https://www.theguardian.com/world/2021/dec/07/scientists-find-stealth-version-of-omicron-not-identifiable-with-pcr-test-covid-variant -

https://www.thenational.scot/news/19768203.stealth-version-omicron-variant-harder-track-scientists-warn/ - https://www.thenational.scot/news/19768203.stealth-version-omicron-variant-harder-track-scientists-warn/

https://sydneynewstoday.com/scientists-have-discovered-that-the-stealth-version-of-omicron-cannot-be-identified-by-pcr-tests-coronavirus/454390/ - https://sydneynewstoday.com/scientists-have-discovered-that-the-stealth-version-of-omicron-cannot-be-identified-by-pcr-tests-coronavirus/454390/

The discovery of a new form of Omicron is for researchers https://github.com/cov-lineages/pango-designation/issues/361 - B.1.1.529 Divide the system To the standard Omicron known as BA.1 and a new variant known as BA.2.Professor François Barrow, director of the University College London Institute of Genetics, said that 42 or about 6% of the submitted 709 Omicron genome was https://www.gisaid.org/hcov19-variants/ - Gisaid Genome Database It was BA.2.

“Omicron has two strains, BA.1 and BA.2, which are genetically quite distinct,” he said. “The two lines may behave differently.”

Scientists use whole-genome analysis to determine which mutants caused the Covid infection, but PCR tests may provide suggestions. About half of UK PCR machines look for three genes in the virus, but Omicron (and its predecessor, the alpha variant) is positive in only two of them. This is because, like alpha, Omicron has a genetic alteration called an “S” or deletion of the spike gene. Glitch means that PCR tests showing so-called “S gene target failure” strongly suggest Omicron infection.

Informally, some researchers call the new variant “Stealth Omicron.” This is because there are no deletions that can be found in the PCR test. A concern among some researchers is that stealth variants can go unnoticed while public health authorities focus on standard Omicron PCR tests.

One of the big unknowns is how new variants emerged. It is classified as Omicron, but if it spreads rapidly, it is genetically distinguished so that it may qualify as a new “variant of concern”. According to one researcher, it is “worried” that two variants, BA.1 and BA.2, occur in succession and the mutations are shared, and public health surveillance “misses a large part of the puzzle.” It suggests that there is.

Scientists have discovered that the “stealth” version of Omicron cannot be identified by PCR tests | Coronavirus

Pixie wrote: Scientists have discovered that the “stealth” version of Omicron cannot be identified by PCR tests | Coronavirus

Wow, that is important information. Every country in the world relies on PCR testing to identify cases. The alternative is either clinical diagnosis or genetic sequencing, and obviously we can't do genetic sequencing on everyone. I wonder if the lateral flow tests still work. 

What would be really good information to have is what percentage of Omicron cases are B1 and B2. I really can't think how it can be contained or even monitored if it can't be easily tested for. 

Over here we're all being urged to get tested if we have a mild sore throat and a tickly cough, but where I live, everybody has that at the moment because the grasses have just started flowering and hayfever is rife. Despite the government urging, I know that at our local surgery, the only place where you can get tested, they tell you it's probably hayfever and send you home. lol.

I think I did put this link in scenario's this morning...[url]https://github.com/cov-lineages/pango-designation/issues/361[/url] or https://github.com/cov-lineages/pango-designation/issues/361 - https://github.com/cov-lineages/pango-designation/issues/361 ;

In the last few days a number of genomes have been uploaded by South Africa, Australia and Canada that whilst having many of the defining mutations of B.1.1.529 (Omicron) do not have the full set and also have a number of their own unique mutations. This was first described in Issue #359

where the yellow column gives the mutations unique to the new 'BA.2' lineage, blue column the mutations unique to the original 'BA.1' lineage of Omicron and the green column those shared by both - i.e. inferred to have arisen prior to the split.

A CSV version of this table is available here:  https://github.com/cov-lineages/pango-designation/files/7668225/Omicron_BA.1_BA.2_mutations.csv" style="box-sizing: border-box; background-color: transparent; color: var(--color-accent-fg); text-decoration: none; - Omicron_BA.1_BA.2_mutations.csv

Here we propose expanding the breadth of the B.1.1.529 lineage to include all of these variants. Then 2 sub-lineages created - BA.1 for the original globally-distributed lineage and BA.2 for the new outlier lineage. The names BA.1 and BA.2 follows the Pango convention to avoid more than three numerical fields, an alias is made for the parent lineage.

A couple of observations -

Both sub-lineages (and thus we assume the common ancestor) carry almost all the spike RBD mutations first noted for Omicron and both furin cleaveage adjacent mutations. They both have the NSP6 deletion seen in other VOCs.

The new sub-lineage (putative BA.2) does not carry the spike:69/70del deletion and will thus not be detectable by SGTF (S-gene target failure).

Pangolin currently assign the outlier lineage as B.1.1.529 but Scorpio will give the additional label 'Probable Omicron' because the outlier lineage is missing many of the original defining mutations.

DJ from same link ; Hi Andrew, In addition to this finding, there are some B.1.1.529 lineages that do not have the N440K and K417N mutation (336 entries in GISAID) and form a separate clade when analysed with other sequences that do contain these mutations.

So we have another 3rd strain with a switch in position for N and K  at positions 417 and 440...(related ?) 

[url]https://github.com/cov-lineages/pango-designation/issues/360[/url] or https://github.com/cov-lineages/pango-designation/issues/360 - https://github.com/cov-lineages/pango-designation/issues/360 and another one ?  

Too early for a lineage designation but worth watching:

About 10% of Omicrons (47) have the mutation S:346K which has already been seen in Mu and B.1.640.

Using the available sequences from GISAID it seems possible that Omicrons with S:346K grow faster than Omicrons without.

high speed spread=high mutations=high sub variants ! 

So what does the third strain mean or do? Is that info available yet or did I miss it.

This explains why the PCR test is missing about 30% of the cases.