Coronavirus

[Giles]

very enlightening post; thanks monkie

[L19MUD]

9 hours ago, reb78 said:

Its a shame this thread was ever started on here. Its not the place for it.

I understand where you are coming from but I have found this thread very interesting. There is a diverse group of people on this thread spread in both the UK and abroad and it has been interesting to see how things are affecting others differently. I hold the opinion of a lot of members on here in high regard (certainly more so that a random person down the pub) and we have some people with very relevant experience that have provided so great insights such as Monkie.

[landroversforever]

1 hour ago, L19MUD said:

I understand where you are coming from but I have found this thread very interesting. There is a diverse group of people on this thread spread in both the UK and abroad and it has been interesting to see how things are affecting others differently. I hold the opinion of a lot of members on here in high regard (certainly more so that a random person down the pub) and we have some people with very relevant experience that have provided so great insights such as Monkie.

Exactly my thoughts too. Whilst I've got experience of working with surface contamination, I haven't got knowledge like Monkie. I think it's a good discussion to have, I'm certainly finding it an interesting one.

[Bigj66]

On 9/22/2020 at 11:18 PM, monkie said:

Again, please let me shed some light on the true situation regarding testing in hospital labs by removing any current politics. I work for one of the largest clinical diagnostics companies in the PCR section.

The virus is detected (from swabs taken from the nose and throat) by PCR. Not all hospital labs are set up to do this specialist test. Let me assure you that the company I work for (and others) and NHS England have been putting additional capacity for this type of testing in place all throughout the summer as well additional biomedical scientist staff being retrained from other areas of pathology to do this testing.

Most labs can only process a few thousand tests a day - a limitation of the technique of PCR. The PCR test is not quick but it is highly sensitive and specific. It can take anywhere between 6 and 2 hours from sample in to result out. This is because the sample itself can not undergo PCR straight away. Firstly the sample must be deactivated by heat or chemical treatment so it is safe for the lab staff to handle. This deactivated sample must be extracted - that is the virus (if present) chemically broken open (lysis) to release the RNA and then purified to remove it from substances that may interfer with the test. This "extracted" sample then can undergo the PCR test. If an analyser goes down (they are not designed to run 24/7 for months on end doing just one type of test) then the lab find it very difficult to catch up. They cannot accept more samples and therefore if you require a test you will not be able to get swabbed during this period, other than being offered a swab potentially miles away from your home.

This is what happens at the moment when a hospital lab needs more equipment:

NHS England decide if that lab in that geographical area needs the additional capacity over another area (the instruments and tests are in very limited supply as global demand is massive). The order is placed and it takes between 4-6 weeks to get the instrument shipped, delivered, alteration work to the lab (additional power supply, IT network points, moving walls, shelves benches etc) completed and the instrument placed in the lab. A further week or maybe 2 elapses whilst an engineer (in between dealing with breakdowns elsewhere) to install, calibrate and comission the instrument ready for use. Lab staff then take about 1 week to be trained and evaluate the test (to prove it works in their lab by testing known panels). They then get the green light to use the instrument for clinical diagnostic use. Fortunately it is not possible for any old idiot to set up a lab and start turning our tests, it is quite rightly a heavily regulated environment and a lab cannot just start a new type of test without providing evidence the test is reliably working without contamination or producing false results as a result of the lab staff not using the test and handling the sample correctly.

To run the test, the instruments use >95% Ethanol, lysis buffers, wash buffers, elution buffers, RNase free water, SARS-CoV-2 primer/probes, control material, 1,000s and 1,000s and 1,000s of disposable pipette tips and loads more other consumable plasticwear. If any one of these items is in limited supply then the testing can not run at full capacity and decisions have to be made as to where to send the limited consumables as to best serve the hardest hit areas where testing demand is needed most.

PCR is the gold standard of testing because it looks directly for the viral RNA (or DNA for some other viruses), it can detect as little as <100 bits or copies of viral RNA in 1ml of sample. The rapid tests that are talked about are starting to come through but so far the sensitivity of these tests lags far behind that of PCR which is why they are not being used. Antibody testing is different and is not used to diagnose a current infection. At the moment we don't know what having antibodies to SARS-CoV-2 means exactly so this testing has dropped off. Some people thought if they tested positive for antibodies they were immune so went back to life as normal, making the problem worse.

I hope this illustrates that no matter what your political opinion and no matter who was running the country - nothing regarding testing would be different today in the middle of this pandemic. NHS pathology labs have been shaped by years of policy across several governments to consolidate testing to a few specialist labs (which in many ways makes sense and saves the NHS a lot of money). It is called the Carter review if you are interested and outlined how the NHS could save £0.2 billion by consolidating pathology.

Excellent and very informative post. I wish someone would tell the media this although we should never let the truth get in the way of a good rumour 🙄

I’m interested in this comment “Firstly the sample must be deactivated by heat or chemical treatment so it is safe for the lab staff to handle.”

Can you explain this a bit more please? How does the deactivation process make the sample safe for the lab staff? Can/is this used elsewhere to prevent transmission?

[monkie]

Thank you for the responses to my post. I'm pleased that it has given you an insight into what the media aren't interested in telling the public. I think a news special showing people what the inside of a molecular lab looks like or a day in the life of would be helpful. 

6 hours ago, Bigj66 said:

Excellent and very informative post. I wish someone would tell the media this although we should never let the truth get in the way of a good rumour 🙄

I’m interested in this comment “Firstly the sample must be deactivated by heat or chemical treatment so it is safe for the lab staff to handle.”

Can you explain this a bit more please? How does the deactivation process make the sample safe for the lab staff? Can/is this used elsewhere to prevent transmission?

Good question. You are already (I hope!) doing this in a way.

Firstly for those who aren't sure let's call the virus by its correct name because the media often are not: Covid-19 is the term to used for the disease state or illness not the virus. Covid-19 is caused by the virus SARS-CoV-2 which is severe acute respiratory syndrome - Coronavirus 2. Just how AIDS is the disease but is caused by the virus HIV.

Basically viruses contain their genetic material in a shell (capsid). The capsid contains proteins and a load of other stuff the virus needs do it's job and infect a host. The best way to picture the capsid on SARS-CoV-2 is like a fatty layer. 

If you can open this layer then you have deactivated the virus i.e rendered it unable to function correctly. 

As it is a fatty layer on SARS-CoV-2, soap will do this nicely. This is why it is very important to properly wash your hands as soap will break apart the virus's fatty layer rendering it useless or dead. 

In the lab, because using a molecular technique (PCR) which is used to detect the presence of the virus by amplifying and detecting its nucleic acids (RNA in this case for SARS-CoV-2), it doesn't matter if the virus is dead or alive in terms of the test. 

As respiratory viruses are spread to humans mainly by aerosol, the samples can be easily aerosoled by opening tubes out in the open in the lab to put on the instrument performing the test. For the safety of the lab staff they open the tubes in a special biological safety cabinet and either heat them (not a great method, so isn't often used in the UK) or add something called lysis buffer. Lysis buffer essentially does what soap does and destroys the viruses capsid. This kills the virus but importantly for PCR it does not destroy the RNA which then goes through a clean up process and then the amplification/detection process. 

I hope this detail answers your question? 

[Bowie69]

All good stuff Minnie, and backs up some of my understanding.

One of the things that has intrigued me on the rumour mill, is the suggestion that the current UK spec PCR testing is picking up old, dead, virus that is being expelled by the body. This is leading to many false positives, weeks or months after the host is infectious, or so they say. It is suggested that the tests are overly sensitive, and can detect even fragments of the virus.

Are you able to shed any light on this?

[monkie]

6 minutes ago, Bowie69 said:

All good stuff Minnie, and backs up some of my understanding.

One of the things that has intrigued me on the rumour mill, is the suggestion that the current UK spec PCR testing is picking up old, dead, virus that is being expelled by the body. This is leading to many false positives, weeks or months after the host is infectious, or so they say. It is suggested that the tests are overly sensitive, and can detect even fragments of the virus.

Are you able to shed any light on this?

Yes, you are right as PCR is so sensitive it is important to establish a cut off to the test so it only flags clinically relevant infections. I'm afraid the studies are still ongoing as to where this cut off should be as the tests which usually take months or years to develop were all developed in a few weeks and given emergency FDA clearance. 

There have though been studies on where to take the sample for PCR. Typically in most people with the infection you can detect the virus in a nasopharyngeal swab (the one up your nose) within a few days of infection. After a few weeks post infection the virus is no longer detected in the nose but sometimes can be in a stool sample but not reliably so. 

For a strong, current infection the PCR test should pick up a positive amplification signal in fewer cycles than others. But the test is qualitative, not quantitative so you just get a positive or negative result. Past infections if detected will have a high cycle number. This is why a cut off is established. 

[Bowie69]

Ah, thanks mobile, that helps, also explains the cycles too.

[monkie]

14 minutes ago, Bowie69 said:

Ah, thanks mobile, that helps, also explains the cycles too.

Your autocorrect is running well this morning

With each cycle in PCR the quantity of nucleic acid doubles, the tests have around 40 or 45 cycles usually. The signal has to cross a threshold to be considered positive. The point at which this happens is called the cyclic threshold (ct). The more nucleic acids in the original sample means the signal will cross the threshold for detection earlier (lower cycler number), the lower the ct number the stronger the signal. If the signal crosses the threshold just before the end of the test (high ct) then you have to question the clinical relevance of the result. It could signal contamination or just a very low level of virus present which might signify a past infection. 

[Bigj66]

2 hours ago, monkie said:

Thank you for the responses to my post. I'm pleased that it has given you an insight into what the media aren't interested in telling the public. I think a news special showing people what the inside of a molecular lab looks like or a day in the life of would be helpful. 

Good question. You are already (I hope!) doing this in a way.

Firstly for those who aren't sure let's call the virus by its correct name because the media often are not: Covid-19 is the term to used for the disease state or illness not the virus. Covid-19 is caused by the virus SARS-CoV-2 which is severe acute respiratory syndrome - Coronavirus 2. Just how AIDS is the disease but is caused by the virus HIV.

Basically viruses contain their genetic material in a shell (capsid). The capsid contains proteins and a load of other stuff the virus needs do it's job and infect a host. The best way to picture the capsid on SARS-CoV-2 is like a fatty layer. 

If you can open this layer then you have deactivated the virus i.e rendered it unable to function correctly. 

As it is a fatty layer on SARS-CoV-2, soap will do this nicely. This is why it is very important to properly wash your hands as soap will break apart the virus's fatty layer rendering it useless or dead. 

In the lab, because using a molecular technique (PCR) which is used to detect the presence of the virus by amplifying and detecting its nucleic acids (RNA in this case for SARS-CoV-2), it doesn't matter if the virus is dead or alive in terms of the test. 

As respiratory viruses are spread to humans mainly by aerosol, the samples can be easily aerosoled by opening tubes out in the open in the lab to put on the instrument performing the test. For the safety of the lab staff they open the tubes in a special biological safety cabinet and either heat them (not a great method, so isn't often used in the UK) or add something called lysis buffer. Lysis buffer essentially does what soap does and destroys the viruses capsid. This kills the virus but importantly for PCR it does not destroy the RNA which then goes through a clean up process and then the amplification/detection process. 

I hope this detail answers your question? 

Great explanation, thanks for taking the time.

 

[Peaklander]

Thank you @monkiefor providing further detailed explanations. It's very helpful to read this in the light of so much chatter elsewhere about testing and helps me understand the challenges around providing mass testing.

[monkie]

Also I should mention another thing people are rightly questioning as we are going into winter which is peak season for respiratory viruses: if you have a high temperature, cough, sore throat etc. It isn't necessarily coronavirus. 

True. 

Diagnostic companies are starting to release variants of their SARS-CoV-2 tests on the market that multiplex other targets into a single test so they can detect other common respiratory viruses like Flu A/B, RSV (common in small children), human metapneumovirus and maybe even rhinovirus (common cold). This would be helpful if you test negative for SARS-CoV-2 but positive for something else, it explains your symptoms. Particularly helpful for parents of small children who have to work. If your child is ill and is positive for RSV, it will explain why they are ill and you are fine so good to go to work.

I think it will also increase people's confidence in the test as I think there is some doubt about how good they are if you feel ill but test negative. 

[Stellaghost]

In light of the latest news stay safe guys especially those of you in the worst hit areas regards Stephen

[Bowie69]

Have a good one, if you possibly can... I expect my Christmas to be mostly in the shed.

[Eightpot]

Mrs Eightpot and I have an interesting little challenge to run over the next two days, passing various covid tests, dodging tier restrictions, national lockdowns, borders, getting through airports and trying to avoid the plague to get reunited with my S2a in South Africa and disappearing into the bush with a fridge full of steak & wine, hopefully popping our heads back out in a few weeks to find it's all over 😆  nerve racking watching the restrictions build up hour by hour 😬

[reb78]

50 minutes ago, Eightpot said:

Mrs Eightpot and I have an interesting little challenge to run over the next two days, passing various covid tests, dodging tier restrictions, national lockdowns, borders, getting through airports and trying to avoid the plague to get reunited with my S2a in South Africa and disappearing into the bush with a fridge full of steak & wine, hopefully popping our heads back out in a few weeks to find it's all over 😆  nerve racking watching the restrictions build up hour by hour 😬

Sounds very perfect!! Good luck!

[Happyoldgit]

I had another Covid swab at the local drive through today, standard procedure for anyone having hospital treatment - in my case chemo on Tuesday.

As I kept the A&M team briefed throughout so will now let you all know that I was discharged from hospital a couple of weeks or so ago after being in for nearly a month. I  self admitted suffering from severe stomach pains and unable to keep any food or drink down. The initial diagnosis was bleak, very bleak. However after more investigations, tests etc they came up with a treatment plan that if successful may, may provide a less bleak outlook. May - nothing is guaranteed.

As my immune system is now shot I have to continue to isolate. I've lost a huge amount of weight due to no food and just sips of water for days was  - just IV hydration. They eventually put a permanent PICC line in my arm and then I was able to recieve liquid nutrition 24/7.

So now you know.

All the staff from consultants to nurses, ancillaries, porters, cleaners etc were lovely. 

While in hospital they were Covid testing patients every two days.

Try and have a good Christmas but above all stay safe guys.  

[Mo Murphy]

Try and enjoy Christmas MOG and continue to recover 👍

Best wishes

Mo

[SteveG]

Good luck with the treatment Steve. Every case and person is naturally very different, but my Dad lived with a terminal diagnosis for prostate cancer for 8 years. At first any physical change you start to suspect it may have spread somewhere else and suspecting the worse. After a short while he soon moved into a mode of what will be, will be and started to live again, and even when it spread multiple times he just moved into a mode of fitting the treatments around his life, rather than fitting his and everyone else’s life around the various phases of treatment.

Not saying this is the best way to do it, but it’s remarkable how quickly we can all adapt.

Enjoy Christmas and New Year with your family and friend. My time in the garage will be directly proportional to how cold it is 😉

cheers, Steve 

[Stellaghost]

7 hours ago, Mo Murphy said:

Try and enjoy Christmas MOG and continue to recover 👍

 

All of this from I'm quite sure all of us take care regards LR4X4

[JohnnoK]

9 hours ago, Eightpot said:

Mrs Eightpot and I have an interesting little challenge to run over the next two days, passing various covid tests, dodging tier restrictions, national lockdowns, borders, getting through airports and trying to avoid the plague to get reunited with my S2a in South Africa and disappearing into the bush with a fridge full of steak & wine, hopefully popping our heads back out in a few weeks to find it's all over 😆  nerve racking watching the restrictions build up hour by hour 😬

You should still be OK to get in, but depending when you plan to leave, you may be in lockdown again.

I predict SA will be back to a hard lockdown by mid Jan-early Feb at the very latest.

[Happyoldgit]

3 hours ago, SteveG said:

Good luck with the treatment Steve. Every case and person is naturally very different, but my Dad lived with a terminal diagnosis for prostate cancer for 8 years. At first any physical change you start to suspect it may have spread somewhere else and suspecting the worse. After a short while he soon moved into a mode of what will be, will be and started to live again, and even when it spread multiple times he just moved into a mode of fitting the treatments around his life, rather than fitting his and everyone else’s life around the various phases of treatment.

Not saying this is the best way to do it, but it’s remarkable how quickly we can all adapt.

Enjoy Christmas and New Year with your family and friend. My time in the garage will be directly proportional to how cold it is 😉

cheers, Steve 

Thanks Steve 🙂

Yeah, I'm a pretty pragmatic sort and live by the one day at a time/ what will be will be approach. I'll just have to come to terms with the new me much as I did after the accident I had 30 years ago.

Not sure why I felt the need to spill it all last night, but a lot of us have been here a long time, and its good to share with friends right 🙂

 

 

[monkie]

@Happyoldgit I'm very sorry to hear this. All I can say is I hope 2021 brings much better news for all of us no matter where we are. 

[geoffbeaumont]

@Happyoldgitsorry to hear that Steve 😟 Keep your head up and enjoy what's good in your life. 

[Eightpot]

My old man had to go in recently after an xray for something else showed up a massive tumor covering quite a few necessary bits. Treatment was actually pretty amazing and he seems fine now. Hard work and not something you'd want to trade places for, but the time passes quickly and the future looks better.  Our flights finally got cancelled today so my safari trip and more importantly reunion with my lovely S2a is punted off to another future but can't really moan, maybe I'll put the tent up, have a bbq and paint spots on the cat and not grumble about the heat 🙂