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Health ministry confirms RT-PCR test can detect Omicron variant


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BANGKOK (NNT) - People have expressed concerns about whether the RT-PCR test method for the virus that causes COVID-19 is able to detect the recently-surfaced Omicron variant of the virus. Public health authorities have now confirmed that the RT-PCR method is capable of detecting the new variant and the method is still in use globally.

 

Department of Medical sciences Director-General Supakit Sirilak said his department has been constantly checking the genomes of the coronavirus and feeding reports into the GISAID global database that provides access to genomic data of influenza viruses. With the appearance of the Omicron variant of the virus that causes COVID-19, which is considered a variant of concern by the World Health Organization, the department has yet to discover the variant among 8 recently collected samples or from the 75 other samples collected since Thailand’s reopening to international visitors on November 1. All of the said samples were of the Delta variant and subvariants.

 

Dr. Supakit asserted that if Omicron variants make their way into the country, his department will quickly discover them as the variant identification process at 15 medical science centers nationwide is now being adjusted to focus on the Omicron variant. He explained that genomic sequencing of the virus that causes Covid generally takes 1 week, while targeted sequencing can determine the variant in 3 days. However, the science centers are now using an approach that can flag the Omicron variant in samples in 1-2 days.

 

Addressing concerns over the effectiveness of the ATK and RT-PCR test methods on the Omicron variant, Dr. Supakit said these methods are capable of identifying Covid infections caused by the Omicron variant. However, the Department of Medical sciences is aware that 2 out of 104 RT-PCR test liquids approved by the Food and Drug Administration identify the coronavirus via the spike protein and this could be an issue if the virus mutates beyond the detection ability of the liquids.

 

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7 minutes ago, Big Bert said:

Yesterday it was a different story and to identify new variant was taking extra testing. Genome sequencing I think was the term, not in a regular RT-PCR test

 

From when it was found actually:

 

World Health Organisation has stated that the Polymerase Chain Reaction (PCR) tests are well effective in detecting the B.1.1.529 Omicron strain as well. In addition, it has said that there are studies ongoing on whether other tests such as Rapid Antigen Tests (RAT) could provide effective diagnosis as well.

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3 minutes ago, Bkk Brian said:

From when it was found actually:

 

World Health Organisation has stated that the Polymerase Chain Reaction (PCR) tests are well effective in detecting the B.1.1.529 Omicron strain as well. In addition, it has said that there are studies ongoing on whether other tests such as Rapid Antigen Tests (RAT) could provide effective diagnosis as well.

It can detect it as Covid but cannot differentiate between strain. That takes more investigation.

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Just now, Big Bert said:

It can detect it as Covid but cannot differentiate between strain. That takes more investigation.

No PCR can detect the actual strain without sequencing because Omicron is so unique in its mutations.

 

PCR tests are being touted as cheaper, quicker alternatives to “laborious” genome sequencing when trying to identify the new Omicron variant.

A mutation in the Omicron variant, called the S-gene dropout, could be identified through the widely-used polymerase chain reaction (PCR) test, the World Health Organisation (WHO) said. This is because the S-gene on the spike protein doesn’t amplify well and won’t be detected when the test is processed.

As Professor Mike Bunce, a principal scientist in genomics for ESR, explained: “This means if two – separate – PCRs are run on a single sample, and one fails, it likely indicates Omicron is present.”

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I don't think your quite getting this, a PCR test can be used to identify the actual Omicron variant. That will then be classified as a probable case. To confirm then a full genome sequence can be carried out.

 

This makes identification of this variant far simpler and far quicker to help stop its spread:

 

"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."

 

https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern

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13 minutes ago, Bkk Brian said:

I don't think your quite getting this, a PCR test can be used to identify the actual Omicron variant. That will then be classified as a probable case. To confirm then a full genome sequence can be carried out.

 

This makes identification of this variant far simpler and far quicker to help stop its spread:

 

"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."

 

https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern

 and this test can be used as a marker for this variant, pending sequencing confirmation

 

So it flags it for further investigation, not confirmation of Omicron.

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10 minutes ago, Big Bert said:

 and this test can be used as a marker for this variant, pending sequencing confirmation

 

So it flags it for further investigation, not confirmation of Omicron.

It flags it as a probable case..................similar to how they use the rapid ATK test here to look for covid in general.  

 

Its a quick, cheap and easy way to identify cases, isolate them and then do a full sequence.

 

Makes surveillance far easier to track the spread and identify any new cases. Its about the only piece of solid good news we have about Omicron

image.png.c85fd07f8f023526bf7d200021b39706.png

https://newsnodes.com/nu_tracker

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1 hour ago, Bkk Brian said:

akes surveillance far easier to track the spread and identify any new cases. Its about the only piece of solid good news we have about Omicron

image.png.c85fd07f8f023526bf7d200021b39706.png

Great but unless it shows deaths its missing the most important piece of data required in the rush to to lock up countries and destroy the economy even more than necessary . 

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So going by his statement have they only sequenced 83 samples since 1st November and then only incoming "tourists". No information on how many home grown cases they are sequencing. Chances are it's probably already in the population, they just haven't detected it yet. This is the risk of low testing numbers, you just don't know what's out there.

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So the virus is carrying a passport with here in Thailand It says.. hee I am Covid and I am Delta, and I am Covid and I am Omricon, I am Covid and I am Apha..... PCR tests only shows if you are infected with which strain needs more investigation, but in here is everything different. Better read the nws of the rest of the world.

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9 hours ago, Petey11 said:

So going by his statement have they only sequenced 83 samples since 1st November and then only incoming "tourists". No information on how many home grown cases they are sequencing. Chances are it's probably already in the population, they just haven't detected it yet. This is the risk of low testing numbers, you just don't know what's out there.

The low Genome Sequencing test rate, which is an early warning system for any possible new Variants within a Countries Population, was one of the primary reasons that Thailand was placed on the original UK Red List.

South Africa to their credit have a high Genome Test rate, which is the reason this new Variant has been found so quickly.

There is a high probability that the Omicron Virus is already within Borders of Countries that do not G Test to a high degree, and Thailand, with its " Open Border " policy on Tourists, and only proposed ATK testing for them on arrival, are leaving themselves wide open to an outbreak of this Virus Variant sooner, rather than later.

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