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Now tracking the new emerging South Africa Omicron Variant

Deltacron

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Dutch Josh View Drop Down
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    Posted: January 08 2022 at 11:14pm

[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/ ;

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

 

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

DJ Maybe using the Greek AlphaBet is not such a good idea ? See also [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 

(Will post more info at New Variants later on...) 

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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 4:48am

Maybe the discussion on "Deltacron" has to split; 








Small update: the Cypriot 'Deltacron' sequences reported by several large media outlets look to be quite clearly contamination - they do not cluster on a phylogenetic tree and have a whole Artic primer sequencing amplicon of Omicron in an otherwise Delta backbone.

DJ There may not be a "Deltracon" variant....[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/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.

DJ So is it a Delta-subvariant ? Is it a co-infection with both Delta and Omicron ? 


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Post Options Post Options   Thanks (0) Thanks(0)   Quote cobber Quote  Post ReplyReply Direct Link To This Post Posted: January 11 2022 at 4:23am

DeltaCon

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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 16 2022 at 7:59am

No not realy Delta"con" but co-infection. I do not know if co-infection is "better news" then an DeltaCron variant. It may bring more severe disease for those that catch both, a form of "Delta" and a form of "Omicron" (wonder what sub variants are involved)  but also may indicate "Delta" sticking around, mutating further, co-existing...

[url]https://www.coronaheadsup.com/science/co-infection/italy-2-cases-of-deltacron-reported-but-theyre-not-recombinant-variants/[/url] or https://www.coronaheadsup.com/science/co-infection/italy-2-cases-of-deltacron-reported-but-theyre-not-recombinant-variants/ ;

Italy: 2 cases of Deltacron reported, but they’re NOT recombinant variants

Two Deltacron cases have been reported in Italy, one in Padua and the other in Trento. They are NOT recombinant variants however, they are coinfections with both the Delta and Omicron variants.

The samples were found by Experimental Zooprophylactic Institute of the Venezie (IZSVe) in Legnaro at the beginning of January. The two infected are a patient residing in the province of Padua and one in the province of Trento.

Il Tiempo report (in Italian)

 

Doctor Antonia Ricci, director of the Zooprophylactic Institute of the Venezie, said “we do not have a sequence generated by the acquisition of mutations between two different variants. What we have found is not a new strain of Sars Cov-2 that combines Delta and Omicron – the only ones currently in circulation – creating a virological bomb in the common imagination, but rather they are samples that have both variants. In short, Delta and Omicron can co-infect the same person”

Larena.it report (in Italian)

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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 31 2022 at 4:55am

[url]https://github.com/cov-lineages/pango-designation/issues/422[/url] or https://github.com/cov-lineages/pango-designation/issues/422

Sequences:
hCoV-19/England/ALDP-2F86D33/2021|EPI_ISL_8166781|2021-12-19
hCoV-19/England/QEUH-312A66E/2022|EPI_ISL_8610834|2022-01-02
hCoV-19/England/ALDP-31AE19E/2022|EPI_ISL_8865709|2022-01-06
hCoV-19/England/ALDP-325CFB2/2022|EPI_ISL_8898412|2022-01-11

The ORF1ab region of these 4 genomes is more similar to Delta, while the remaining regions are more similar to Omicron. It seems that these genomes are recombinants of Delta and Omicron. Or just contamination?

DJ Most likely Deltacron recobinations just a matter of time...lots of Delta still aroung with Omicron variants also massive...not "if" but "when" in my opinion...

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Post Options Post Options   Thanks (1) Thanks(1)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: February 14 2022 at 11:58pm

First the github-links; 

Australia [url]https://github.com/cov-lineages/pango-designation/issues/437[/url] or https://github.com/cov-lineages/pango-designation/issues/437 

US [url]https://github.com/cov-lineages/pango-designation/issues/439[/url] or https://github.com/cov-lineages/pango-designation/issues/439 

UK [url]https://github.com/cov-lineages/pango-designation/issues/422[/url] or https://github.com/cov-lineages/pango-designation/issues/422 

[url]https://twitter.com/EnemyInAState/status/1492529796731002886[/url] or https://twitter.com/EnemyInAState/status/1492529796731002886 ; It's OFFICIAL, DELTACRON IS HERE IN THE UK: AND IT'S WORSE THAN WE THOUGHT: Delta has merged with Omicron and is now an official variant under investigation:

Kostrikis, has previously stated that he believed that Delta was taking on features of Omicron: rather than a true re-combination event in which the viruses merged: the UK has gone one better and shown that the two viruses have recombined to produce a new variant.

(DJ (Kostrikus-in Cyprus-was the first Dr. to detect cases of Deltacron...much discussion on the samples; was it co-infection, bad sampling ?)

Deltacron, is likely to be much more infectious and as severe as Delta, if not more so: based on what has been observed in Greek data.

Paul Hunter, who along side Tom Peacock, is one of the few people the media goes to for comment on a new variant, says that 'he's not overly worried about Deltacron' due to past immunity

So at the moment I'm not overly worried at the moment. If both Delta and Omicron are falling then, in theory, this [variant] should struggle to take off," Hunter said.

Nothing could be further from the truth: a hybrid virus could easily evade immunity.

'The new variant is believed to have evolved in a patient who caught both the Omicron and Delta variants at the same time'

This is just the worst thing you could imagine. There's no sugar coating it.

(DJ-Since Delta-sub-variants still are widespread and Omicron sub-variants still are spreading in high numbers there must be lots of recombinations...)

If the patient was immunocompromised and it lead to this recombination event spewing out Deltacron then God knows what we are dealing: this is potentially a true nightmare situation.

Chris Turnbull@EnemyInAState·Feb 12I'm actually super fucking angry right as well. This is happening a few weeks BEFORE they want to end all safety measures! Which means it's likely to spread as fast as fucking possible.

Deaths, admissions, cases, have all been at record highs in Greece and Cyprus since the announcement of Kostriki's Deltacron—which would be mild compared to this true recombination:

(DJ, Greece cases now at +0,7%,  deaths -15%, Cyprus cases-0,9%, deaths +144% (last 7 days 39, week before 16 population 1,2 million)


DJ, Writer of this twitterthread is a journalist, trying to make sense...The picture I have BA.2 will show how "bad" these forms of Deltacron are...I expect BA.2/BA.2+ (when will it become BA.2.1 ?) may dominate these forms of "Deltacron"...however if they (also) would be able to recombinate...with most countries now dropping restrictions-we may be in "very serious problems"...

One may claim "Omicron" itself could be seen as a "sort of SARS-3"...with most likely mice playing a role in development..."Deltacron" could be even further away from the Wuhan-starter-virus...(making immunity even less effective...). 

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: March 23 2022 at 5:33am

DJ;

[url]https://www.coronaheadsup.com/science/variants/deltacron/china-cdc-deltacron-is-a-grey-rhino-event/[/url] or https://www.coronaheadsup.com/science/variants/deltacron/china-cdc-deltacron-is-a-grey-rhino-event/ ;

Although the emergence and subsequent spread of these VOCs has had a huge impact on global health and economy, it may not have been the worst case until now, as recombination (a major mechanism bringing genetic diversity to coronaviruses) has not really emerged on a large scale and shown its power before the emergence of “Deltacron.” The emergence of “Deltacron” is therefore a “grey rhino” rather than “black swan” event.

Deltacron Is Just the Beginning

With the advent of “Deltacron,” further concerns are coming. According to our preliminary analysis on the first “Deltacron” genome, recombination event only occurs in S gene. However, recombination events involving all types of genes encoded by CoVs have been found in nature.  Consequently, the genetic recombination events involving other genes and/or the combination of other genes would also occur with high probability. Furthermore, the genetic recombination event of “Deltacron” occurs at the inter-lineage level, that is the parents of the “Deltacron” came from different lineages of the same species (AY.4 and BA.1), respectively.

-

In addition, the spillover events of SARS-CoV-2 between humans and animals in both directions (for example transmission of SARS-CoV-2 from humans to minks and then back to humans and further community transmission) have been found in nature.

Taken together, the probability of co-infection with SARS-CoV-2 and other types of CoVs or even other viruses in a single host would be high, leading to the occurrence of cross-species recombination with high probability. Therefore, it is difficult to predict which viral species SARS-CoV-2 will recombine with, and on which genes future recombination will occur. This kind of uncertainty is doomed to increase the likelihood of generating a novel recombinant virus with unknown risk to humans.

China CDC: Perspectives: The “Wolf” Is Indeed Coming: Recombinant “Deltacron” SARS-CoV-2 Detected (in English)

 

On "grey rhino's" [url]https://wisdomproject.substack.com/p/of-black-swans-and-grey-rhinos?s=r[/url] or https://wisdomproject.substack.com/p/of-black-swans-and-grey-rhinos?s=r ; Gray Rhino is a term used to define a danger that’s slow moving, obvious and yet is conveniently ignored. Somewhat of an opposite of a Black Swan.

We are actually talking about the concept of Black Swan Events.

Its a term used to define highly improbable events, impossible to predict, which have a massive impact on the world, but which seem obvious in hindsight.

DJ "unknown unknowns" may be another description...

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: March 23 2022 at 5:49am

[url]https://www.coronaheadsup.com/coronavirus/india-568-deltacron-cases-being-investigated/[/url] or https://www.coronaheadsup.com/coronavirus/india-568-deltacron-cases-being-investigated/ 

It’s beginning to look like Deltacron could be the next big thing….

“Genetic sequencing data from Indian SARS-CoV-2 Genomics Consortium (INSACOG) and GSAID indicates that there are 568 Covid sequences under investigation in various genetic laboratories in India that contain both the Delta and Omicron variants”

Telanganatoday.com

[url]https://telanganatoday.com/covid-sequences-under-scanner-telangana-reports-25-deltacron-cases[/url] or https://telanganatoday.com/covid-sequences-under-scanner-telangana-reports-25-deltacron-cases ;

Hyderabad: The imminent threat of new variants of coronavirus with a potential to fuel fresh surge in Covid infections continues to remain a cause of worry, as the latest genetic sequencing data from Indian SARS-CoV-2 Genomics Consortium (INSACOG) and GSAID indicates that there are 568 Covid sequences under investigation in various genetic laboratories in India that contain both the Delta and Omicron variants.

Popularly referred to as Deltacron, 25 such cases have been reported so far in Telangana while Karnataka remains a hotspot with 221, followed by 90 in Tamil Nadu, 66 in Maharashtra, 33 in Gujarat, 32 in West Bengal and 20 in New Delhi.

The presence of genetic signatures of both Delta and Omicron variants in 568 Covid sequences is an indication of the presence of recombinant virus, which means it contains genetic elements of both Delta and Omicron or contains genes from both the variants.

Health officials in Hyderabad assert that the growing evidence of recombination of Delta and Omicron suggests the coronavirus is constantly evolving, a good enough reason for people to be cautious and realise that the pandemic is hardly over.

DJ-I am NOT an expert, just trying to make sense; still a few remarks/questions;

-How good is present (very limited) testing able to detect "Deltacron"?

-Omicron did see high spread, Delta did see higher viral load/more severe disease (and over 220 Delta subvariants) , will "Deltacron" be able to result in a virus/variant(s0 with both high spread and high(er) viral load ? 

-If we stop all restrictions in most countries are recombinations now unstopable ?

-How much Delta (sub)variants are still around? Did chance of recombining Delta and Omicron become a risk of recent past ?

DJ-IF virus/variants "stay behind" in hosts then most likely a lot of hosts still may have forms of Delta...on top of that catching an Omicron variant may-still-result in "Deltacron" sub/new variants...and maybe spread undetected because tests miss it, non-human hosts etc...

I think another risk still may be in people catching Omicron-subvariants becoming easy "targets" for "out of season" flu...Not very likely/maybe even impossible to "re-combine" but very well able to "co-infect" and spread linked to Omicron spread...

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: March 23 2022 at 6:05am

[url]https://asia.nikkei.com/Spotlight/Coronavirus/Deltacron-variant-5-things-to-know-as-experts-downplay-danger[/url] or https://asia.nikkei.com/Spotlight/Coronavirus/Deltacron-variant-5-things-to-know-as-experts-downplay-danger ;

The new variant has been dubbed "deltacron," or "deltamicron," mainly by the media. Some scientists insist it is inappropriate to use such terms, which sound much scarier than the variant is likely to be in reality.

The WHO says it is "aware" of the recombinant, which combines the delta AY.4 and omicron BA.1 strains. But it has not adopted a formal name for it.

Amesh Adalja, senior scholar at the Johns Hopkins Center for Health Security, told Nikkei Asia in an email: "There's not enough information on cases, or virologically, to know what traits recombinant delta/omicron possesses. Because these recombinant forms differ in their recombination, the term "deltacron" doesn't make sense (except as clickbait). Which genes are recombined differs in these hybrids."

-

However, a small number of recombinant cases have continued to turn up, from Europe to the Americas.

This week in Brazil, the governments of two northern states informed the Health Ministry that they had found cases of deltacron. According to local media, a 34-year-old man and a 26-year-old woman were infected.

The ministry's investigation, however, appeared to find that at least one of the cases was not deltacron but rather a "co-infection" by omicron and delta, Brazilian media said on Friday. The investigation was ongoing.

-

According to GISAID, an international database of COVID-19 genomic information, the hybrid variant has cropped up in France, Denmark, Germany, the Netherlands and Belgium. As of this week, France had found the highest number of cases, 38, followed by Denmark, with eight. Cases had yet to be reported in Asia.

A paper suggesting that at least two cases have been found in the U.S. was released on medRxiv, a website that publishes pre-peer-reviewed medical papers.

How worrying is it?

Not very, at least for now.


DJ-I think "Delta-cron" is downplayed in the media...because it would indicate pandemic-strategies are "not very effective"....The new BA.2 subvariants may spread even faster/more (30-45%) then BA.1 (sub)variants did...I think maybe other subtypes of "Delta" then only AY.4 may be able to "recombine"...

For that matter one could wonder if Hong Kong [url]https://www.coronaheadsup.com/asia/hong-kong/hong-kong-omicron-ba-2-with-si1221t-mutation-designated-ba-2-2/[/url] or https://www.coronaheadsup.com/asia/hong-kong/hong-kong-omicron-ba-2-with-si1221t-mutation-designated-ba-2-2/ AY.127 "hamster-delta" managed to get into Omicron ? 


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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: March 23 2022 at 9:02am

Maybe two stories related to Deltacron;

[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 @nzm8q


and the "BA.4" [url]https://www.coronaheadsup.com/science/variants/omicron/ba-4/ba-4-recombinant-of-omicron-ba-1-and-ba-3/[/url] or https://www.coronaheadsup.com/science/variants/omicron/ba-4/ba-4-recombinant-of-omicron-ba-1-and-ba-3/

Potential BA.4 lineage with a mix of BA.1 and BA.3 mutations, 5 sequences found in South Africa and USA.

Cornelius Roemer on Github: I’m breaking this post from @c19850727 into a separate issue to allow for dedicated discussion.

Below is the original post from Sakaguchi:

Hi I came across the following 5 sequences:
Accession Virus name
EPI_ISL_8262451 hCoV-19/USA/CO-CDC-MMB12218639/2021
EPI_ISL_8439638 hCoV-19/South Africa/NICD-N23764/2021
EPI_ISL_8402519 hCoV-19/Puerto Rico/PR-CDC-S874/2021
EPI_ISL_9962725 hCoV-19/South Africa/NICD-N29342/2022
EPI_ISL_10210515 hCoV-19/South Africa/NICD-N29407/2022

They are all classified as BA.1 by Pango/Nextstrain, but with G2832A reversed. Instead, they have T670G (BA.2 and BA.3 defining ), C832T (BA.3 defining ), G4184A (BA.2 and BA.3 defining) and C4321T (BA.2 defining).
Downstream from T5386G it’s all BA.1, but with a few private mutations: G7684A, C29167T, G29734A.

Github issue page

 

William Haseltine at Forbes.com

“The simplest interpretation of the origin of BA.4 is a recombination event between BA.1 and BA.3. It is likely that BA.3 contributes the portion of the genome extending from the 5’ end halfway through the NSP3 gene of the replication complex (about 2,000 amino acids). The remainder is plausibly contributed by BA.1”

Forbes.com article

DJ, Did some BA.1 subvariants pick up Delta-parts-now showing up via recombinations in BA.2 subvariants ?

BA.2 + ORF3a:D173Y mutation ⚠️ 67% of sequences uploaded from Vietnam Regional growth advantage: 47% And that’s vs BA.2! 

If you want to find links with Delta you need to have sequences in a data-base...we may be simply missing to much information...(My fear is Deltacron may be allready spreading high speed-but under other names, BA.2.1/BA.2.2, BA.2.3 etc....Maybe even not recognized as having Delta-segments/(re)actions...)

[url]https://www.thailandmedical.news/news/sars-cov-2-ba-2-variant-continues-to-rise-globally,-constantly-spawning-newer-subvariants-and-causing-reinfections--new-surge-expected-in-america[/url] or https://www.thailandmedical.news/news/sars-cov-2-ba-2-variant-continues-to-rise-globally,-constantly-spawning-newer-subvariants-and-causing-reinfections--new-surge-expected-in-america

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