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 ? 

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.

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...

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, E272G; NSP3 – 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 – Δ106-108, T181I; 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...). 

[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.

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

[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  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 . 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...

Oliver Alexander

@OAlexanderDK

·

2 jan.

A 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.

An update from the same newspaper

https://www.dailymail.co.uk/news/article-10367101/French-Covid-variant-NOT-worth-worrying-scientists-say.html

Flo Débarre

@flodebarre

·

6 jan.

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. 7/7

2

14

26

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...

Josette Schoenmakers

@JosetteSchoenma

·

3 u

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 ). Newest graphs based on 

@GISAID

 data here, based on 700+ samples on the 2nd of January)

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..

[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 ?

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"....

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

  Cubic growth

  Linear 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 !

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

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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 ?)

[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..

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...

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

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

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; 

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

Raj Rajnarayanan

@RajlabN

 · 23h

and 

shay fleishon 

@shay_fleishon

·

36m

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