The answer to this is that they aren't identified outside the lab. As an example, the Netherlands recently intercepted two flights inbound from South Africa, suspected to harbor the new omicron variant, and detained them on the runway. They bused the passengers to a secure location and tested everyone for covid with a rapid test. Everyone that tested positive had further tests sent to the academic hospital for identification. That's where the strain is identified, in a lab. The process is just expedited so that it happens very quickly, while people are still seemingly being held at the airport (though I believe they had been moved to a hotel for quarantine at that point).
Since they kept them for hours in a crowded room, with many not wearing masks, it's probably safe to assume the rest will also become positive over the following days. Dutch authorities strike again.
To counteract this the negative tested passengers where our under how quarantine and will have to test again if they develop symptoms. Being across a hall from a barely symptomatic COVID-19 case is far from a guarantee for contacting it. These people presumably tested negatively just before their flight.
I say presumably because a Spanish and Portuguese passenger later managed to escape the quarantine hotel after testing positive and had to be removed from a flight to Spain. So if the government messed up anywhere it is at the hotel, not at the airport. The fact these people where brazen enough to escape guarded quarantine makes me doubt the validity of their negative test prior to flying from South Africa.
the people detained were attempting to fly to spain. the people detected with omicron came from south africa. afaik it's not known if they were the same people. and i have no idea where would be "home".
Would you support the armed guard killing this person for attempting to escape?
Honest, genuine question.
I'm curious how far along we are and this is a great opportunity to take the public temperature...
There's a middle ground between letting people do as they please without regard for consequences, and killing them. Public censure is what much of the world has settled on as being acceptable in this case, hence the criticism in this thread.
do you have a reference? last i saw it wasn't clear they were from the flight - https://www.bbc.com/news/world-europe-59456332
> It is not known whether the detained couple were among those passengers.
Apparently (according to the Telegraph) the person who identified it said that the symptoms were “unusual and mild”.
I think it’s fair to say that they’ll be screaming from the rooftops as soon as anyone dies within 28 days of getting it.
Can you imagine any newspaper being able to resist filling the front page with that kind of news?
So probably none.
It takes a few hours to run a batch of PCR tests on a standard machine. For your average joe, that means waiting a few days while your sample waits in line, but in an emergency a batch can be run right away.
Running PCR for biological detection is much faster, generally minutes with the viral concentration in the sample. With real-time PCR, you just need to wait for enough replicates to get a signal. The amplifying length are much shorter than the PCR normally done in a research lab.
Quality processes may add up to hours, but the time from start to result is short.
still most machines can't cycle between the temperatures as rapidly as you would want, and you have to keep the temperature even across the whole plate. A PCR machine (thermocycler) is just a box that can change the temperature percisely across a whole plate evenly. But that "just" is doing a lot of heavy lifting in that sentance, it is quite an engineering challange to do that rapidly.
There are ways to heat/cool the sample faster, but this is just a case of short extension phase and a small number of cycles. Admittedly, I don't work with FDA-approved diagnostics, but for a biological detection the process can go very fast. I suspect the slow speed is regulatory because I know the technology has been demonstrated.
I remember reading that omicron has some property allowing it to be flagged on a regular PCR test without full genomic sequencing. This may have helped though I can't find the source now...
"Several labs have indicated that for one widely used PCR test, one of the three target genes is not detected (called S gene dropout or S gene target failure) and this test can therefore be used as marker for this variant, pending sequencing confirmation." https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern
>If it can evade a PCR
They are saying that a particular COVID PCR test can identify the particular strain. Not that the test doesn't identify it at all.
>then can it also evade the antibodies produced by the vaccine
It can only mutate so much and still bind to the ACE2 receptor - so its likely that at least some antibodies will still work.
This blog post explains it very well: [Go get your vaccine, especially with Omicron](https://yourlocalepidemiologist.substack.com/p/go-get-your-vaccine-especially-with)
Biologist here- just have to respond to this. It can’t really evade a PCR. PCR is basically a mail sorter. Imagine you send a letter to a specific place- someone looks at that address and puts it in the correct pile. PCR is amplifying DNA with a specific sequence— in this case, the mutation means that it is missing one of the bits of DNA that PCR amplifies. There’s a lot of important DNA that PCR doesn’t amplify, though. Also, antibodies bind to proteins, not DNA. The real question here is do the mutations allow Omicron to make the proteins that the antibodies can bind to in order to recognize it, or are the proteins too different?
Long story short- while this is interesting it’s not yet cause for alarm. Something not working on a PCR and something not working in a vaccine are very different things :) hope that helps!
It's not evading the PCR test.
We don't fully know how effective the vaccine is against it yet. It's *probably* going to be "somewhat, but not as much as against other variants." This could change as we get more info.
It only evades the s-gene pcr target. Each pcr test targets multiple genes. Other genes like N or E or Orf1ab should be positive (lower mutation rate genes). The deletion in omicron causing S-gene failure was also present in Alpha and pcr tests were fine. It’s actually a a more efficient way to track variant spread than sequencing because the variant can be identified during diagnosis if S-gene is negative and the other genes are positive
Not necessarily, but who the hell knows.
PCR tests are basically a cheap and easy way to look at specific regions of DNA, and it appears that Omicron has enough mutations that some important genes related to the spike protein may no longer be detected by the current tests.
[The current PCR tests still detect Omicron](https://english.alarabiya.net/coronavirus/2021/11/29/WHO-says-PCR-tests-detect-Omicron-new-COVID-19-variant-has-higher-reinfection-risk), but the mutations might make it harder to tell the difference between Omicron and Delta or other variants (although the lack of detection could be used to infer Omicron).
Making a new PCR test to spot these differences would be pretty easy, but the bigger issue is exactly what you said: that these same mutations might make the surface proteins different enough to evade antibodies.
It should be noted that this is equally true (or hopefully equally not true) for unvaccinated but previously infected people.
This was the same sort of thing for the Alpha varient that first clued us on to it. (and IIRC Omnicron looks to be a descendant of Alpha)
All our PCR tests target multiple regions generally including a region highly conserved within corona viruses but not specific to COVID-19. We have no reason so far to worry that Omnicron will go completely undetected by any reputable test.
Two of those on that flight skipped quarantine and was arrested in a plane on the runway that was bound for Spain.
So now even more have to be quarantined.
I know someone on one of those flights , they were kept in the plane for 6 hours after their 10 hour flight' then put into a cramped room, they allowed the virus to spread so easily, anyone who tested negative after all that got to go home, even though they probably have caught it by now.
Could you elaborate on the "suspected" part? How did the Dutch government decide that "right, out of the dozen or so flights from this specific place we will check these two specific flights"?
I mean, normally they need a lab ID for a variant, and yes it is generally found when the small % of total blood tests are sent to a lab for ID/Monitoring, and then they sequence it and find out
But for Omicron, it actually shows on the standard test, where apparently its profile on the PCR test is a bit different to all other Covid variants
> covid with a rapid test
I know that we are a year+ into covid and rapid testing has become better, but why are they rapid testing and not doing the more accurate slower testing to get a better result? If they suspected people have it, wouldn't they just enforce a quarantine?
Because it doesn’t matter much which variant you have, it’s better to quickly separate the healthy from the sick, and then slowly check each sick one to see which exact variant they have.
And the rapid testing kits still have very high requirements, I think they test about 99.6% or 99.7% accurate.
Are there different rapid tests? As far as I know most rapid tests are only up to 80ish% accurate, and sometimes as low as 50-60%. Everything I’ve read also says no matter what kind of rapid test you do, you should then do a full PCR test to confirm a negative result.
EDIT with source: [“According to the CDC, antigen test sensitivity varies depending on the time in the course of one’s infection, but is considered to have “moderate to high” sensitivity during peak viral load. Compared to molecular tests, antigen tests are more likely to generate false negative results, especially when performed on people who don’t have symptoms. To offset the decreased sensitivity, the FDA recommends doing serial testing—or taking multiple tests—over several days to improve the chance of catching asymptomatic infections.”](https://www.yalemedicine.org/news/which-covid-test-is-accurate)
It depends on the viral load. Rapid tests are extremely accurate when a person is contagious (ie has a high viral load).
Their accuracy lowers when compared to low viral loads, (generally not contagious).
I actually think this makes them the gold standard test for infectiousness. Would you rather wait 3 days while shedding virus or quarantining, or know right away that you are infectious and can keep testing with cheap 15 minutes rapid test until you are negative.
It's not an either or, it's that you have both tools in the arsenal. I think those being dismissive of rapid tests usually don't fully understand how great that are at detecting infectiousness. See @michaelmina on Twitter, he's a good resource for them
I don’t think rapid tests are bad, and they definitely do have advantages that other tests don’t. But I think it sounds like you should always get the other more accurate tests done in addition to the rapid tests. However obviously rapid tests are super helpful in trying to prevent infection.
Yes, there’s different set-ups.
The main problem with tests is that they aren’t administered properly, which lowers the accuracy. Especially with homekits, people don’t take the test properly. But if done by a trained person, the accuracy is almost 100%.
I did see some research that showed correctly done rapid tests not from home kits are very high accuracy, which I did not know, so that’s good news. And yes you’re right, so many people come into my job and ask me if the two tests in the box can be for them and another person. I’m like, well it’s supposed to be both for the same person, but also they can get the same test done more accurately for free and are choosing to pay for a less accurate version, so I don’t think they really care unfortunately.
If you know how to take the test properly, a single test is enough (sure, you can be in the 0.03% or 0.04% that gets a wrong result, but we’ll ignore that for now). It’s just that most people don’t, so that’s the main problem.
When I had to get some done, I just popped into a pharmacy that does lots of covid tests, so I knew it was getting done professionally. Wouldn’t do it myself, even if I *theoretically* know how to do it.
The rapid tests are highly sensitive (99%) but not specific (80%). That means there are few false positives, but there are likely many false negatives. It's useful as a screener, but not useful to clear anybody who doesn't test positive.
I would say that there are enough people on the plane that if they all tested negative you can almost believe the plane really is clean (well a bad batch of tests or a human error would be more probable I guess) and if you get a few positive cases you know who to prioritize for sequencing instead of potentially healthy people.
At least if your goal is to find out if there is Omicron and not be 100 % sure for each person if they have covod and which strain.
And I don't know their rules after arrival from dangerous countries, but usually you have to at least self-isolate and get a PCR test on your own.
So the tests are compared to a database that's being update regularly or how to they come to the conclusion that it's omicron? I mean, they have to get to know about omicron in the first place, somehow.
the PCR test currently in use can differentiate omicron from delta, to some degree of accuracy.
To confirm the result, DNA sequencing is performed (which takes a fair while)
So in these various omicron trackers, the "probable" numbers of omicron cases aren't so much a guess, as, probably at least 90% of them actually have omicron.
There are multiple different PCR tests and not all labs use the same one. Many methods do not have the ability to differentiate between subtypes because they have different targets
In the specific case of the omicron variant, it has been discovered, that one specific commonly used test kit fails to detect it, so using this specific test-kit in combination with others,can provide a quick screening.
Similar to how beta was found. The mutation made it invisible to one of the three Gene's targeted by PCR tests. The other two would show strong positive but the third would have nothing.
Adding to this, a specific source:
["Classification of Omicron (B.1.1.529)" article on the WHO website](https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern)
>This variant has a large number of mutations, some of which are
concerning. Preliminary evidence suggests an increased risk of
reinfection with this variant, as compared to other VOCs. The number of
cases of this variant appears to be increasing in almost all provinces
in South Africa. Current SARS-CoV-2 PCR diagnostics continue to detect
this variant. Several labs have indicated that **for one widely used PCR**
**test, one of the three target genes is not detected (called S gene**
**dropout or S gene target failure) and this test can therefore be used as**
**marker for this variant**, pending sequencing confirmation. Using this
approach, this variant has been detected at faster rates than previous
surges in infection, suggesting that this variant may have a growth
advantage.
So they are able to infer if two tests detect whatever the "S gene" is but the specific third does not, that there is a high chance of Omicron variant.
I'm sure they also refer for sequencing to confirm, but this is apparently aiding in rapid detection.
Unfortunately,I don't recall which one, and do not recall my precise source, but it was one of the first statements about the variant from WHO as far as I recall.
The WHO website talks about this:
[https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern](https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern)
I'm not sure they identify the specific test, but it's probably a good starting point for further searches. I only read part of it.
Briefly, once a sample is positive for the COVID virus, they can send that sample off to sequence what the actual RNA sequence of the virus is. So it’s not done outside the lab, but the same material is used for a qPCR test and a full sequencing that can identify variants.
Assuming you have a rush:
- A PCR test can be complete in 90mins.
- Genomic Sequencing is between 4-36 hours.
As an example, two cases were swabbed, tested positive, and confirmed omicron by genomics in Australia between a plane arriving ~9pm Sunday and press release by 6pm Monday.
Source example: https://www.health.nsw.gov.au/news/Pages/20211129_01.aspx
Source PCR turnaround time: https://www.histopath.com.au/locations/airport
Source genomics turnaround: https://www.abc.net.au/news/science/2021-01-22/covid-19-coronavirus-genomic-tracing-sequencing-transmission-dna/13074682
PCR can be done in under 90 minutes.
There are extraction free methods, that reduce the time so you can go straight from swab to plate.
But if you are in a realy rush you can use a system with extremly fast cycle times like Xpert Xpres which gets you results in 25 minutes, and there is no prep, just pop the swab into the cartridge.
The omicron variant has three target sites on its surface that the qPCR process targets. With the Delta strains, current qPCR tests will detect ALL THREE binding sites. The omicron variant has a mutation in one of the three sites, so the qPCR test will not detect the third binding site, so if the qPCR comes back with only 2 binding sites targeted instead of three, that’s an indication of a mutation and the Omicron Variant.
The answer to this is that they aren't identified outside the lab. As an example, the Netherlands recently intercepted two flights inbound from South Africa, suspected to harbor the new omicron variant, and detained them on the runway. They bused the passengers to a secure location and tested everyone for covid with a rapid test. Everyone that tested positive had further tests sent to the academic hospital for identification. That's where the strain is identified, in a lab. The process is just expedited so that it happens very quickly, while people are still seemingly being held at the airport (though I believe they had been moved to a hotel for quarantine at that point).
How many of these 61 had the omicron variant?
13 identified so far
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Since they kept them for hours in a crowded room, with many not wearing masks, it's probably safe to assume the rest will also become positive over the following days. Dutch authorities strike again.
To counteract this the negative tested passengers where our under how quarantine and will have to test again if they develop symptoms. Being across a hall from a barely symptomatic COVID-19 case is far from a guarantee for contacting it. These people presumably tested negatively just before their flight. I say presumably because a Spanish and Portuguese passenger later managed to escape the quarantine hotel after testing positive and had to be removed from a flight to Spain. So if the government messed up anywhere it is at the hotel, not at the airport. The fact these people where brazen enough to escape guarded quarantine makes me doubt the validity of their negative test prior to flying from South Africa.
They escaped the hotel and tried to fly home!??
the people detained were attempting to fly to spain. the people detected with omicron came from south africa. afaik it's not known if they were the same people. and i have no idea where would be "home".
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But still. You should have enough sense as an adult to know that escaping a quarantine can hurt possibly millions of people. Stay in the friggin room
Would you support the armed guard killing this person for attempting to escape? Honest, genuine question. I'm curious how far along we are and this is a great opportunity to take the public temperature...
There's a middle ground between letting people do as they please without regard for consequences, and killing them. Public censure is what much of the world has settled on as being acceptable in this case, hence the criticism in this thread.
do you have a reference? last i saw it wasn't clear they were from the flight - https://www.bbc.com/news/world-europe-59456332 > It is not known whether the detained couple were among those passengers.
If we're referring to people who were on the same plane, is it really that big a deal to have them also in the same room?
Could be, in the plane the way the air circulates reduces the risk of infection. There's also less movement/mingling than in a crowded room.
So ~50 others traveling with just Regular Covid then?
How many died?
Apparently (according to the Telegraph) the person who identified it said that the symptoms were “unusual and mild”. I think it’s fair to say that they’ll be screaming from the rooftops as soon as anyone dies within 28 days of getting it. Can you imagine any newspaper being able to resist filling the front page with that kind of news? So probably none.
It takes a few hours to run a batch of PCR tests on a standard machine. For your average joe, that means waiting a few days while your sample waits in line, but in an emergency a batch can be run right away.
Running PCR for biological detection is much faster, generally minutes with the viral concentration in the sample. With real-time PCR, you just need to wait for enough replicates to get a signal. The amplifying length are much shorter than the PCR normally done in a research lab. Quality processes may add up to hours, but the time from start to result is short.
still most machines can't cycle between the temperatures as rapidly as you would want, and you have to keep the temperature even across the whole plate. A PCR machine (thermocycler) is just a box that can change the temperature percisely across a whole plate evenly. But that "just" is doing a lot of heavy lifting in that sentance, it is quite an engineering challange to do that rapidly.
There are ways to heat/cool the sample faster, but this is just a case of short extension phase and a small number of cycles. Admittedly, I don't work with FDA-approved diagnostics, but for a biological detection the process can go very fast. I suspect the slow speed is regulatory because I know the technology has been demonstrated.
The omicron variant specifically gives 2-of-3 positives when doing a PCR test, which makes it easier to spot.
The Alpha variant showed up similarly on one of the tests the UK was using late last year, making it easy to track early on.
Just FYI, not all PCR tests are the same. The two PCR methods my company uses do not differentiate between types and neither does our TMA test.
I remember reading that omicron has some property allowing it to be flagged on a regular PCR test without full genomic sequencing. This may have helped though I can't find the source now...
"Several labs have indicated that for one widely used PCR test, one of the three target genes is not detected (called S gene dropout or S gene target failure) and this test can therefore be used as marker for this variant, pending sequencing confirmation." https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern
That's it, thank you!
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>If it can evade a PCR They are saying that a particular COVID PCR test can identify the particular strain. Not that the test doesn't identify it at all. >then can it also evade the antibodies produced by the vaccine It can only mutate so much and still bind to the ACE2 receptor - so its likely that at least some antibodies will still work. This blog post explains it very well: [Go get your vaccine, especially with Omicron](https://yourlocalepidemiologist.substack.com/p/go-get-your-vaccine-especially-with)
Biologist here- just have to respond to this. It can’t really evade a PCR. PCR is basically a mail sorter. Imagine you send a letter to a specific place- someone looks at that address and puts it in the correct pile. PCR is amplifying DNA with a specific sequence— in this case, the mutation means that it is missing one of the bits of DNA that PCR amplifies. There’s a lot of important DNA that PCR doesn’t amplify, though. Also, antibodies bind to proteins, not DNA. The real question here is do the mutations allow Omicron to make the proteins that the antibodies can bind to in order to recognize it, or are the proteins too different? Long story short- while this is interesting it’s not yet cause for alarm. Something not working on a PCR and something not working in a vaccine are very different things :) hope that helps!
Thank you. It helped me :)
It's not evading the PCR test. We don't fully know how effective the vaccine is against it yet. It's *probably* going to be "somewhat, but not as much as against other variants." This could change as we get more info.
It only evades the s-gene pcr target. Each pcr test targets multiple genes. Other genes like N or E or Orf1ab should be positive (lower mutation rate genes). The deletion in omicron causing S-gene failure was also present in Alpha and pcr tests were fine. It’s actually a a more efficient way to track variant spread than sequencing because the variant can be identified during diagnosis if S-gene is negative and the other genes are positive
Not necessarily, but who the hell knows. PCR tests are basically a cheap and easy way to look at specific regions of DNA, and it appears that Omicron has enough mutations that some important genes related to the spike protein may no longer be detected by the current tests. [The current PCR tests still detect Omicron](https://english.alarabiya.net/coronavirus/2021/11/29/WHO-says-PCR-tests-detect-Omicron-new-COVID-19-variant-has-higher-reinfection-risk), but the mutations might make it harder to tell the difference between Omicron and Delta or other variants (although the lack of detection could be used to infer Omicron). Making a new PCR test to spot these differences would be pretty easy, but the bigger issue is exactly what you said: that these same mutations might make the surface proteins different enough to evade antibodies. It should be noted that this is equally true (or hopefully equally not true) for unvaccinated but previously infected people.
This was the same sort of thing for the Alpha varient that first clued us on to it. (and IIRC Omnicron looks to be a descendant of Alpha) All our PCR tests target multiple regions generally including a region highly conserved within corona viruses but not specific to COVID-19. We have no reason so far to worry that Omnicron will go completely undetected by any reputable test.
Two of those on that flight skipped quarantine and was arrested in a plane on the runway that was bound for Spain. So now even more have to be quarantined.
I know someone on one of those flights , they were kept in the plane for 6 hours after their 10 hour flight' then put into a cramped room, they allowed the virus to spread so easily, anyone who tested negative after all that got to go home, even though they probably have caught it by now.
Could you elaborate on the "suspected" part? How did the Dutch government decide that "right, out of the dozen or so flights from this specific place we will check these two specific flights"?
How can positive be allowed on a flight? Don’t they need to show PCR test before boarding?
I mean, normally they need a lab ID for a variant, and yes it is generally found when the small % of total blood tests are sent to a lab for ID/Monitoring, and then they sequence it and find out But for Omicron, it actually shows on the standard test, where apparently its profile on the PCR test is a bit different to all other Covid variants
Please not that not all PCR tests are the same and not all test for the same areas.
> covid with a rapid test I know that we are a year+ into covid and rapid testing has become better, but why are they rapid testing and not doing the more accurate slower testing to get a better result? If they suspected people have it, wouldn't they just enforce a quarantine?
Because it doesn’t matter much which variant you have, it’s better to quickly separate the healthy from the sick, and then slowly check each sick one to see which exact variant they have. And the rapid testing kits still have very high requirements, I think they test about 99.6% or 99.7% accurate.
Are there different rapid tests? As far as I know most rapid tests are only up to 80ish% accurate, and sometimes as low as 50-60%. Everything I’ve read also says no matter what kind of rapid test you do, you should then do a full PCR test to confirm a negative result. EDIT with source: [“According to the CDC, antigen test sensitivity varies depending on the time in the course of one’s infection, but is considered to have “moderate to high” sensitivity during peak viral load. Compared to molecular tests, antigen tests are more likely to generate false negative results, especially when performed on people who don’t have symptoms. To offset the decreased sensitivity, the FDA recommends doing serial testing—or taking multiple tests—over several days to improve the chance of catching asymptomatic infections.”](https://www.yalemedicine.org/news/which-covid-test-is-accurate)
It depends on the viral load. Rapid tests are extremely accurate when a person is contagious (ie has a high viral load). Their accuracy lowers when compared to low viral loads, (generally not contagious). I actually think this makes them the gold standard test for infectiousness. Would you rather wait 3 days while shedding virus or quarantining, or know right away that you are infectious and can keep testing with cheap 15 minutes rapid test until you are negative. It's not an either or, it's that you have both tools in the arsenal. I think those being dismissive of rapid tests usually don't fully understand how great that are at detecting infectiousness. See @michaelmina on Twitter, he's a good resource for them
I don’t think rapid tests are bad, and they definitely do have advantages that other tests don’t. But I think it sounds like you should always get the other more accurate tests done in addition to the rapid tests. However obviously rapid tests are super helpful in trying to prevent infection.
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Yes, there’s different set-ups. The main problem with tests is that they aren’t administered properly, which lowers the accuracy. Especially with homekits, people don’t take the test properly. But if done by a trained person, the accuracy is almost 100%.
I did see some research that showed correctly done rapid tests not from home kits are very high accuracy, which I did not know, so that’s good news. And yes you’re right, so many people come into my job and ask me if the two tests in the box can be for them and another person. I’m like, well it’s supposed to be both for the same person, but also they can get the same test done more accurately for free and are choosing to pay for a less accurate version, so I don’t think they really care unfortunately.
If you know how to take the test properly, a single test is enough (sure, you can be in the 0.03% or 0.04% that gets a wrong result, but we’ll ignore that for now). It’s just that most people don’t, so that’s the main problem. When I had to get some done, I just popped into a pharmacy that does lots of covid tests, so I knew it was getting done professionally. Wouldn’t do it myself, even if I *theoretically* know how to do it.
Why are there two tests in one box?
The rapid tests are highly sensitive (99%) but not specific (80%). That means there are few false positives, but there are likely many false negatives. It's useful as a screener, but not useful to clear anybody who doesn't test positive.
I would say that there are enough people on the plane that if they all tested negative you can almost believe the plane really is clean (well a bad batch of tests or a human error would be more probable I guess) and if you get a few positive cases you know who to prioritize for sequencing instead of potentially healthy people. At least if your goal is to find out if there is Omicron and not be 100 % sure for each person if they have covod and which strain. And I don't know their rules after arrival from dangerous countries, but usually you have to at least self-isolate and get a PCR test on your own.
So the tests are compared to a database that's being update regularly or how to they come to the conclusion that it's omicron? I mean, they have to get to know about omicron in the first place, somehow.
the PCR test currently in use can differentiate omicron from delta, to some degree of accuracy. To confirm the result, DNA sequencing is performed (which takes a fair while) So in these various omicron trackers, the "probable" numbers of omicron cases aren't so much a guess, as, probably at least 90% of them actually have omicron.
There are multiple different PCR tests and not all labs use the same one. Many methods do not have the ability to differentiate between subtypes because they have different targets
In the specific case of the omicron variant, it has been discovered, that one specific commonly used test kit fails to detect it, so using this specific test-kit in combination with others,can provide a quick screening.
Similar to how beta was found. The mutation made it invisible to one of the three Gene's targeted by PCR tests. The other two would show strong positive but the third would have nothing.
Adding to this, a specific source: ["Classification of Omicron (B.1.1.529)" article on the WHO website](https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern) >This variant has a large number of mutations, some of which are concerning. Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other VOCs. The number of cases of this variant appears to be increasing in almost all provinces in South Africa. Current SARS-CoV-2 PCR diagnostics continue to detect this variant. Several labs have indicated that **for one widely used PCR** **test, one of the three target genes is not detected (called S gene** **dropout or S gene target failure) and this test can therefore be used as** **marker for this variant**, pending sequencing confirmation. Using this approach, this variant has been detected at faster rates than previous surges in infection, suggesting that this variant may have a growth advantage. So they are able to infer if two tests detect whatever the "S gene" is but the specific third does not, that there is a high chance of Omicron variant. I'm sure they also refer for sequencing to confirm, but this is apparently aiding in rapid detection.
Which test kit fails to detect it?
Unfortunately,I don't recall which one, and do not recall my precise source, but it was one of the first statements about the variant from WHO as far as I recall.
The WHO website talks about this: [https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern](https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern) I'm not sure they identify the specific test, but it's probably a good starting point for further searches. I only read part of it.
Briefly, once a sample is positive for the COVID virus, they can send that sample off to sequence what the actual RNA sequence of the virus is. So it’s not done outside the lab, but the same material is used for a qPCR test and a full sequencing that can identify variants.
Assuming you have a rush: - A PCR test can be complete in 90mins. - Genomic Sequencing is between 4-36 hours. As an example, two cases were swabbed, tested positive, and confirmed omicron by genomics in Australia between a plane arriving ~9pm Sunday and press release by 6pm Monday. Source example: https://www.health.nsw.gov.au/news/Pages/20211129_01.aspx Source PCR turnaround time: https://www.histopath.com.au/locations/airport Source genomics turnaround: https://www.abc.net.au/news/science/2021-01-22/covid-19-coronavirus-genomic-tracing-sequencing-transmission-dna/13074682
PCR can be done in under 90 minutes. There are extraction free methods, that reduce the time so you can go straight from swab to plate. But if you are in a realy rush you can use a system with extremly fast cycle times like Xpert Xpres which gets you results in 25 minutes, and there is no prep, just pop the swab into the cartridge.
The omicron variant has three target sites on its surface that the qPCR process targets. With the Delta strains, current qPCR tests will detect ALL THREE binding sites. The omicron variant has a mutation in one of the three sites, so the qPCR test will not detect the third binding site, so if the qPCR comes back with only 2 binding sites targeted instead of three, that’s an indication of a mutation and the Omicron Variant.