shpalman wrote:
Fri Jun 19, 2020 12:11 pm
The first was the presense of viral RNA in waste water indicates that the virus might have been circulating in Milan and Turin back in December: https://medicalxpress.com/news/2020-06- ... ember.html

The second, from the director of the Mario Negri Pharmacological Institute, Giuseppe Remuzzi, is that it's being noted that more PCR cycles are necessary in order to detect the virus from some of the latest swabs, such that they are suggesting that these subjects are not even contagious so could probably be classified as negative.

Something in not-very-well-written English: https://www.web24.news/u/2020/06/the-ne ... gious.html
“there are now cases of positivity with a very low, non-contagious viral load. They call them contagions, but they are buffer positive people.

“We conducted a study on 133 Mario Negri researchers and 298 Brembo employees. In all, forty positive buffer cases – explains Remuzzi in an interview with Corriere della Sera – But the positivity of these buffers emerged only with very amplification cycles high, between 34 and 38 cycles, which correspond to less than ten thousand copies of viral RNA. Commenting on the data that is provided every day is useless, because it deals with positivity that has no effect in real life.”
It's interesting, in that it presents a scenario where levels aren't high enough for it to "break out" and be blatant to healthcare professionals but bubbling along as an "odd flu" until finally it gets to a high enough level.

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shpalman
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Re: SARS-CoV-2 testing

Post by shpalman » Wed Jun 24, 2020 8:57 pm

I think the cases in which a high number of PCR cycles are required are basically people who've beaten the virus and are just excreting non-viable bits of it.
molto tricky

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Re: SARS-CoV-2 testing

Post by jimbob » Wed Jun 24, 2020 9:10 pm

FlammableFlower wrote:
Wed Jun 24, 2020 8:07 pm
shpalman wrote:
Fri Jun 19, 2020 12:11 pm
The first was the presense of viral RNA in waste water indicates that the virus might have been circulating in Milan and Turin back in December: https://medicalxpress.com/news/2020-06- ... ember.html

The second, from the director of the Mario Negri Pharmacological Institute, Giuseppe Remuzzi, is that it's being noted that more PCR cycles are necessary in order to detect the virus from some of the latest swabs, such that they are suggesting that these subjects are not even contagious so could probably be classified as negative.

Something in not-very-well-written English: https://www.web24.news/u/2020/06/the-ne ... gious.html
“there are now cases of positivity with a very low, non-contagious viral load. They call them contagions, but they are buffer positive people.

“We conducted a study on 133 Mario Negri researchers and 298 Brembo employees. In all, forty positive buffer cases – explains Remuzzi in an interview with Corriere della Sera – But the positivity of these buffers emerged only with very amplification cycles high, between 34 and 38 cycles, which correspond to less than ten thousand copies of viral RNA. Commenting on the data that is provided every day is useless, because it deals with positivity that has no effect in real life.”
It's interesting, in that it presents a scenario where levels aren't high enough for it to "break out" and be blatant to healthcare professionals but bubbling along as an "odd flu" until finally it gets to a high enough level.
Do you mean in the population, or in the individual?
Have you considered stupidity as an explanation

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Re: SARS-CoV-2 testing

Post by FlammableFlower » Wed Jun 24, 2020 10:15 pm

Had originally been thinking on a population level - whether, essentially by chance, R was low, so it was about in the population but hadn't reached a sufficient level. But that's pure speculation on my part...

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Re: SARS-CoV-2 testing

Post by jimbob » Wed Jun 24, 2020 11:28 pm

FlammableFlower wrote:
Wed Jun 24, 2020 10:15 pm
Had originally been thinking on a population level - whether, essentially by chance, R was low, so it was about in the population but hadn't reached a sufficient level. But that's pure speculation on my part...
Well that is consistent with the superspreaders being more important than with, say flu.

Most people won't infect anyone else, but there's a chance one might infect dozens.
Have you considered stupidity as an explanation

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Re: SARS-CoV-2 testing

Post by Woodchopper » Sun Jun 28, 2020 10:33 am

Spanish virologists have found traces of the novel coronavirus in a sample of Barcelona waste water collected in March 2019, nine months before the COVID-19 disease was identified in China, the University of Barcelona said on Friday.
https://www.reuters.com/article/us-heal ... SKBN23X2HQ

If true that would be extraordinary.

But as mentioned here, it looks like a false positive combined with flaws in the method may be a more likely explanation.
https://scienceintegritydigest.com/2020 ... na-sewers/

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Re: SARS-CoV-2 testing

Post by headshot » Mon Jun 29, 2020 9:54 pm

I’m taking part n the Zoe/King’s College symptom tracker app and reported a sore throat late last week (I suspect pollen) and today got an email from them asking me to go for a test.

Booked at test at the local drive thru. Went there and back in an hour.

It was a self-administered test and I had to swab my throat and nose, it only said to push into the nose about 2.5cm. I’d heard stories of it going in much further than that. Very specifically it said to push until resistance but not to be uncomfortable. Anyway, I shoved it in until it hit something. I reckon there’ll be a lot of duff self-tests.

Results in 2-3 days.

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Re: SARS-CoV-2 testing

Post by Squeak » Tue Jun 30, 2020 4:51 am

I'll add an Antipodean report of covid testing. I woke up with a sore throat and sniffles this morning - the sort of thing that you couldn't justify as a reason for a day off in any ordinary times.

A quick call to the state health authority this morning to report my illness. 2 hours later, they called back and gave me an appointment in an hour for drive-through testing. I went down, was there for ten minutes, where I got ticked off a couple of lists and had my throat and nose swabbed on both sides (presumably that counts as four tests, if you're counting Matt Hancock stylee). There is no way I could have performed that test with the thoroughness they did. My head was rammed against the headrest as I tried to avoid gagging and then having my sinuses scraped, and my eyes went bright red and I coughed at the poor health worker who was testing me. It was quite remarkably unpleasant and my nose is still irritated half an hour later.

Then, a tissue, a pamphlet, and home to try to keep my distance from Calliope until my results come back in 24-48 hours.

For context, no new cases in my state in almost two months and they're testing ~650 people/day, so the odds of it being anything other than ordinary germs from the small kids I saw (but didn't touch) on Saturday are minuscule.

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Re: SARS-CoV-2 testing

Post by headshot » Tue Jun 30, 2020 8:33 am

Got my result back already. Negative.

Can’t help but think that I and many others who are self-administering tests aren’t doing it properly.

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Re: SARS-CoV-2 testing

Post by sTeamTraen » Tue Jun 30, 2020 5:26 pm

Squeak wrote:
Tue Jun 30, 2020 4:51 am
I'll add an Antipodean report of covid testing. I woke up with a sore throat and sniffles this morning - the sort of thing that you couldn't justify as a reason for a day off in any ordinary times.

A quick call to the state health authority this morning to report my illness. 2 hours later, they called back and gave me an appointment in an hour for drive-through testing.
Given that (AFAIK) neither a sore throat nor sniffles are common symptoms of COVID-19 (fingers crossed for yoU!), this suggests that they must have built up a lot of testing capacity. Back in March there were stories from the UK and Spain (and probably many other places) of people who had slam-dunk symptoms (fever, dry coughing for several days, loss of sense of taste) being told to just stay at home and ride it out, with no tests available.
Careering along in my creosote car

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Re: SARS-CoV-2 testing

Post by Squeak » Tue Jun 30, 2020 5:43 pm

sTeamTraen wrote:
Tue Jun 30, 2020 5:26 pm
Squeak wrote:
Tue Jun 30, 2020 4:51 am
I'll add an Antipodean report of covid testing. I woke up with a sore throat and sniffles this morning - the sort of thing that you couldn't justify as a reason for a day off in any ordinary times.

A quick call to the state health authority this morning to report my illness. 2 hours later, they called back and gave me an appointment in an hour for drive-through testing.
Given that (AFAIK) neither a sore throat nor sniffles are common symptoms of COVID-19 (fingers crossed for yoU!), this suggests that they must have built up a lot of testing capacity. Back in March there were stories from the UK and Spain (and probably many other places) of people who had slam-dunk symptoms (fever, dry coughing for several days, loss of sense of taste) being told to just stay at home and ride it out, with no tests available.
Yup. Australia is testing anyone who even looks like they might have any respiratory illness. We're presumably going to get some great data on colds out of this. Tasmania's testing 650 people a day and haven't had a positive covid result in two months. Even at the start of the outbreak, our positive rate was 2-3%, at a time when they were rationing tests to recent travellers and their contacts and a time that the UK and US (esp. New York) were reporting numbers like 35-60% positive tests. If you want to know what the infection fatality rate is like in a non-overwhelmed rich western country with an average aged population and high obesity rates, Australia's a good place to look. The data are delicious and fairly comprehensive.

Personally, I'm not at all worried that I might have it but I don't want to get tested again and I didn't much enjoy having to text people and apologise for endangering their ability to see elderly family members this week. Therefore, I'm staying away from small germy children until at least summer. They might be cute but they are also pretty gross.

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Re: SARS-CoV-2 testing

Post by jimbob » Tue Jun 30, 2020 6:26 pm

Squeak wrote:
Tue Jun 30, 2020 5:43 pm
sTeamTraen wrote:
Tue Jun 30, 2020 5:26 pm
Squeak wrote:
Tue Jun 30, 2020 4:51 am
I'll add an Antipodean report of covid testing. I woke up with a sore throat and sniffles this morning - the sort of thing that you couldn't justify as a reason for a day off in any ordinary times.

A quick call to the state health authority this morning to report my illness. 2 hours later, they called back and gave me an appointment in an hour for drive-through testing.
Given that (AFAIK) neither a sore throat nor sniffles are common symptoms of COVID-19 (fingers crossed for yoU!), this suggests that they must have built up a lot of testing capacity. Back in March there were stories from the UK and Spain (and probably many other places) of people who had slam-dunk symptoms (fever, dry coughing for several days, loss of sense of taste) being told to just stay at home and ride it out, with no tests available.
Yup. Australia is testing anyone who even looks like they might have any respiratory illness. We're presumably going to get some great data on colds out of this. Tasmania's testing 650 people a day and haven't had a positive covid result in two months. Even at the start of the outbreak, our positive rate was 2-3%, at a time when they were rationing tests to recent travellers and their contacts and a time that the UK and US (esp. New York) were reporting numbers like 35-60% positive tests. If you want to know what the infection fatality rate is like in a non-overwhelmed rich western country with an average aged population and high obesity rates, Australia's a good place to look. The data are delicious and fairly comprehensive.

Personally, I'm not at all worried that I might have it but I don't want to get tested again and I didn't much enjoy having to text people and apologise for endangering their ability to see elderly family members this week. Therefore, I'm staying away from small germy children until at least summer. They might be cute but they are also pretty gross.
Well fancy that:

https://virologydownunder.com/rhinoviru ... riumphant/

Well worth following him on Twitter too

https://twitter.com/MackayIM/status/1277557437420244994
Have you considered stupidity as an explanation

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Re: SARS-CoV-2 testing

Post by Bird on a Fire » Tue Jun 30, 2020 9:16 pm

The Lancet: High COVID-19 testing rate in Portugal
A sense of civic duty and mutual confidence between scientists and health authorities played a role in Portugal high testing rates. Marcia Triunfol reports.

What do a flight attendant, an algebra professor, a 21-year-old man dreaming to be a pilot, and a scientist working with malaria have in common? They have joined the volunteers task force created in Portugal at the beginning of the COVID-19 outbreak to increase the country's capacity to do RT-PCR tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). On March 2, the country testing capacity was around 1500 tests per day. According to Maria Mota, a malaria researcher and the executive director of Instituto de Medicina Molecular (IMM), which is part of the Lisbon University, this scenario would soon change. “I saw Graça Freitas, the director of the Directorate-General of Health, on TV talking about the country limited capacity to test people and then I thought…wait a minute, it is just a PCR!”.

On the same night Maria Mota sent an email to the Ministry of Health stating that her institute had capacity to do the tests. A few minutes later she got a call back. “From this first contact to actually starting testing patients' samples for COVID-19 took only a couple of days”, recalls Mota.

On Mar 13, two researchers from IMM, Vanessa Zuzarte Luis and Miguel Prudêncio, plus Judite Costa, a lab manager, met with doctors at Santa Maria Hospital, the University Hospital of Lisbon University, who suddenly had an overwhelming demand for COVID-19 tests. “Initially we would help with RNA extraction only, but we soon realised that the help they needed was way beyond that”, says Zuzarte Luís. The group created the PCR protocol based on that of the US Centers for Disease Control and Prevention, designed primers and probes in-house using reagents available in Portugal, had the protocol validated by Instituto Ricardo Jorge, a reference state-owned laboratory in the country and the first to do the test, and set up a testing pipeline for COVID-19, all in a matter of days. Portugal has done more than 900 000 tests since March, the beginning of the outbreak, and according to the site Our World in Data, it is among the ten countries doing the highest number of daily tests per thousand individuals (85·7 tests per thousand people as of Jun 2). Of the 91 labs in the country currently testing for COVID-19, 25 are in universities and scientific centres.

“It was clear that this fight would require many people”, declared José Matos, president of Ordem dos Biólogos, a professional association for biologists and other related areas. Knowing that research labs were in lockdown, early on the association sent out a request to all its associates, hoping to recruit volunteers that could operate the many idle PCR machines and do other tasks as needed. In 24 hours, 2300 people had replied. “I was moved when I saw how many people were willing to collaborate!”, confessed Matos.

At the COVID Testing Centre (CTC) at Lisbon University, the group of volunteers included individuals like Ana Caetano, a flight attendant now in lay-off who previously had worked in a lab for more than 10 years. “I worked all my life and didn't want to stay home for months waiting for this to end. Having to leave home everyday to coordinate one of the stations in the PCR pipeline was what kept me going.” Tiago Rosa, a 21-year-old man studying to be a pilot, also heard the call. “I could have stayed home playing video-games, but I wanted to help instead.” Rosa has been responsible for creating bar codes for testing tubes and for implementing management programmes to improve CTC's capacity. For Maria João Gouveia, an algebra professor at Lisbon University, joining the group was a matter of civic duty. “They needed someone with mathematical thought to organise the information related to the materials used, orders, stocks, invoices and that has been my contribution.” According to Ricardo Dias, the CTC coordinator, the initiative recruited 300 volunteers, many through the call sent by Ordem dos Biólogos. Volunteers work 4 hours per day doing around 400 PCR tests daily. “We built a centre from scratch and our goal is to have a resilient structure that can rapidly provide answers to society in emergencies like this”. In the north of Portugal, at University of Porto's i3S scientific institute, more than 150 volunteers have been doing around 350 tests everyday.
More at link.

My university has been running a testing centre as well.

The UK could so, so easily have done something like this, and it would have fit perfectly with the all-mucking-in-together spirit-of-the-Blitz keep-calm-and-carry-on shtick Johnson has been trying to push (when he hasn't been gasping for breath in an ICU due to his own fecklessness).
Born at 356.32 ppm CO2 #ShowYourStripes

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Re: SARS-CoV-2 testing

Post by Squeak » Tue Jun 30, 2020 10:48 pm

jimbob wrote:
Tue Jun 30, 2020 6:26 pm

Well fancy that:

https://virologydownunder.com/rhinoviru ... riumphant/

Well worth following him on Twitter too

https://twitter.com/MackayIM/status/1277557437420244994
Thanks! That blog post is exactly the sort of information I was hoping would come from this mass testing approach. It's a little worrying to consider what things would be like if SARS-COV-2 weren't really disrupted by handwashing, like some of the viruses still in circulation...

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Re: SARS-CoV-2 testing

Post by Squeak » Wed Jul 01, 2020 11:22 am

It took just 27 hours to get my text message confirming that I don't have covid. Quelle surprise.

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Re: SARS-CoV-2 testing

Post by jimbob » Wed Jul 01, 2020 12:22 pm

Squeak wrote:
Wed Jul 01, 2020 11:22 am
It took just 27 hours to get my text message confirming that I don't have covid. Quelle surprise.
That's nothing. I saw on Twitter, someone in the UK say that they got their negative test result before even requesting, let alone receiving a test.
Have you considered stupidity as an explanation

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Re: SARS-CoV-2 testing

Post by Squeak » Wed Jul 01, 2020 11:14 pm

jimbob wrote:
Wed Jul 01, 2020 12:22 pm
Squeak wrote:
Wed Jul 01, 2020 11:22 am
It took just 27 hours to get my text message confirming that I don't have covid. Quelle surprise.
That's nothing. I saw on Twitter, someone in the UK say that they got their negative test result before even requesting, let alone receiving a test.
Geez. I should complain to the Tasmanian Health Authorities. How slack are they?!

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Re: SARS-CoV-2 testing

Post by Woodchopper » Thu Jul 02, 2020 2:03 pm

Deloitte who do the tests is not required to report results to Public HEalth England: https://twitter.com/justinmadders/statu ... 2561153024

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Re: SARS-CoV-2 testing

Post by Woodchopper » Thu Jul 02, 2020 4:59 pm


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Re: SARS-CoV-2 testing

Post by EllyCat » Thu Jul 02, 2020 7:54 pm

headshot wrote:
Tue Jun 30, 2020 8:33 am
Can’t help but think that I and many others who are self-administering tests aren’t doing it properly.
MrCat went for a test today and it was self-administered...but he pointed out since the place was staffed by the army, they aren’t going to be any more qualified to take a swab than he is and at least if he damages himself, he can’t sue :roll:

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Re: SARS-CoV-2 testing

Post by Squeak » Fri Jul 03, 2020 7:20 am

My GP phoned today to chat about my covid result and she told me that Australia is switching to just a nasal swab, rather than the horrible nasopharyngeal swab, for children because it's almost as accurate and because it's easier to convince a kid to get tested a second time if it's a nicer experience. She didn't know the exact figures but she thought it was only a few percent lower. And it's presumably less likely to result in the recipient spluttering in the face of the poor healthcare worker.

So, enjoy your nicer tests that are almost as good. :)

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Re: SARS-CoV-2 testing

Post by headshot » Fri Jul 03, 2020 9:44 am

I’m due to receive a test kit from Imperial College that is asking me to do a nose and throat swab as well as a saliva spit test.

https://www.ipsos.com/ipsos-mori/en-uk/ ... -test-faqs

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Re: SARS-CoV-2 testing

Post by badger » Fri Jul 03, 2020 11:38 am

Woodchopper wrote:
Thu Jul 02, 2020 4:59 pm
Some new UK testing data: https://twitter.com/jburnmurdoch/status ... 38561?s=20
Thanks, very useful.

Most London boroughs are up to 21 June rather than 30 June, but even so I'm amazed at how low the numbers are in the capital. I really thought we'd see more of a bounce as people went back to work, school and public transport was used more. Also given the amount of mass meetings that have occurred.

It'll be interesting to see the change in the coming weeks.

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