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Now tracking the new emerging South Africa Omicron Variant

new variants

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Dutch Josh View Drop Down
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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: September 02 2021 at 9:01pm

good find, bad news badger2 !

[url]https://www.japantimes.co.jp/news/2021/08/31/national/japan-confirms-first-case-new-type-delta-variant/[/url] or https://www.japantimes.co.jp/news/2021/08/31/national/japan-confirms-first-case-new-type-delta-variant/

A research team from the Tokyo Medical and Dental University, headed by associate professor Hiroaki Takeuchi, announced Monday in a statement that the first case of this delta variant sublineage was confirmed in a COVID-19 patient in mid-August.


Based on genome analysis, “it is highly likely the latest case mutated domestically,” the researchers said, adding that the patient had no history of traveling abroad.

The latest case contains the N501S mutation, which is similar to the mutation in the alpha variant known as N501Y that was first identified in Britain last year. At least a dozen submutations of the delta variant have been confirmed worldwide so far, in countries such as India and Israel, according to media reports.

When a patient is infected with a coronavirus variant carrying the N501Y mutation, they have a higher risk of secondary infection as well as of developing severe symptoms and dying. Due to the similarities between N501Y and N501S, researchers believe patients infected with N501S could face a similar prognosis.

-

The analysis also showed that patients with the delta variant rapidly increased between late June and late July due to community spread.

DJ This mutation may further increase infectiousness/severity...increase the R0. 

Also from the article; 

Separately, the researchers have also concluded that at least two sublineages of the delta variant — AY.4 and B.1.617.2 — may have existed in Japan in July. But now, they only detect the B.1.617.2 strain of the delta variant.

The first infection with the delta variant in Japan was found on April 20. Delta has been classified as one of four variants of concern by the World Health Organization, and it has quickly outpaced other versions in some parts of Japan — it is now estimated to account for 95% of all cases in Tokyo.

With the delta variant making up a growing share of cases in Japan, the number of patients age 19 and younger is on the rise, a health ministry panel on the coronavirus said last week, calling for schools to take appropriate measures to prevent the spread of infections.

The U.S. Centers for Disease Control and Prevention believes the delta variant is as transmissible as chickenpox and about twice as contagious as previous variants.

DJ AY.4 the newest Delta+ variant ? [url]https://en.wikipedia.org/wiki/SARS-CoV-2_Delta_variant#%22Delta_plus%22_variant[/url] or https://en.wikipedia.org/wiki/SARS-CoV-2_Delta_variant#%22Delta_plus%22_variant

Delta with K417N corresponds to lineages AY.1 and AY.2[44] and has been nicknamed "Delta plus" or "Nepal variant".[45] It has the K417N mutation[46] which is also present in the Beta variant.[47] The exchange at position 417 is a lysine-to-asparagine substitution.[48]

As of late July 2021, the AY.3 variant accounted for approximately 15% of cases in the United States.[49]

As of 30 August 2021, the AY.4 variant accounted for approximately 59% of cases in the United States

DJ [url]https://outbreak.info/situation-reports?loc=USA&pango=AY.4&selected=USA[/url] or https://outbreak.info/situation-reports?loc=USA&pango=AY.4&selected=USA One reason for high US cases could be in the Delta+/AY.4 variant. 

The Japan N501S mutation becoming AY.5-variant in the Delta+ series ? 

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Post Options Post Options   Thanks (0) Thanks(0)   Quote badger2 Quote  Post ReplyReply Direct Link To This Post Posted: September 03 2021 at 5:18am

The CDC changed their published mutation for P.1 Brazil-Japan, which was originally on its page as K417N/T, showing that the virus indeed can use either threonine or asparagine. When they changed it to K417T, they removed the link to increased potency of fentanyl:

Oct 2001 Leuven, Belgium: Asn230 / Mu-Opioid Receptor Increased Potency of Fentanyl

https://pubmed.ncbi.nlm.nih.gov/11588103

’....Potency of fentanyl and morphine can be explained by mutating this residue towards more hydrophobic amino acids.’


Janssen first synthesized fentanyl. Janssen Pharmaceutica, Belgium, is a division of Johnson & Johnson.

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Post Options Post Options   Thanks (0) Thanks(0)   Quote badger2 Quote  Post ReplyReply Direct Link To This Post Posted: September 03 2021 at 8:49am

Mu variant links, without mutating, are:


Fathead minnow nidovirus: S144, Y501, N109. Not only does SARS-CoV-2 think it’s in a fish, that same fish is also reservoir to a picornavirus, of which poliovirus is a member.


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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: September 10 2021 at 2:22am

DJ, 

[url]https://en.wikipedia.org/wiki/SARS-CoV-2_Mu_variant[/url] or https://en.wikipedia.org/wiki/SARS-CoV-2_Mu_variant and [url]https://www.gisaid.org/hcov19-variants/[/url] or https://www.gisaid.org/hcov19-variants/ 

Lots of info on Mu spread [url]https://en.wikipedia.org/wiki/SARS-CoV-2_Mu_variant#Statistics[/url] or https://en.wikipedia.org/wiki/SARS-CoV-2_Mu_variant#Statistics via "other sources"...; 

September 8:

September 9:

  • Twenty-six cases of the Mu variant have been confirmed in Jamaica from a total of 92 samples which were sent for testing to the Atlanta-based Centers for Disease Control on August 21.[23][24][25]

DJ It may be indicating we are missing many cases...or not ? Do we have any realistic picture on what this variant is doing in numbers ? 

[url]https://www.nbcchicago.com/news/coronavirus/mu-delta-lambda-what-we-know-so-far-about-the-most-recent-covid-variants/2606891/[/url] or https://www.nbcchicago.com/news/coronavirus/mu-delta-lambda-what-we-know-so-far-about-the-most-recent-covid-variants/2606891/ "general info" seems to be the best available yet...

From wikipedia; The Mu genome has a total number of 21 mutations, including 9 amino acid mutations, all of which are in the virus's spike protein code: T95I, Y144S, Y145N, R346K, E484K or the escape mutation, N501YD614GP681H, and D109N.[8]

-

On August 31, 2021, the WHO released an update which stated that the "Mu variant has a constellation of mutations that indicate potential properties of immune escape", noting that preliminary studies showed some signs of this but that "this needs to be confirmed by further studies."[9]

One such study conducted in a lab in Rome tested the effectiveness of sera collected from recipients of the BioNTech-Pfizer vaccine against the Mu variant, and found that "neutralization of SARS-CoV-2 B.1.621 lineage was robust", albeit at a lower level than that observed against the B.1 variant.[10]


DJ I would expect to see more urgency in learning more on new variants....

With 2,461 detections in the US, 516 in Spain, 375 in Mexico, 128 in Canada, 84 in (NL)Aruba, 8 in Bonaire, 20 in Curacou (NL ABC Islands) and 75 in NL, 82 in Italy, 62 in the UK, Belgium 41, France 22, Germany 14 cases one of my questions would be how many of the cases were vaccinated ? Re-infections ? 

[url]https://www.ndtv.com/world-news/who-designates-mu-a-variant-of-concern-know-all-about-it-here-2526194[/url] or https://www.ndtv.com/world-news/who-designates-mu-a-variant-of-concern-know-all-about-it-here-2526194 does not give much answers...

[url]file:///home/chronos/u-6a204c8e63e7def0ddbd413be1e353ce67875461/MyFiles/Downloads/20210831_Weekly_Epi_Update_55.pdf[/url] or file:///home/chronos/u-6a204c8e63e7def0ddbd413be1e353ce67875461/MyFiles/Downloads/20210831_Weekly_Epi_Update_55.pdf ;

"Based on the latest round of assessments, B.1.621 was classified as a VOI on 30 August 2021 and given the WHO label “Mu”. This includes the descendent Pango lineage B.1.621.1. This variant is known as 21H in Nextstrain nomenclature. 

The Mu variant has a constellation of mutations that indicate potential properties of immune escape. Preliminary data presented to the Virus Evolution Working Group show a reduction in neutralization capacity of convalescent and vaccinee sera similar to that seen for the Beta variant, but this needs to be confirmed by further studies.

Since its first identification in Colombia in January 2021, there have been a few sporadic reports of cases of the Mu variant and some larger outbreaks have been reported from other countries in South America and in Europe. As of 29 August, over 4500 sequences (3794 sequences of B.1.621 and 856 sequences of B.1.621.1) have been uploaded to GISAID from 39 countries. 

Although the global prevalence of the Mu variant among sequenced cases has declined and is currently below 0.1%, the prevalence in Colombia (39%) and Ecuador (13%) has consistently increased. 

The reported prevalence should be interpreted with due consideration of sequencing capacities and timeliness of sharing of sequences, both of which vary between countries. More studies are required to understand the phenotypic and clinical characteristics of this variant. The epidemiology of the Mu variant in South America, particularly with the co-circulation of the Delta variant, will be monitored for changes."

DJ This weekly WHO update was from August 31...

latest-september 7 update [url]file:///home/chronos/u-6a204c8e63e7def0ddbd413be1e353ce67875461/MyFiles/Downloads/20210907_Weekly_Epi_Update_56.pdf[/url] or file:///home/chronos/u-6a204c8e63e7def0ddbd413be1e353ce67875461/MyFiles/Downloads/20210907_Weekly_Epi_Update_56.pdf ;

DJ Only focus at Variants Of Concern (VOC)... 

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: September 13 2021 at 2:19am

Good video/info from "drbeen"-All about the Mu variant [url]https://www.youtube.com/watch?v=P59E2bUBXjw[/url] or https://www.youtube.com/watch?v=P59E2bUBXjw conclusion; The Mu variant did have over 8 months to spread-"only" made it to 39% of cases in Colombia...

If it was a more dangerous, infectious variant it would have shown by now. Delta started later and still is dominant-able to start several waves if room is provided (by reopening schools etc...). 

DJ When I look at trends for some "countries of concern";

India cases -18%, deaths -12%

Brazil cases -27%, deaths -24%

South Africa cases -30%, deaths -20%

Colombia cases -13%, deaths -21%

the numbers for these vulnarable countries would go up if some new, more infectious variant was around...

Still; Peru cases +4%, deaths -1%

Philippines cases +15%, deaths -19%

Ukraine cases +43%, deaths +37%

Egypt cases +38%, deaths +21%

and several other regions may indicate some new variant may be increasing....

With decrease in testing-and because of that sequencing, increase of (asymptomatic often) spread in vaccinated it may take time before we "see" /detect a new, worse, variant...but I expect it will show up this year...looking at the history of this pandemic, limited level of immunity worldwide...

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: January 02 2022 at 1:04am

DJ-I see Omicron was not in this "new variants" latest news [url]https://flutrackers.com/forum/forum/europe-aj/europe-covid-19-sept-13-2020-may-31-2021/933598-southern-france-reports-of-new-variant-with-46-mutations[/url] or https://flutrackers.com/forum/forum/europe-aj/europe-covid-19-sept-13-2020-may-31-2021/933598-southern-france-reports-of-new-variant-with-46-mutations may have also a lot of similarities....

Southern France reports of new variant with 46 mutations


https://www.thailandmedical.news/new...-from-cameroon

This article states that 67 patients have been identified with this variant - all suffering moderate to severe symptoms. The variant first came to light at the end of November 2021 with the initial case being from Cameroon.

https://www.medrxiv.org/content/10.1....24.21268174v1

Emergence in Southern France of a new SARS-CoV-2 variant of probably Cameroonian origin harbouring both substitutions N501Y and E484K in the spike protein

Their analysis revealed 46 mutations and 37 deletions resulting in 30 amino acid substitutions and 12 deletions. Fourteen amino acid substitutions, including N501Y and E484K, and 9 deletions are located in the spike protein.

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https://www.express.co.uk/news/scien...b16402-omicron from December 10th. Covid warning as ANOTHER new variant discovered in France – scientists sound alarm



ANOTHER variant of coronavirus has been detected by experts working in Marseille, France, as the world continues to battle the deadly virus.

The alarm was sounded by experts at the IHU Mediterranee Infection in Marseille. They announced on their Twitter that they had detected a new variant in Covid-19 patients from Forcalquier, in the Alpes-de-Haute-Provence region. Dubbed "IHU," the variant has been registered under the name B.1.640.2 on the GISAID network (Global Initiative on Sharing Avian Influenza Data).

DJ [url]https://en.wikipedia.org/wiki/Variants_of_SARS-CoV-2#Variants_under_monitoring_(WHO)[/url] or https://en.wikipedia.org/wiki/Variants_of_SARS-CoV-2#Variants_under_monitoring_(WHO) has a B.1.640 from Congo september 2021...the Cameroon link to B.1.640.2 may indicate this new variant has been spreading in central/western Africa for a few months...France and Italy cases going up may not only be related to Omicron...

A lot of good info on [url]https://www.thailandmedical.news/news/breaking-southern-france-reports-spread-of-new-sars-cov-2-variant-b-1-640-2-with-46-mutations-and-37-deletions-originating-from-cameroon[/url] or https://www.thailandmedical.news/news/breaking-southern-france-reports-spread-of-new-sars-cov-2-variant-b-1-640-2-with-46-mutations-and-37-deletions-originating-from-cameroon 

But the news is "fresh" so I expect to hear/learn a lot more the coming days....46 mutations, 37 deletions, N501Y, and E484K mutations are well known-have their own names "NellY and EeK"....

E484K

The name of the mutation, E484K, refers to an exchange whereby the glutamic acid (E) is replaced by lysine (K) at position 484.[216] It is nicknamed "Eeek".[228]

E484K has been reported to be an escape mutation (i.e., a mutation that improves a virus's ability to evade the host's immune system[229][230]) from at least one form of monoclonal antibody against SARS-CoV-2, indicating there may be a "possible change in antigenicity".[231] The Gamma variant (lineage P.1),[115] the Zeta variant (lineage P.2, also known as lineage B.1.1.28.2)[118] and the Beta variant (501.V2) exhibit this mutation.[231] A limited number of lineage B.1.1.7 genomes with E484K mutation have also been detected.[232] Monoclonal and serum-derived antibodies are reported to be from 10 to 60 times less effective in neutralising virus bearing the E484K mutation.[233][234] On 2 February 2021, medical scientists in the United Kingdom reported the detection of E484K in 11 samples (out of 214,000 samples), a mutation that may compromise current vaccine effectiveness.[235][236]


N501Y

N501Y denotes a change from asparagine (N) to tyrosine (Y) in amino-acid position 501.[239] N501Y has been nicknamed "Nelly".[228]

This change is believed by PHE to increase binding affinity because of its position inside the spike glycoprotein's receptor-binding domain, which binds ACE2 in human cells; data also support the hypothesis of increased binding affinity from this change.[29] Molecular interaction modelling and the free energy of binding calculations has demonstrated that the mutation N501Y has the highest binding affinity in variants of concern RBD to hACE2.[1] Variants with N501Y include Gamma,[231][115] Alpha (VOC 20DEC-01), Beta, and COH.20G/501Y (identified in Columbus, Ohio).[1] This last became the dominant form of the virus in Columbus in late December 2020 and January and appears to have evolved independently of other variants.[240][241]

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: January 02 2022 at 3:30am

Well the news is not that fresh...[url]https://github.com/cov-lineages/pango-designation/issues/362[/url] or https://github.com/cov-lineages/pango-designation/issues/362 early december; 

In a similar vein to the recent split of B.1.1.529(Omicron) into two sister sublineages it appears B.1.640 may also have a similar issue with a major group constating of the vast majority of sequences and a small outgroup which appears related but has a very different set of mutations (EPI_ISL_7181977; EPI_ISL_7156959; EPI_ISL_7156955; EPI_ISL_6315910; EPI_ISL_5926666) and includes sequences from France and England, indicating some degree of spread.

Defining mutations (mutations not shared between both groups shown in bold):
Major lineage:
Spike - P9L, E96Q, Δ136-144, R190S*, I210T, R346S, N394S, Y449N, F490R, N501Y, D614G, P681H, T859N, D936H
Non-spike - NSP2 – P129L, E272GNSP3 – L1301F, A1537S; NSP4 – S386F, R401H, T492I; NSP6 – V149A; NSP12 – P323L; T32I, Q57H; M – I82T; ORF8 – Q27*STOP; N- D22Y, T205I, E378Q; S2m deletion

Minor lineage:
Spike - P9L, E96Q, Δ136-144, R190S, D215H, R346S, N394S, Y449N, E484K, F490S, N501Y, D614G, P681H, T859N, D1139H
Non-spike - NSP2 – P129L; NSP4 – D459N; NSP6 – Δ106-108T181I; NSP12 – P323L; NSP13 – V371A; NSP14 – P46S, V437F; ORF3a – T32I, Q57H; M – I82S; ORF8 – Q27*STOP; N – D22Y, T205I

DJ See also [url]https://twitter.com/peacockflu[/url] or https://twitter.com/peacockflu maybe this B.1.640.2 variant now detected more ? Mistaken for Delta ?

[url]https://trialsitenews.com/new-variant-emerges-in-france-b-1-640-2-not-clear-if-of-concern/[/url] or https://trialsitenews.com/new-variant-emerges-in-france-b-1-640-2-not-clear-if-of-concern/

The IHU Mediterranee Infection in Marseille reported recently on a new SARS-CoV-2 variant in France recently. Announced on Twitter, the group identified the new variant in the Forcalquier commune in this beautiful part of southern France. The variant is formally registered as B.1.640.2 on the GISAID network.

On Dec. 6, the IHU Mediterranee Infection announced via a tweet their first encounter with the Omicron variant. Then on Dec. 9, the French organization reported they had detected what is now called the IHU variant or B.1.640.2.

Recently, scientists posted that Omicron (B.1.1.529) was split into two sub-lineages identifying that “B.1.640 may also have similar issue with a major group constating of the vast majority of sequences and a small outgroup, which appears related but has a very different set of mutations.” This includes sequences from France and England.

TrialSite picked up the story from La Figaro in France.

The French media reported that they are not certain whether the new variant falls under the category of variant of concern (Delta or Omicron) or variants of interest (Lambada or Mu). It remains to be seen which category B.1.640.2 will fall under.

DJ article from december 10....[url]https://www.deseret.com/coronavirus/2021/11/16/22785162/new-covid-19-variant-france-spike-protein-mutations[/url] or https://www.deseret.com/coronavirus/2021/11/16/22785162/new-covid-19-variant-france-spike-protein-mutations goes back even further, november 16....; 

European countries have detected a new coronavirus variant that has some mutations that scientists have never seen before.

What is the new Europe COVID-19 variant?

French paper Le Telegramme reported that the new variant — called B.1.X or B.1.640 — infected 24 people in a French school in October. Since then, a handful of cases have been discovered in the United Kingdom, Switzerland, Scotland and Italy.

  • The variant hasn’t spread too far because the delta variant is so dominant.
  • Why is the new Europe COVID-19 variant dangerous?

    Cyrille Cohen, a professor at Bar-Ilan University in Israel, told The Jerusalem Post that the B.1.640 variant has some new mutations we haven’t seen.

    • For example, the spike protein, which allows the virus to latch onto the human cell and infect people, has deletions that haven’t been noticed before. This could make it harder for vaccines to identify the spike protein before it infects people.

  • Where did the Europe COVID-19 variant come from?

    Cohen told The Jerusalem Post the variant likely came from Africa, which probably wouldn’t have happened if the world had more access to vaccines.

    • “This variant exemplifies that if you leave some of the world’s population without access to vaccines, then the virus will continue to multiply and it will lead to more variants,” Cohen said.
  • Why should you keep an eye on this variant?

    The new variant emerges as cases across Europe have spiked. Experts said there could be a new COVID variant circulating in Europe right now, which is why cases have surged so fast, according to CNBC.

So what to think of it all ? [url]https://www.coronaheadsup.com/europe/france/france-new-sars-cov-2-variant-detected-with-n501y-and-e484k/[/url] or https://www.coronaheadsup.com/europe/france/france-new-sars-cov-2-variant-detected-with-n501y-and-e484k/ ;

UPDATE 31/12/2021 – from the French Public Health Department

The B.1.640 variant is classified as a variant under investigation (VUM) by Public Health France (at 12/11/2021) as well as by WHO, ECDC and UKHSA. Since December 8, 2021, the B.1.640 lineage has been divided into two sublines: B.1.640.1 and B.1.640.2.

B.1.640.1 corresponds to the sequences of B.1.640 initially detected, and is majority. B.1.617.2* was detected within a cluster at the end of November 2021 in the Provence-Alpes-Côte region Azure.

B.1.640.2 is characterized by the presence of the E484K mutation (one of the targets of the current strategy screening), which is not present in B.1.640.1. The discrimination between these two sub-lineages is not still included in bioinformatic analysis tools. In this risk analysis, no difference is made between the two sublineages of B.1.640 and all cases are considered 20A / C variants B.1.640.

Public Health Document: Mise à jour de l’analyse de risque sur les variants émergents du SARS-CoV-2 du 01/12/2021  réalisée conjointementpar Santé publique France et le CNR des virus des infections respiratoires   (PDF download in French)

It is not "recycling of older news" French Public Health Department did give an extra warning december 31....[url]https://outbreak.info/location-reports?loc=FRA[/url] or https://outbreak.info/location-reports?loc=FRA has B.1.640 (allready) at 1%. [url]https://outbreak.info/situation-reports?loc=FRA&pango=B.1.640&selected=FRA[/url] or https://outbreak.info/situation-reports?loc=FRA&pango=B.1.640&selected=FRA gives 1-2% in Normandy. Outbreak not detecting B.1.640.2 in Italy or Belgium....

So lots of ?????  [url]https://www.worldometers.info/coronavirus/country/cameroon/[/url] or https://www.worldometers.info/coronavirus/country/cameroon/ also-yes increase of cases end of september 2021....[url]https://outbreak.info/location-reports?loc=COG[/url] or https://outbreak.info/location-reports?loc=COG Congo reporting 47% B.1.640 but Omicron taking over there (and French B.1.640.2 may be different...). 

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: January 02 2022 at 4:49am

DJ-I go on about the French B.1.640.2 story with French Healthcare giving a warning december 31....I think that is "unexpected" since Omicron was supposed to be the main-if not only-news....

Diving a bit further in the French B.1.640 story; [url]https://www.connexionfrance.com/French-news/French-Minister-Detection-of-Covid-Congo-strain-shows-tracking-works[/url] or https://www.connexionfrance.com/French-news/French-Minister-Detection-of-Covid-Congo-strain-shows-tracking-works  from november 18;

France’s health minister has used an example of a Covid variant thought to have originated in the Republic of Congo as an example of the country’s ability to track mutations of the virus.

A small number of cases of the variant have been detected in France and in other European countries, such as Italy, Netherlands and Spain.

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The variant, which has been denoted B.1.640, was added to France’s list of “variants under monitoring” on November 12. 

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Scientists have reported that it has a surprising genomic diversity, meaning that the variant has several diverging mutations, but they can all be classified under the variant of B.1.640.

This diversity suggests that the variant is not necessarily new, as it takes time for mutations in a variant to occur. 

“One possibility is that this variant has been potentially circulating at low levels for some time, in Africa or elsewhere, in places where genome surveillance is lower,” Étienne Simon-Lorière, a virologist at the Pasteur Institute, told HuffPost.

He said that it is very difficult to know exactly where it came from or how it will spread. 

"We are currently unable to say whether this variant will die out or develop," he said. 

Florence Débarre, a scientist and researcher at France’s national research centre, the Centre national de la recherche scientifique, told HuffPost that it served as a reminder that other variants are circulating, despite the dominance of Delta.

“It was said that Delta had become hegemonic and that the next variant would be one of its descendants. This [B.1.640] is another very different branch, a lineage that seems to have lived its life off the radar,” she said.

“It is a reminder that several versions of coronavirus are circulating in many parts of the world where there is very little genomic surveillance and few vaccine doses have been administered.”

DJ (More or less the story was claiming France doing a very good job in testing/sequencing...not yet at UK/US level....with the US not doing very great...)

[url]file:///home/chronos/u-6a204c8e63e7def0ddbd413be1e353ce67875461/MyFiles/Downloads/analyse_risque_variants_20211201_maj_20211215.pdf[/url] or file:///home/chronos/u-6a204c8e63e7def0ddbd413be1e353ce67875461/MyFiles/Downloads/analyse_risque_variants_20211201_maj_20211215.pdf In French (I will translate it via google put it under this post)

[url]https://www.thailandmedical.news/news/breaking-updates-on-new-b-1-640-2-variant-spreading-in-southern-france-number-of-cases-growing-and-variant-now-detected-in-united-kingdom-as-well[/url] or https://www.thailandmedical.news/news/breaking-updates-on-new-b-1-640-2-variant-spreading-in-southern-france-number-of-cases-growing-and-variant-now-detected-in-united-kingdom-as-well ....if this story would be about renaming Delta variant cases....it does NOT look that way however. 

952 cases per 1-1-2022, last earlier number was december 13 with 323 cases-all cases detected after hospital admission with 315 of them on ventilators. 

UK would have (at least) 17 B.1.640.2 cases. 

Just as transmissable as Delta but resulting in more severe disease, better in evading immunity with most cases in hospital vaccinated 2x, some of them even had a booster....

Also another warning [url]https://www.thailandmedical.news/news/warning-omicron-is-still-evolving-the-world-will-pay-dearly-for-assuming-it-is-mild-[/url] or https://www.thailandmedical.news/news/warning-omicron-is-still-evolving-the-world-will-pay-dearly-for-assuming-it-is-mild- 

DJ.....Christmas/New Year may have made keeping an eye for new developments even harder....The B.1.640 itself is not that new, some of its mutations may be just start showing up fairly recent....

On top of Omicron and Delta still not gone, very bad news ! It could be Omicron will end B.1.640.2...? Good info-in English-so the international community can get the info-would be welcome ! It would be so nice if-at least during the pandemic-medical science could agree on a basic international language for major findings....

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: January 02 2022 at 5:04am

[url]https://www.santepubliquefrance.fr/dossiers/coronavirus-covid-19[/url] or https://www.santepubliquefrance.fr/dossiers/coronavirus-covid-19 

Google Translation of [url]file:///home/chronos/u-6a204c8e63e7def0ddbd413be1e353ce67875461/MyFiles/Downloads/analyse_risque_variants_20211201_maj_20211215.pdf[/url] or file:///home/chronos/u-6a204c8e63e7def0ddbd413be1e353ce67875461/MyFiles/Downloads/analyse_risque_variants_20211201_maj_20211215.pdf (The B.1.640.2 part) ;

3. Additional data on B.1.640
This chapter is an update of the data presented in the risk analysis of 12/01/2021.
3.1. Classification
The B.1.640 variant is classified as a variant under investigation (VUM) by Public Health France (at
12/11/2021) as well as by WHO, ECDC and UKHSA. Since December 8, 2021, the B.1.640 lineage has been
divided into two sublines: B.1.640.1 (“major group” in Figure 5) and B.1.640.2 (“minor group”
in Figure 5) (23). B.1.640.1 corresponds to the sequences of B.1.640 initially detected, and is
majority. B.1.617.2 was detected within a cluster at the end of November 2021 in the Provence-Alpes-Côte region
Azure. B.1.640.2 is characterized by the presence of the E484K mutation (one of the targets of the current strategy
screening), which is not present in B.1.640.1. The discrimination between these two sub-lineages is not
still included in bioinformatic analysis tools. In this risk analysis, no difference is
made between the two sublineages of B.1.640 and all cases are considered 20A / C variants
B.1.640.
3.2. International epidemiology
This variant was detected for the first time in the Republic of Congo at the end of September 2021. As of 12/14/2021 in
2 p.m., 205 sequences were deposited in GISAID by 14 countries. The majority of samples come from
from France (n = 129), followed by the Republic of Congo (n = 36) then Italy (n = 13, Figure 6).

3.3. Circulation in France - sequencing data
The first cases of infection with VUM B.1.640 in France, identified at the end of October by sequencing, came from
mostly from Brittany and were associated with a cluster in a school.
As of 12/13/2021 at 12 noon, 323 sequences of B.1.640 have been deposited in the EMERGEN database. This variant has
was detected in 12 regions. Île-de-France is the region with the greatest number of sequences identified
(n = 84), followed by Hauts-de-France (n = 79) and Normandy (n = 74, Figures 7 and 8). This variant was detected
during the last 8 Flash surveys. The median age of sequenced cases (44 years) was comparable to that of
other variants circulating over the same period (43 years).

3.4. Circulation in France - investigations
For some B.1.640 samples, patients could be contacted to determine their status
vaccination, the severity of their symptoms and their travel history as well as that of their contacts. Among
of the 123 cases for which information was available, 84 had a full vaccination (68%). A total
of 10 hospitalized patients was reported (including 2 in intensive care) among the 129 for whom information was
could be harvested (8%). For 103 cases out of 118, no notion of travel was found, indicating a
potential circulation of this variant in France, even at low levels. For the 15 cases for which it
there was a notion of travel, 7 were returning from the Republic of Congo, two from Belgium, one from Cameroon,
one from Morocco and one from India. The proportion of cases linked to a return from abroad has fallen since
start of this data collection at the end of November, indicating that the circulation of this variant is no longer carried by
ad hoc imports but relies on indigenous circulation. Most of the cases involving
of an investigation (85 out of 122, or 70%) belonged to clusters (family, professional, friends).
Important clusters of this variant have been investigated in Hauts-de-France and Normandy. In
Hauts-de-France, a hospital cluster of 26 cases was reported, among which 11 were sequenced and
confirmed B.1.640. Three cases have died, but the deaths are not necessarily attributable to infection with
SARS-CoV-2. In Normandy, a cluster of B.1.640 linked to a meal for 139 people has been described;
the average age of the participants was 74 years; among the 101 people tested and contacted, 57 were
positive and 3 hospitalized. Two-dose vaccination coverage in this cluster was 100%.
These data are preliminary and relate to a small number of cases and it is therefore advisable to remain cautious
as to interpretations. It is important to continue this data collection because France is the only country
among those where this variant circulates capable of conducting epidemiological investigations guided by surveillance
genomics. These epidemiological analyzes will be supplemented by in vitro studies, which are underway at
CNR.

The 20A / C B.1.640 variant, classified as VUM, is also the subject of enhanced surveillance in France. In
Indeed, the majority of confirmed cases of B.1.640 infection have been detected in France. Health authorities
public organizations are therefore counting on these data to clarify the questions
characteristics of this variant. In France, B.1.640 is detected in the most recent Flash surveys at
low levels, but which could indicate community circulation in certain areas. Cases
infection with B.1.640 were confirmed in 11 of the 13 regions of metropolitan France and Réunion. This
variant is the first to be able to circulate at low levels since the Delta variant circulates from
almost exclusively, indicating potential competitiveness against Delta. Careful monitoring, carried by the
genomic surveillance and epidemiological investigations, will better characterize this variant. From
In vitro studies are also planned to complement the epidemiological analyzes.
These new elements complete the overall analysis of the circulation of variants carried out on
12/01/2021. The conclusions of this risk analysis remain valid, because while the number of confirmed cases
infection with Omicron and B.1.640 has increased over the past two weeks, Delta VOC remains
very large majority in France and internationally. The emergence and beginning of dissemination of the VOC
Omicron in France is however confirmed and is expected to ramp up in the coming weeks.
The enhanced surveillance that has been deployed around the Omicron VOC illustrates the robustness of the
genomic monitoring, and its ability to increase its activity to meet specific needs. In
the current context, characterized both by the emergence of new variants with still poorly
described and by a circulation of Delta at high levels, it is necessary to strengthen the vaccination efforts,
compliance with barrier gestures and adherence to isolation measures in the event of a diagnosis of infection or
close contact with a case.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote KiwiMum Quote  Post ReplyReply Direct Link To This Post Posted: January 03 2022 at 12:04pm
"Once you've decided that something's absolutely true, you've closed your mind on it, and a closed mind doesn't go anywhere. Question everything. That's what education's all about." ~ David Eddings
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Post Options Post Options   Thanks (0) Thanks(0)   Quote roni3470 Quote  Post ReplyReply Direct Link To This Post Posted: January 03 2022 at 1:53pm

Kiwi - that seems scary.....anyone have anything additional?

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Post Options Post Options   Thanks (0) Thanks(0)   Quote KiwiMum Quote  Post ReplyReply Direct Link To This Post Posted: January 03 2022 at 3:30pm

Originally posted by roni3470 roni3470 wrote:

Kiwi - that seems scary.....anyone have anything additional?

It's the first I'd heard of it. I agree, it does sound scary. I'll keep my eyes peeled for more info on it.

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: January 03 2022 at 11:59pm

[url]https://www.livemint.com/news/world/more-severe-than-omicron-new-covid-variant-ihu-worries-global-health-experts-11641279345140.html[/url] or https://www.livemint.com/news/world/more-severe-than-omicron-new-covid-variant-ihu-worries-global-health-experts-11641279345140.html has some links to [url]https://twitter.com/drericding[/url] or https://twitter.com/drericding january 2/ recent tweets;

Another source says the rise in ICUs and deaths in Southeast France Vlag van Frankrijk are still due to Delta - possible. I’m not that worried about #B16402 yet—i doubt it will win over Omicron (5-6x faster than Delta) or Delta (which is 2x faster than original).

-

10) the Provence-Alpes-Côte d'Azur region also has a steeper #COVID19 death climb than the rest of Vlag van Frankrijk. Not sure if this is #Omicron or if it’s the new variant (unclear), but still not good regardless even if Omicron.


DJ Most info so far coming from France...[url]https://www.santepubliquefrance.fr/dossiers/coronavirus-covid-19[/url] or https://www.santepubliquefrance.fr/dossiers/coronavirus-covid-19 having their own database and going for French as the global language....

[url]https://twitter.com/OAlexanderDK[/url] or https://twitter.com/OAlexanderDK could have more info...








CollectieA few days ago, I like many read about a new variant of COVID discovered in Provence-Alpes-Côte d'Azur. I didn't pay much attention to it at the time. Now though data from the region is starting to look quite different from the rest of France.

But info is delayed....hope we get some more info soon.

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Post Options Post Options   Thanks (0) Thanks(0)   Quote roni3470 Quote  Post ReplyReply Direct Link To This Post Posted: January 04 2022 at 8:38am

So do we have conflicting stories?  One saying the deaths are rising but not sure what variant and one saying the new variant won't change things because its still D and O that are causing things?

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: January 04 2022 at 9:15pm

Maybe a few remarks;

January 4 had over 2 million new cases....10,000 cases would be 0,5% so say those 10,000 cases would not be Omicron....In such high numbers 1% may seem low but could still be 10,000+....

Besides that, I (DJ) think it is an "old" -very likely by now incorrect-way of thinking....Omicron, B.1.640.2 may be that different from most Delta subvariants that they may co-infect hosts...In a bad case a person could end up-in that way of thinking-with ALL THREE !!! Some form of Delta, BA.1 or BA.2 (or a new other) Omicron AND B.1.640.2....

It is easy to miss...just like one could miss flu when a person is positive for CoViD...

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: January 08 2022 at 2:47am







The data are compatible with a small blip of B.1.640.2 (maximum 5% of cases) in the Provence-Alpes-Côte d'Azur (PACA) region towards the end of December. Omicron is now taking over in frequency space. Klein wit vierkant7/7


proportions of L452R, E484K and their combination in PACA region, over time (mid Nov to now). See tweets for explanations

2

14

26








I cannot directly plot E484K-nonL452R, because sample sizes are not the same between data with single and double mutations, unfortunately (NAs are not reported). But we can inspect the data that we have and infer the presence of B.1.640.2 by comparing them

DJ Looks like B.1.640.2 was pushed aside by-most-Omicron...still France is seeing over 300,000 cases for days now...extreme ! 

Maybe [url]https://github.com/cov-lineages/pango-designation/issues/394[/url] or https://github.com/cov-lineages/pango-designation/issues/394 is related : A sub-lineage of AY.122 was first detected in the Republic of Congo in September 2021 harboring the S:E484A escape mutation seen in Omicron. It quickly rose to a significant portion of sequences from the Republic of Congo throughout September and October, consistently accounting for a 20% proportion. It began to grow in France in October 2021 and has reached a peak of 1.7% proportion in week 49 (starting 12-06). It has persisted as Omicron has continued to reach dominance and the most recent sample was collected on December 30.

DJ Yet another sign Delta may not be gone completely...also Africa link...

[url]https://github.com/cov-lineages/pango-designation/issues/395[/url] or https://github.com/cov-lineages/pango-designation/issues/395 ;

With this proposal i would like to highlight that, as @zach-hensel pointed to me, there are multiple emerging sublineage of BA.1 carrying the mutation Orf1A:K3353R.
We met this mutation before in AY.124 sublineage of Delta , dominant in Portugal for a long time, and earlier in sublineages of Alpha and Beta.

Here i propose one of them mainly from New York city:
Mutations:
Nuc: C2407T (Orf1a:714)
then nuc: A14940G (Orf1b:491) and A10323G (ORF1ab: K3353R)

Interestingly one sample was collected in Japan (Dont know if this is linked with the outbreak in the american army)

DJ So Omicron BA.1 may be splitting up in further subvariants...








I still dare say BA.2 has become the dominant variant in Denmark in the last couple of days! (But I accidentally removed my last tweet about it Omgekeerd gezicht). Newest graphs based on  data here, based on 700+ samples on the 2nd of January)


Afbeelding

Omicron is not only spreading fast...also mutating high speed with BA.2 very likely also major in India a.o. 

Sublineages and stealth variant

Researchers have established the existence of three sublineages of Omicron. The 'standard' sublineage is now referred to as BA.1/B.1.1.529.1, and the two other sublineages are known as BA.2/B.1.1.529.2 and BA.3/B.1.1.529.3.[39]

All three can be detected by full sequencing, but BA.2 has been nicknamed 'Stealth Omicron' because it differs from the 'standard' variety by not having the characteristic S gene target failure (SGTF)-causing deletion (Δ69-70) by which many PCR tests are able to detect a case as an Omicron, or Alpha, variant. Thus, countries that primarily rely on SGTF for detection may overlook BA.2.[40] Some countries, including Denmark, use a variant qPCR that tests for several mutations, including Δ69-70, E484K, L452R and N501Y.[41] It can also distinguish Delta (the heavily dominant variant worldwide, prior to the spread of Omicron), which has L452R but not N501Y,[42] and all Omicron sublineages, which have N501Y but not L452R.[43][44] As of 19 December 2021, BA.2 appears to be very rare with about twenty known cases from half a dozen countries.[39][44] The third sublineage, BA.3, is also very rare and it does not represent the same potential problem in detection since it has the SGTF deletion (Δ69-70), similar to BA.1.[39][45]

From [url]https://en.wikipedia.org/wiki/SARS-CoV-2_Omicron_variant#Sublineages_and_stealth_variant[/url] or https://en.wikipedia.org/wiki/SARS-CoV-2_Omicron_variant#Sublineages_and_stealth_variant 

[url]https://outbreak.info/situation-reports?pango=BA.2&loc=ZAF&loc=GBR&loc=USA&selected=Worldwide&overlay=false[/url] or https://outbreak.info/situation-reports?pango=BA.2&loc=ZAF&loc=GBR&loc=USA&selected=Worldwide&overlay=false running behind with data..

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: January 09 2022 at 1:26am

Limited info so far on both "DeltaCron-Cyprus" and China-Omicron...

-[url]https://www.coronaheadsup.com/coronavirus/deltacron-a-new-variant-that-combines-omicron-and-delta-discovered-in-cyprus/[/url] or https://www.coronaheadsup.com/coronavirus/deltacron-a-new-variant-that-combines-omicron-and-delta-discovered-in-cyprus/

Cypriot authorities have reported the detection of up to 25 cases of infection with a combined version of the Delta and Omicron variants of the SARS-CoV-2 coronavirus which they have named “Deltacron”.

“Currently there are coinfections of Omicron and Delta. We have found a variant that is a combination of both,” explained Leondios Kostrikis, professor of Biology at the University of Cyprus and director of the Laboratory of Biotechnology and Molecular Virology.

Kostrikis and his team have highlighted that they are more frequent in hospitalized patients for COVID-19 than in non-hospitalized positives. “We will see in the future if this variant is more pathological or contagious or if it will be imposed” on Delta and Omicron, he has indicated, although in his opinion it is most likely that it will be overshadowed by the Omicron variant as it is more contagious.

El Periodico report

and  

UPDATE 1 – 8th January 2022

“Dr Leontios Kostrikis, who leads the team of scientists working at the University of Cyprus’ biotechnology and molecular virology lab, said a new coronavirus variant has been identified in the community.

Speaking to local media, Kostrikis explained that the new variant, which has been dubbed Deltacron, shares the genetic background of the Delta variant along with some of the mutations of Omicron.

“We have found a significant number of mutations only previously found in Omicron cases, which is different from other variants as it has 30 mutations,” he said. “Ten of these were identified in these samples taken in Cyprus”.

Cyprus-Mail.com report

[url]https://www.thailandmedical.news/news/breaking-recombinant-delta-and-omicron-variant-called-deltacron-has-finally-emerged-in-cyprus-according-to-documented-genomic-data[/url] or https://www.thailandmedical.news/news/breaking-recombinant-delta-and-omicron-variant-called-deltacron-has-finally-emerged-in-cyprus-according-to-documented-genomic-data ,

See also ;[url]https://flutrackers.com/forum/forum/middle-east-aa/middle-east-covid-19-sept-13-2020-may-31-2021/934560-cyprus-finds-covid-19-infections-that-combine-delta-and-omicron-%E2%80%9Cdeltacron%E2%80%9D[/url] or https://flutrackers.com/forum/forum/middle-east-aa/middle-east-covid-19-sept-13-2020-may-31-2021/934560-cyprus-finds-covid-19-infections-that-combine-delta-and-omicron-%E2%80%9Cdeltacron%E2%80%9D trying to follow the story...

-China Omicron sub-variant [url]https://flutrackers.com/forum/forum/china-other-health-threats/china-covid-19-sept-13-2020-may-31-2021/934559-china-tianjin-officials-imposing-a-graduated-covid-19-semi-lockdown-4-districts-today-and-the-rest-of-the-districts-tomorrow-12-january-9-2022[/url] or https://flutrackers.com/forum/forum/china-other-health-threats/china-covid-19-sept-13-2020-may-31-2021/934559-china-tianjin-officials-imposing-a-graduated-covid-19-semi-lockdown-4-districts-today-and-the-rest-of-the-districts-tomorrow-12-january-9-2022 ; January 8th, Tianjin detected two cases of positive COVID-19 nucleic acid test among the personnel willing to do the inspection and the active visits of the fever clinic. After comprehensive research and judgment by the city-level expert group, they were determined to be local confirmed cases of new coronary pneumonia (light type).

DJ Even less info....may have some mutations showing up in other places as well..All variants have/had "weak spots" resulting in more mutations in those segments...(So the China mutation may not be that new....[url]https://github.com/cov-lineages/pango-designation/issues/395[/url] or https://github.com/cov-lineages/pango-designation/issues/395; 

With this proposal i would like to highlight that, as @zach-hensel pointed to me, there are multiple emerging sublineage of BA.1 carrying the mutation Orf1A:K3353R.
We met this mutation before in AY.124 sublineage of Delta , dominant in Portugal for a long time, AY.113 and earlier in sublineages of Alpha and Beta.

Here i propose one of them mainly from New York city:
Mutations:
Nuc: C2407T (Orf1a:714)
then nuc: A14940G (Orf1b:491) and A10323G (ORF1ab: K3353R)

Interestingly one sample was collected in Japan (Dont know if this is linked with the outbreak in the american army)

ORF1a:K3353R (NSP5_K90R) is also ~defining for B.1.351.

The Japan sequence metadata says it's a sequence found in airport test/quarantine for international arrivals.

Separately and without ORF1a:K3353R, recent BA.1 domestic cases in Yamanashi and Shizuoka, Japan (e.g. EPI_ISL_8439369) contain ORF1a:T3432S (NSP5_T169S) which may have originated in Hawaii and could be linked to nearby base cases. However, there were also several cases of this sub-lineage caught in airport testing earlier in December so it's unclear.

or others Omicron mutations ? Tianjin Epidemic Timeline

January 9, 2022

Most of the 20 new cases of positive infections in Tianjin are primary and middle school students. One picture to understand the relationship between the cases

Two local cases in Tianjin were infected with Omi Keron, or have been spreading in the community for some time

More info to come...no doubt. 

-[url]https://github.com/cov-lineages/pango-designation/issues/396[/url] or https://github.com/cov-lineages/pango-designation/issues/396 ;

I have been watching this small subclade since it's first submitted on December 1st, 2021.
It spread from Connecticut to New Jersey, the US, and then to Gujarat, India within a month.
There are 5 sequences at the moment but considering its unusual set of substitutions, it might be woth being monitored closely.

Description
Sub-lineage of: AY.3
Earliest sequence: 2021/11/15 (the US-CT)
Most recent sequence: 2021/12/26 (India-Gujarat)
Countries circulating: the US and India

Substitutions on top of AY.3:

GeneMutations
ORF1a:E102K, T1682I, S2839N, R3164H
ORF9b:V96A
N:N196I
Spike:L18F, Y144del, G181V, G446V, R452Q, Y453F, E484Q, D936H
nucG569A, T4066C, T11731C, C18681T, C21614T

DJ So (at least) 19 mutations in this Delta AY.3 subvariant ????

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[url]https://github.com/cov-lineages/pango-designation/issues/400[/url] or https://github.com/cov-lineages/pango-designation/issues/400 ;

Pango/Nextstrain unclassified lineage with high mutational load including S:F490R, S:N501Y, S:p681H and 9 aa deletion Spike aa 136-144, sharing mutations with B.1.640.2 (South of France/Cameroon) #400

Case [description]
The AZ Delta COVID Genomics Core (Roeselare, Belgium) identified N=1 SARS-CoV-2 isolate with aberrant mutation profile. The patient was a 39 year old woman from Menen, Belgium. She traveled to Paris on Dec 22-23, 2021 and developed mild respiratory symptoms and fatigue without anosmia on Dec 31, 2021. Besides a trip to Paris, she had limited contacts since she is a teacher and infection occurred in the holiday. She had no known contacts with other people with a travel history outside Europe. She tested positive on Seegene Allplex with Ct E/N/RdRP-S= 18/23/29. She was doubly vaccinated by Pfizer/BioNTech, with last dose on July 17, 2021. Her partner and 2 children also tested positive (no samples available for sequencing). Mutation-specific Seegene Novaplex indicated an abnormal profile in an epidemiologic context of 90% Omicron/10% Delta in baseline surveillance by whole genome sequencing: S:N501Y(+), E484K (-) and del69/70 (-), hence selection of sample for whole genome sequencing using Illumina SARS-CoV-2 Research panel.

Sequencing QC metrics were good:
Total number of reads: 118226
Error rate:0.72%
Median/Mean/Q25/Q75 depth of sequencing: 642/755/418/775
Number of missing nucleotides: 182
Number of variant positions: 60 (Freebayes and GATK Mutect2)
Possibly contaminated positions: 3 (ok)

The consensus FASTA sequence showed a very high mutational load, and a profile that was distinct from the epidemiologically prevailing Omicron and Delta lineages, with absence of typical amplicon dropouts in the SARS-CoV-2 Research panel amplicon design, that was indicative for an older, ancestral lineage.
Overall QC: good
Total substitutions: 58
Total deletions:58
Total insertions:0
Total missing: 182
Mutations of interest: N501Y, R346S, F490R
Absence of L452R and other Delta-defining mutations
Absence of Omicron defining mutations

Manual curation indicated a relatively high degree of resemblance to the B.1.640.2 lineage originated from South of France/Cameroon idenfied by IHU Marseille (D. Raoult et al. MedRxiv : https://doi.org/10.1101/2021.12.24.21268174 ) but also clear divergence with > 20 additional/different amino acid substitutions and a remarkable 9 amino acid deletion in Spike affecting amino acid 136-144. As compared to the B.1.640.2, also the E484K mutation was missing, tested both by Novaplex and by WGS (good coverage at 23012-23014 corresponding to ORF2 amino acid 484.

Mutation analysis was done by in-house developed pipeline using FreeBayes and GATK-Mutect2

The amino acid substitutions in this unclassified isolate were:
M:I82T,N:D22Y,N:T205I,N:K373N,N:E378Q,ORF1a:M85V,ORF1a:P309L,ORF1a:E452G,ORF1a:S1188L,ORF1a:L2119F,ORF1a:A2355S,ORF1a:S3149F,ORF1a:R3164H,ORF1a:T3255I,ORF1a:V3718A,ORF1b:P314L,ORF1b:D884Y,ORF1b:K2557R,ORF3a:T32I,ORF3a:Q57H,ORF8:Q27*,ORF9b:I5T,ORF9b:Q18H,S:P9L,S:V11F,S:E96Q,S:R190S,S:I210T,S:R346S,S:N394S,S:Y449N,S:F490R,S:N501Y,S:D614G,S:P681H,S:T859N,S:D936H,S:A942S

The amino acid deletions in this unclassified isolate were:
ORF1a:G82-,ORF1a:H83-,ORF1a:V84-,S:C136-,S:N137-,S:D138-,S:P139-,S:F140-,S:L141-,S:G142-,S:V143-,S:Y144-

To date, we have no proof of additional local transmission, though we will monitor the situation by a combination of Novaplex and WGS. We submit this issue to ask support by Pango designation comittee in assigning this isolate, and potentially finding other similar cases.

DJ Lots of mutations and deletions-again-making this variant a big ?








Also a B1.1 ?

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: April 03 2022 at 12:28am

Recombinations;

[url]https://www.coronaheadsup.com/science/recombination/recombination-details-on-xd-xe-and-xf-recombinants-by-tom-peacock/[/url] or https://www.coronaheadsup.com/science/recombination/recombination-details-on-xd-xe-and-xf-recombinants-by-tom-peacock/ 

There’s a new thread on Twitter by Tom Peacock of Imperial College covering the latest information on the SARS-CoV-2 recombinants XD, XE and XF.

XD is the new name for the French Delta x BA.1 lineage.

XE is a large UK BA.1 x BA.2 lineage. Sequenced and verified by @UKHSA and @sangerinstitute, first identified by @nzm8qs

XF is a UK Delta x BA.1 lineage. Again sequenced and verified by @UKHSA and first identified by @nzm8qs

and [url]https://www.coronaheadsup.com/science/recombination/netherlands-ba-1-1-ba-2-recombinant-designated-xm/[/url] or https://www.coronaheadsup.com/science/recombination/netherlands-ba-1-1-ba-2-recombinant-designated-xm/

A recombinant SARS-CoV-2 variant originally sequenced in the Netherlandshas been designated XM. It’s a combination of the Omicron BA1.1 and BA.2 subvariants.

From Gisaid:

Recombinant between: BA.1.1 & BA.2
Earliest sequence: 2022/2/21 (NL-NH)
Most recent sequence: 2022/3/04 (NL-NH)
Countries circulating: Netherlands (NH)
Likely breakpoint: between 17410 and 19995 (NSP13 or NSP14 or NSP15, ORF1b).
Cov-spectrum query: C15240T, C2470T, A18163G, C19955T, A20055G

Genomes:
hCoV-19/Netherlands/NH_AUMC-004734/2022 EPI_ISL_10925473 2022-03-04
hCoV-19/Netherlands/NH_AUMC-004178/2022 EPI_ISL_10925492 2022-02-21

https://cov-spectrum.org/explore/Netherlands/AllSamples/Past6M/variants?nucMutations=C15240T%2CC2470T%2CA18163G%2CC19955T%2CA20055G

See also [url]https://twitter.com/PeacockFlu/status/1510233225595174913[/url] or https://twitter.com/PeacockFlu/status/1510233225595174913 ;

BA.1 x BA.2 recombinants. Includes 2 more UK recombinants (XP, XQ & XR - all spotted by ). XP is interesting as it actually has the Spike from BA.1.1 (ie R346K)


Image

DJ, Some of the recombinations show "better spread "...could become next Variants Of Concern....[url]https://twitter.com/josetteschoenma[/url] or https://twitter.com/josetteschoenma very active here....

BA.2 subvariants;

[url]https://twitter.com/RajlabN/status/1507751923151216658?ref_src=twsrc%5Etfw%7Ctwcamp%5Etweetembed%7Ctwterm%5E1507751923151216658%7Ctwgr%5E%7Ctwcon%5Es1_&ref_url=https%3A%2F%2Fwww.coronaheadsup.com%2Fcoronavirus%2Findia-first-delta-ba-2-recombinant-recorded-in-karnatka%2F[/url] or https://twitter.com/RajlabN/status/1507751923151216658?ref_src=twsrc%5Etfw%7Ctwcamp%5Etweetembed%7Ctwterm%5E1507751923151216658%7Ctwgr%5E%7Ctwcon%5Es1_&ref_url=https%3A%2F%2Fwww.coronaheadsup.com%2Fcoronavirus%2Findia-first-delta-ba-2-recombinant-recorded-in-karnatka%2F ;

New #PANGO designations - BA.2.* BA.2.4Alias of B.1.1.529.2.4, #Singapore lineage BA.2.5Alias of B.1.1.529.2.5, lineage in #Portugal and other countries BA.2.6Alias of B.1.1.529.2.6, lineage in #France and other countries BA.2.7Alias of B.1.1.529.2.7, #USA lineage

DJ, It would be very optimistic to believe this is even the tip of the iceberg...

[url]https://github.com/cov-lineages/pango-designation/issues[/url] or https://github.com/cov-lineages/pango-designation/issues also did see further BA.2 subvariants, possible BA.4 

It looks like they are simply ignored by the "main stream" since the "pandemic has to be over"....


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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: April 03 2022 at 2:05am

DJ, BA.2.1 = UK linked, BA.2.2 Hong Kong, BA.2.3 Philippines

[url]https://www.coronaheadsup.com/health/children/hong-kong-ba-2-causes-7-times-more-deaths-among-hospitalised-children-than-flu/[/url] or https://www.coronaheadsup.com/health/children/hong-kong-ba-2-causes-7-times-more-deaths-among-hospitalised-children-than-flu/ 

[url]https://www.thailandmedical.news/news/breaking-american-scientist-from-arkansas-state-university-alerts-scientific-community-of-numerous-ba-2-subvariants-that-have-alarmingly-emerged[/url] or https://www.thailandmedical.news/news/breaking-american-scientist-from-arkansas-state-university-alerts-scientific-community-of-numerous-ba-2-subvariants-that-have-alarmingly-emerged 

DJ-[url]https://www.coronaheadsup.com/health/animals/deer/us-delta-variant-found-in-utah-mule-deer/[/url] or https://www.coronaheadsup.com/health/animals/deer/us-delta-variant-found-in-utah-mule-deer/ ;

“On March 22, the APHIS’ National Veterinary Services Lab in Ames, Iowa confirmed a case of the SARS-CoV-2 delta variant in one of the samples submitted from a female mule deer in Morgan County. Only one deer tested positive for the virus from the nasal samples, but several other Utah deer had the antibodies in their blood samples, indicating the virus had been in the deer population prior to the capture.”

Officials don’t yet know how the deer were originally exposed to the virus and are investigating further to determine whether it was from another animal or a human.

Wildlife.Utah.gov report

 

SARS-CoV-2 virus in Saskatchewan white-tailed deer

A team from the University of Saskatchewan (USask) found positive results in viral RNA swabs taken from four white-tailed deer harvested in 2021.

The National Centre for Foreign Animal Disease confirmed the results, which represent two percent of 227 white-tailed deer tested in Saskatchewan. Ten percent of 62 white-tailed deer tested also had SARS-CoV-2 antibodies—indicating previous exposure or active infection.

University of Saskatchewan article

 

94.4% of captive deer at a Texas park seropositive for SARS-CoV-2

Through a cross-sectional study of 80 deer at three captive cervid facilities in central and southern Texas, we provide evidence of 34 of 36 (94.4%) white-tailed deer at a single captive cervid facility seropositive for SARS-CoV-2 by neutralization assay (PRNT90), with endpoint titers as high as 1,280.

Preprint: High Seroprevalence of SARS-CoV-2 in White-Tailed Deer (Odocoileus virginianus) at One of Three Captive Cervid Facilities in Texas 

CoViD/SARS-2 is now widespread in animals...with very likely some of the variants becoming better able to (re)infect humans...

So;

-recombinations ; XA to XR often BA variants involved

-BA. variants, BA.2.1 to at least BA.2.7 very likely a lot more

-animal SARS-2 variants....

DJ We are now in a phase were the virus may be in "hundreds of millions of hosts" (far more then the close to 60 million "active cases") spreading, mutating, recombinating etc....

Of course, this is just an opinion/observation...I am NOT an expert, also NOT objective, neutral etc...

This pandemic is like a "climate change on stroids" risk for humans...so "we look away"....

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Post Options Post Options   Thanks (0) Thanks(0)   Quote KiwiMum Quote  Post ReplyReply Direct Link To This Post Posted: April 03 2022 at 1:27pm

I just posted this on another thread but it's relevant here as I suspect this is the new B2.2

A sister of mine in Australia went to her choir practice 2 weeks ago. They met outside and stood 2 metres apart from each other and sang for 30 minutes. She wore her mask the entire time, no one else did. Two days later she started to feel unwell with a sore throat, by the end of the week 16 out of the 20 people present had tested positive to Covid. And they were outside!!!!!

That's how contagious it is!

"Once you've decided that something's absolutely true, you've closed your mind on it, and a closed mind doesn't go anywhere. Question everything. That's what education's all about." ~ David Eddings
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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: April 03 2022 at 9:58pm

KiwiMum, the idea that "6 feet" social distance would do "the work" by now is unrealistic...

New variants [url]https://en.wikipedia.org/wiki/Exponential_growth[/url] or https://en.wikipedia.org/wiki/Exponential_growth 

The graph illustrates how exponential growth (green) surpasses both linear (red) and cubic (blue) growth.
  Exponential growth

Exponential growth is a process that increases quantity over time. It occurs when the instantaneous rate of change (that is, the derivative) of a quantity with respect to time is proportional to the quantity itself.


DJ With cases going up, variants went up...


We may soon be in an "Ocean" of variants able to co-infect..

So you may not only catch BA.2.1 but also recombination XC or XE...at the same time..

possibly creating yet another (sub)variant...while you catch BA.2.17 "new" or yet another recombi-type 

next week...


Of course I hope to be totally wrong !

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: April 04 2022 at 8:00am

[url]https://www.pango.network/summary-of-designated-omicron-lineages/[/url] or https://www.pango.network/summary-of-designated-omicron-lineages/ ;

We’ve added a number of lineages within BA.1 and BA.2. As previously outlined for Delta lineages, these lineages have been designated to enable researchers to track the virus on a finer scale. Their designation does not imply any biological difference and, like BA.1 and BA.2, they correspond to the WHO-defined Omicron variant (https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/)

Below is a summary of the lineages within BA.1 and BA.2 that have been designated to date, including their dominant geographical locations and associated mutations. We anticipate that additional lineages within BA.1 and BA.2 will continue to follow and will add any future lineages to this table.

Table of currently designated BA.1 and BA.2 lineages, their predominant geographical location(s) and their associated mutation(s). Note that the listed mutations are those that occurred along the phylogenetic branch immediately preceding the common ancestor of the lineage. These mutations are therefore those that separate the lineage from closely related sequences but may not be all of the mutations that separate them from other lineages.

BA.1.1MultipleG22599A (S:R346K)
BA.1.1.1EuropeA16064G (Orf1ab:Q5267R)
BA.1.1.2JapanC10560G (Orf1ab:T3432S)
BA.1.1.3SwitzerlandC23934T (ST791I), A28416G (N:N48S)
BA.1.1.4UKT25711C (Orf3a:Y107H)
BA.1.1.5South KoreaA2589G (Orf1ab:E775G)
BA.1.1.6CanadaC28757T (N:P162S)
BA.1.1.7India and other countriesC2453T (Orf1ab:L730F)
BA.1.1.8USAC1766A (Orf1ab:Q501K)
BA.1.1.9New ZealandC13421T (Orf1ab:L4386F)
BA.1.1.10CanadaC12513T (Orf1ab:T4083M)
BA.1.1.11EuropeG2354A (Orf1ab:G697R)
BA.1.1.12UKC2942A (Orf1ab:L893M)
BA.1.1.13UKC26078T (Orf3a:T229I)
BA.1.1.14Europe, paricularly UKA14107G (Orf1ab:I4615V)
BA.1.1.15Europe, AustraliaG13570A (Orf1ab:G4436S)
BA.1.1.16Canada, USAC27509G (Orf7a:T39R)
BA.1.2Mayotte, ReunionC7420T (synonymous), C11669T (Orf1ab:R3802C)
BA.1.3CanadaA3481G (synonymous), C8645T (Orf1ab:H2794Y)
BA.1.4FranceG23351A (S:V597I)
BA.1.5UKC24054T (S:A831V)
BA.1.6Canada, Sint MaartenC17639T (Orf1ab:S5792L)
BA.1.7UKC27686T (Orf7a:S98F)
BA.1.8EuropeC23987T (S:P809S)
BA.1.9BrazilC23673T (S:S704L)
BA.1.10UKA17042G (Orf1ab:Y5593C)
BA.1.12UKG22487C (S:E309Q)
BA.1.13Europe, particularly FranceG1957T (Orf1ab:K564N)
BA.1.13.1IndonesiaG19684T (Orf1ab:V6474L)
BA.1.14Brazil and other countriesC12786T (Orf1ab:T4174I)
BA.1.15USA and other countriesC25708T (Orf3a:L106F)
BA.1.15.1UKA24803G (S:I1081V)
BA.1.16UKT3104C (Orf1ab:Y947H)
BA.1.16.1Thailand, Singapore, IndonesiaG9758A (Orf1ab:V3165I)
BA.1.17Europe, North America, AustraliaG5924A (Orf1ab:V1887I)
BA.1.17.1AustraliaC4683T (Orf1ab:A1473V)
BA.1.17.2MultipleC23664T (S:A701V)
BA.1.18Europe, North AmericaC5730T (Orf1ab:T1822I)
BA.1.19EuropeC21034T (Orf1ab:L6924F)
BA.2.1UKC12789T (Orf1ab:T4175I)
BA.2.2Hong KongC12525T (Orf1ab:T4087I)
BA.2.3Philippines and other countriesC8991T (Orf1ab:A2909V)
BA.2.3.1JapanC23591G (S:Q677E)
BA.2.4SingaporeT27374A (Orf6:M58K)
BA.2.5Europe, particularly PortugalC3317T (Orf1ab:P1018S)
BA.2.6France and other countriesG25471C (Orf3a:D27H)
BA.2.7USAC6636T (Orf1ab:T2124I)
BA.2.8UKG25483A (Orf3a:A31T)
BA.2.9EuropeC25624T (Orf3a:H78Y)
BA.2.10MultipleT16342C (Orf1ab:S5360P)








#NewCoV2Lineages #Alert  BA.2.10.1Alias of B.1.1.529.2.10.1, Prevalent in #Singapore and other countries BA.2.3.2Alias of B.1.1.529.2.3.2, Prevalent in #Vietnam and #Japan  Summary of PANGO designations: https://pango.network/summary-of-designated-omicron-lineages/

DJ [url]https://github.com/cov-lineages/pango-designation/issues[/url] or https://github.com/cov-lineages/pango-designation/issues lots of new subvariants/recombinations being detected...however most will not be found soon due to lack of testing...

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: April 05 2022 at 12:13am

New subvariants BA.2.3.2 and BA.2.10.1

BA.2.3.2 (aka B.1.1.529.2.3.2) | Prevalent in #Vietnam #Japan and other countries Key mutations: E:S55F COV-spectrum predicts a global growth advantage of 12% over BA.2 and 64% over BA.1.1

-








#NewCoV2Lineages #Alert  BA.2.10.1Alias of B.1.1.529.2.10.1, Prevalent in #Singapore and other countries BA.2.3.2Alias of B.1.1.529.2.3.2, Prevalent in #Vietnam and #Japan  


See also [url]https://www.pango.network/summary-of-designated-omicron-lineages/[/url] or https://www.pango.network/summary-of-designated-omicron-lineages/  being updated. 

With potential much more in [url]https://github.com/cov-lineages/pango-designation/issues[/url] or https://github.com/cov-lineages/pango-designation/issues 

[url]https://outbreak.info/situation-reports[/url] or https://outbreak.info/situation-reports now over 50 Omicron BA. subvariants...real number may be in the thousends...

B.1.1.529



DJ BA.2.3.2, BA.2.10.1 not yet included (BA.4 South Africa [url]https://github.com/cov-lineages/pango-designation/issues/455[/url] or https://github.com/cov-lineages/pango-designation/issues/455 under discussion ?)

Recombinations have a "X" name (so from "XA" to at least "XM"...)-however may also become a "BA" subvariant (or another non-Omicron named variant ?)

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: April 07 2022 at 3:01am

From [url]https://twitter.com/RajlabN[/url] or https://twitter.com/RajlabN doing a lot of good hard work resulting in bad news...


BA.4  alias of BA.1.1.529.4 

BA.5  alias of BA.1.1.529.5 

BA.2.11 alias of BA.1.1.529.2.11 

BA.2.12 alias of BA.1.1.529.2.12 

BA.2.12.1 alias of BA.1.1.529.2.12.1

DJ both [url]https://outbreak.info/situation-reports[/url] or https://outbreak.info/situation-reports and [url]https://www.pango.network/summary-of-designated-omicron-lineages/[/url] or https://www.pango.network/summary-of-designated-omicron-lineages/  no doubt will be updated further...

Of course BA.4, BA.5 is bad news ! [url]https://twitter.com/RajlabN/status/1511699260265353223[/url] or https://twitter.com/RajlabN/status/1511699260265353223 (more updates on its way...)

[url]https://twitter.com/PeacockFlu/status/1511732151447953412[/url] or https://twitter.com/PeacockFlu/status/1511732151447953412








There is propensity to hop H->Z in Mink, White Tail Deer. Variants seen in WTD indicate ongoing hops. Analysis of BA.1's affinity for native mouse ACE2 strongly suggests zoonotic pool (African mouse?) Ongoing H-Z hops with Z-H return fits observations. Who searches for  pool?

-










Mogelijke BA.4 en BA.5 gevonden. Voornamelijk in Zuidelijk Afrika.

DJ, "Possible BA.4 and BA.5 detected. Mostly in southern Africa. Namibia cases +163%, Eswatini +81%, Congo +43%, Kenya +36%, Zambia +10%, South Africa +2%, Zimbabwe however -37%, Malawi -21%, Lesotho -42% (but test availability will be a major factor...)


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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: April 11 2022 at 4:50am

[url]https://www.coronaheadsup.com/asia/china/china-omicron-subvariant-detected-in-beijing/[/url] or https://www.coronaheadsup.com/asia/china/china-omicron-subvariant-detected-in-beijing/ 

Chinese state news has announced that they have uncovered new Covid cases in Beijing caused by a subvariant of Omicron. They haven’t said exactly which subvariant of Omicron though.

DJ....is it "new" as not seen anywhere else yet...or new to Bejing ? 

[url]https://www.abc.net.au/news/2022-04-09/qld-coronavirus-covid-new-variant-deltacron/100958122[/url] or https://www.abc.net.au/news/2022-04-09/qld-coronavirus-covid-new-variant-deltacron/100958122 ; The new variant was initially detected in February in the north of France and has been steadily popping up around the world, particularly in Europe and the United States.

DJ, So the Australian "new variant" has been around two months but is new for Australia...

[url]https://github.com/cov-lineages/pango-designation/issues[/url] or https://github.com/cov-lineages/pango-designation/issues two new BA.4 and 2 new BA.5 subvariants detected....

[url]https://www.thailandmedical.news/news/breaking-debut-of-sars-cov-2-ba-4,-ba-5-variants,-recombinant-xe-variant-and-more-than-34-other-subvariants-heralds-doomsday-scenario[/url] or https://www.thailandmedical.news/news/breaking-debut-of-sars-cov-2-ba-4,-ba-5-variants,-recombinant-xe-variant-and-more-than-34-other-subvariants-heralds-doomsday-scenario an overload of new sub-variants recombinations etc...

DJ-It will get much harder to follow new variants;

-Less (PCR) testing means also less sequencing...so we may simply not know what variants are spreading where..

-Sewage sampling-good early warning for variants-is not increasing enough to compensate for less testing (???)

-With this many subvariants, recombinations etc you may end up in an "ocean" of different types..









#CoronavirusUpdates #HospitalCapacity #UnitedStates  Are we ready to handle another #COVID #WAVE? In-patients beds are >75% full in 25 States + DC ICU beds are >75% full in 16 States + DC https://public.tableau.com/app/profile/raj.rajnarayanan/viz/HospitalCapacity-USA/HospitalCapacity

DJ North America could be facing another-more serious-wave...some of the variants seem more dangerous BA.2.12.1 (spreading in New York-Thailand Medical News-link).[url]https://outbreak.info/location-reports?loc=USA_US-NY&dark=true[/url] or https://outbreak.info/location-reports?loc=USA_US-NY&dark=true still not included in the Outbreak.info subvariants...

We cannot solve our problems with the same thinking we used when we created them.
~Albert Einstein
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Post Options Post Options   Thanks (0) Thanks(0)   Quote roni3470 Quote  Post ReplyReply Direct Link To This Post Posted: April 11 2022 at 7:36pm

Wait....so is it or isn't it that latest one we know about.....or do we know?

NOW is the Season to Know

that Everything you Do

is Sacred
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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: April 20 2022 at 1:47pm

[url]https://www.pango.network/summary-of-designated-omicron-lineages/[/url] or https://www.pango.network/summary-of-designated-omicron-lineages/ ;

BA.1.1MultipleG22599A (S:R346K)
BA.1.1.1EuropeA16064G (Orf1ab:Q5267R)
BA.1.1.2JapanC10560G (Orf1ab:T3432S)
BA.1.1.3SwitzerlandC23934T (ST791I), A28416G (N:N48S)
BA.1.1.4UKT25711C (Orf3a:Y107H)
BA.1.1.5South KoreaA2589G (Orf1ab:E775G)
BA.1.1.6CanadaC28757T (N:P162S)
BA.1.1.7India and other countriesC2453T (Orf1ab:L730F)
BA.1.1.8USAC1766A (Orf1ab:Q501K)
BA.1.1.9New ZealandC13421T (Orf1ab:L4386F)
BA.1.1.10CanadaC12513T (Orf1ab:T4083M)
BA.1.1.11EuropeG2354A (Orf1ab:G697R)
BA.1.1.12UKC2942A (Orf1ab:L893M)
BA.1.1.13UKC26078T (Orf3a:T229I)
BA.1.1.14Europe, paricularly UKA14107G (Orf1ab:I4615V)
BA.1.1.15Europe, AustraliaG13570A (Orf1ab:G4436S)
BA.1.1.16Canada, USAC27509G (Orf7a:T39R)
BA.1.1.17USAG1659T (Orf1ab:G465V)
BA.1.1.18USAC7926T (Orf1ab:A2554V)
BA.1.2Mayotte, ReunionC7420T (synonymous), C11669T (Orf1ab:R3802C)
BA.1.3CanadaA3481G (synonymous), C8645T (Orf1ab:H2794Y)
BA.1.4FranceG23351A (S:V597I)
BA.1.5UKC24054T (S:A831V)
BA.1.6Canada, Sint MaartenC17639T (Orf1ab:S5792L)
BA.1.7UKC27686T (Orf7a:S98F)
BA.1.8EuropeC23987T (S:P809S)
BA.1.9BrazilC23673T (S:S704L)
BA.1.10UKA17042G (Orf1ab:Y5593C)
BA.1.12UKG22487C (S:E309Q)
BA.1.13Europe, particularly FranceG1957T (Orf1ab:K564N)
BA.1.13.1IndonesiaG19684T (Orf1ab:V6474L)
BA.1.14Brazil and other countriesC12786T (Orf1ab:T4174I)
BA.1.14.1BrazilC11109T (Orf1ab:A3615V)
BA.1.14.2BrazilC1812T (Orf1ab:A516V)
BA.1.15USA and other countriesC25708T (Orf3a:L106F)
BA.1.15.1UKA24803G (S:I1081V)
BA.1.15.2USAC23444A (S:Q628K)
BA.1.16UKT3104C (Orf1ab:Y947H)
BA.1.16.1Thailand, Singapore, IndonesiaG9758A (Orf1ab:V3165I)
BA.1.16.2GreeceA28254G (Orf8:I121V)
BA.1.17Europe, North America, AustraliaG5924A (Orf1ab:V1887I)
BA.1.17.1AustraliaC4683T (Orf1ab:A1473V)
BA.1.17.2MultipleC23664T (S:A701V)
BA.1.18Europe, North AmericaC5730T (Orf1ab:T1822I)
BA.1.19EuropeC21034T (Orf1ab:L6924F)
BA.1.20USAC28472T (N:P67S)
BA.1.21EuropeG27762T (Orf7b:E3*)
BA.1.21.1ItalyT15685A (Orf1ab:L5141M)
BA.1.22PeruG3182A (Orf1ab:E973K)
BA.2.1UKC12789T (Orf1ab:T4175I)
BA.2.2Hong KongC12525T (Orf1ab:T4087I)
BA.2.3Philippines and other countriesC8991T (Orf1ab:A2909V)
BA.2.3.1JapanC23591G (S:Q677E)
BA.2.3.2Vietnam, JapanC26408T (E:S55F)
BA.2.3.3Papua New Guinea, AustraliaA28881G (N:K203R)
BA.2.3.4CanadaA23484G (S:N641S)
BA.2.4SingaporeT27374A (Orf6:M58K)
BA.2.5Europe, particularly PortugalC3317T (Orf1ab:P1018S)
BA.2.6France and other countriesG25471C (Orf3a:D27H)
BA.2.7USAC6636T (Orf1ab:T2124I)
BA.2.8UKG25483A (Orf3a:A31T)
BA.2.9EuropeC25624T (Orf3a:H78Y)
BA.2.9.1UKC22916A (S:L452M)
BA.2.10MultipleT16342C (Orf1ab:S5360P)
BA.2.10.1Singapore and other countriesG23955A (S:G798D)
BA.2.11FranceT22917G (S:L452R)
BA.2.12North America, EuropeC23673T (S:S704L)
BA.2.12.1USAT22917A (S:L452Q)
BA.2.13EuropeC22916A (S:L452M)
BA.2.14DenmarkG21753T (S:W64L)
BA.2.15South AfricaC9714T (Orf1ab:T3150I), G21753T (S:W64L)
BA.2.16UKC29160T (N:T296I)
BA.2.17Vietnam, JapanG25909T (Orf3a:D173Y)
BA.2.18UKA22812C (S:N417T)
BA.2.19GermanyC1263T (Orf1ab:T333M)
BA.2.20CanadaA22005C (S:N148T), C28498T (synonymous)
BA.2.21Canada, USAA8763G (Orf1ab:D2833G), G12160A (synonymous)
BA.2.22UKT22119C (S:F186S)
BA.2.23UKG670T (Orf1ab:R135S)
BA.2.24JapanG22577A (S:D339N)
BA.2.25SwedenA1652G (Orf1ab:I463V)
BA.2.25.1SlovakiaC22624T (synonymous), G25681A (Orf3a:V97I)
BA.2.26USAC2003T (Orf1ab:L580F)
BA.2.27ThailandG3514A (Orf1ab:M1083I)
BA.2.28SingaporeA6610C (Orf1ab:R2115S)
BA.2.29JapanG2012A (Orf1ab:A583T)
BA.2.30CuracaoG26109T (Orf3a:E239D)
BA.2.31IsraelG12071A (Orf1ab:D3936N)
BA.2.32IndonesiaG27589T (Orf7a:A66S)
BA.2.33AustraliaC3903T (Orf1ab:P1213L)
BA.2.34NorwayG29000A (N:G243S)
BA.2.35USAC6285T (Orf1ab:T2007I)


DJ recombinations is another list... These are far from complete, BA.3, BA.4 and BA.5 is not yet in this list

We cannot solve our problems with the same thinking we used when we created them.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: May 07 2022 at 10:40am







#OmicronUpdates #NewLineagesAlert BA.2.33 - prevalent in #Australia BA.2.32 - #Indonesia BA.2.31 - #Israel BA.2.30 - #Curacao BA.2.29 - #Japan BA.2.28 - #Singapore BA.2.27 - #Thailand BA.2.3.3 - #PapuaNewGuinea

-

#OmicronUpdates #NewLineagesAlert BA.3.1  alias of B.1.1.529.3.1 | Prevalent in #Poland Key mutations: S:K417T and ORF1a:A1176N PANGO issues: #540 | https://github.com/cov-lineages/pango-designation/issues/540

and

#NewLineagesAlert #OmicronUpdates  BA.2.38   Alias of B.1.1.529.2.38 | Prevalent in #India  (Key mutation: Spike K417T) BA.2.12 sequences with Spike L452Q from #Canada now designated as BA.2.12.1 Pango issues: https://github.com/cov-lineages/pango-designation/issues/541 and https://github.com/cov-lineages/p

see also [url]https://outbreak.info/situation-reports[/url] or https://outbreak.info/situation-reports still missing a lot of new ones...

[url]https://www.coronaheadsup.com/science/variants/recombinants/brazil-2-cases-of-xq-omicron-recombinant-reported/[/url] or https://www.coronaheadsup.com/science/variants/recombinants/brazil-2-cases-of-xq-omicron-recombinant-reported/ 

BREAKING🔔 The 9th preprint from G2P-Japan🇯🇵 is out at . We evaluated the effects of 8 therapeutic monoclonal antibodies against new #Omicron subvariants such as BA.2.11, BA.2.12.1, BA.4 and BA.5. Please RT. 1/5

[url]https://www.biorxiv.org/content/10.1101/2022.05.03.490409v1[/url] or https://www.biorxiv.org/content/10.1101/2022.05.03.490409v1 

We cannot solve our problems with the same thinking we used when we created them.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: July 13 2022 at 8:16am

Since the WHO is simply not doing its job (as well) "someone"named BA.2.75 "Centaurus" (It may be named BA.2.73...DJ No idea if BA.2.74 and 2.76 to 2.79 +? also may be redifined as "Centaurus"...the WHO may stick to "politics" of naming all new variants "Omicron"...) 

[url]https://public.tableau.com/app/profile/raj.rajnarayanan/viz/TrackingBA_2_75LineageOverTime/BA_2_75[/url] or https://public.tableau.com/app/profile/raj.rajnarayanan/viz/TrackingBA_2_75LineageOverTime/BA_2_75; 

Tracking BA.2.75 Lineage Over Time

byRaj Rajnarayanan






DJ (follow link-may be updated later on...) 






Raj Rajnarayanan

@RajlabN
 · 
Tracking #Centaurus (BA.2.75) #SARSCoV2 #lineage over time Hotspots: #Maharastra#Delhi#WestBengal#Karnataka  (#India) Key signature mutations (for tracking purpose) - NSP3_S403L, NSP8_N118S   Other mutations: Spike 147E, 152R, 446S & 493Q https://public.tableau.com/app/profile/raj.rajnarayanan/viz/TrackingBA_2_75LineageOverTime/BA_2_75

and 

Yep. If the WHO will continue to believe there is only one Omicron variant, the social network will fill the gap.

-

Ed Yong

@edyong209
 · 
It is wild to me that some random guy on Twitter decided that the BA.2.75 variant was going to be known as "Centaurus" and it completely worked.

so...I think scientists may be fed up with the WHO "name everything Omicron" policy...

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: July 13 2022 at 8:29am
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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: August 26 2022 at 10:11am