Delta and Omicron's hybrid "Deltacron" is a mystery

On January 8, 2022, Bloomberg reported that Leondios Kostikis, a professor of biological sciences at the University of Cyprus, and his team discovered a new variant of the new coronavirus.
Because the variant has Omicron-like genetic characteristics in the Delta genome, the variant was named "Deltacron"
.

 Kostikis said Deltacron combines the genes of Delta and Omicron, possibly from a patient infected with both Delta and Omicron
.

The study's 25 mutation samples were collected from Cyprus, of which 11 samples were collected from hospitalized COVID-19 patients and 14 samples were collected from the general infected population
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In comparison, the higher mutation frequency in hospitalized patient samples may imply a correlation between Deltacron and hospitalization, and therefore, the pathogenicity and infectivity of Deltacron need attention
.

In addition, research data on Deltacron was submitted to the GISAID global database on January 7
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The proportion of data sources in the GISAID global database (source: GISAID official website) The emergence of the new coronavirus recombinant variant has attracted widespread attention, and some experts have discussed the authenticity of the variant
.

Fatima Tokhmafshan, a geneticist at the McGill University Health Center Research Institute in Montreal, tweeted that the virus was not recombined but caused by laboratory contamination.
Looking at the GISAID clustering and mutation profiles recently submitted by Cyprus did not find a mutation consensus; the world WHO Covid expert Dr Krutika Kuppalli agreed, tweeting that the Omicron components detected in the Delta samples may have been due to sequencing artifacts caused by contamination of the samples in the laboratory, rather than the emergence of new At the same time, Dr.
Tom Peacock, a virologist at Imperial College London, also tweeted that the Deltacron sequence reported by the media was obviously caused by contamination of the sample
.

Other experts have also seen the sequence information of Deltacron, and we have come to the same conclusion: Deltacron does not look like a real virus recombination, but more like the result of sample contamination; another well-known scientist-Emory University in Atlanta contamination Disease expert Dr.
Boghuma Kabisen Titanji was cautious, tweeting on Sunday that conclusions about Deltacron remain cautious, and that the information currently available points to contamination of the samples rather than true recombination of delta and omicron
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Prior to this, genetic recombination for the new coronavirus has been reported
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The article published on Medrxiv on October 11, 2021, entitled "Genome Recombinationbetween Delta and Alpha Variants of Severe Acute Respiratory SyndromeCoronavirus 2 (SARS-CoV-2)" reports the recombination variants of Delta and Alpha discovered in Japan (AY .
29+B.
1.
1.
7)
.

Phylogenetic tree analysis of the data for this finding by Nexstrain confirmed that the recombinant viral sequences could be found in the same cluster
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However, the same analysis of Deltacron data found that it was distributed in almost every branch, and did not have the cluster distribution characteristics of recombinant viruses found in Japan
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In addition to this, complete ARTIC primers with Omicron sequenced amplicons in other Delta clades due to the failure of amplicon 72 in the ARTIC primer protocol because of all Omicron mutations in these sequences (i.
e.
A67V, H69_V70del, T95I, G142D, V143_Y145del) were all in this amplicon, however low-level contaminants from other samples filled in the gaps, so the probability of recombining the amplicon is about 0
.

Research results (Image source: Medrxiv) Phylogenetic tree analysis of Delta and Alpha recombination variants reported in Japan (Image source: Nexstrain) Phylogenetic tree analysis of Delta and Omicron recombination variants reported in Cyprus (Image source: Nexstrain) ARTIC primers In response to the doubts of experts, Kostikis stated on January 9 that the emergence of Deltacron was not a single recombination event, but a mutation of the new coronavirus due to its adaptation to the environment.
The collected samples Tests were not only carried out in laboratories in Cyprus, but also in laboratories in other countries, and the recombination signature of Deltacron was also detected in laboratories in Israel
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The Deltacron infection rate of hospitalized patients was significantly higher than that of non-hospitalized patients, which also ruled out the hypothesis of sample contamination
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Meanwhile, his team found 52 recombinant samples in addition to the original 25 Deltacron samples
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In response to this, Tom Peacock said that the popularity of Omicron did not allow it to produce any recombinants, and the phylogenetic tree also showed that Deltacron did not have clustering characteristics, and true recombinant variants would have common clusters
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Tokhmafshan pointed out that if the original sample had been contaminated when it was collected and processed, even if it was sent to 10 other laboratories, it was the same sample, and they would have gotten the same result
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If Israeli labs give the same test results, are Israeli samples taken independently in other regions and get the same results as Cyprus? As of this writing, Kostikis has not responded
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The authenticity of Deltacron still needs to be observed continuously.
Objectively speaking, there is still the possibility of recombination of delta and omicron that continue to spread around the world.
The enzyme that replicates its genes has a tendency to slip off the RNA strand it replicates, and then land on the spot.
reconnect
.

The probability of such recombination is greatly increased when delta and omicron are simultaneously infected
.

Written|Writing Competition Typesetting|Mu ZijiuEndReference:[1]TsuyoshiSekizuka, Kentaro Itokawa, et al.
Genome Recombination between Delta and AlphaVariants of Severe Acute Respiratory Syndrome Coronavirus 2(SARS-CoV-2).
MedRxiv.
doi:10.
1101 /2021.
10.
11.
21264606.
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