French Scientist Warns Of New Delta Sub-Variant Possessing Kappa’s S:E484Q Mutation And Iota’s S:T95I Mutation That Is Linked With Breakthrough Infections!
: French researchers in a new study have identified a new Delta sub-variant that is of concern as it not only possess the unique mutation S:E484Q found on the Kappa variant but it also has the S:T95I mutation found on the Iota variant that is associated with breakthrough infections!
Alarmingly other mutations were also found on the new Delta sub-variant phylogenetic cluster including the following substitutions that are not found in most of the other Delta sequences ie: ORF1a:T403I, ORF1a:D1167N and ORF1b:A1219S.
More worrying was the fact that these new Delta-subvariants were associated with doubling times and transmission advantage.
The study findings were published on a preprint server in the last 36 hours and are currently being peer reviewed.
The French researchers from Laboratoire Cerba, Université de Montpellier and Laboratoire de Virologie-CHU de Montpellier had been analyzing 92,598 variant screening tests performed on SARS-CoV-2 positive samples collected in France between 1 July and 31 August 2021.
The analysis showed an increase of Kappa-like infections but full genome sequencing revealed that most of these sequencings corresponded to Delta variants bearing the S:E484Q mutation.
Interestingly most of these sequences also belonged to a phylogenetic cluster and also bears the S:T95I mutation which has been associated with breakthrough infections according to a previous study. https://www.nejm.org/doi/full/10.1056/NEJMoa2105000
The study team noticed an increase in infections caused by the Delta variants bearing the E484Q mutation in the Paris area. The significant transmission advantage they estimated for this mutation is consistent with it being associated with immune evasion and with the high vaccination coverage in France.
Note that other lineages bearing a mutation in position S:484 were found to spread earlier in 2021 but their transmission advantage was more limited (approximately 17% versus 35 to 63% here) and the reference strain was the Alpha variant, whereas is less contagious that the Delta variant and has less immune evasion properties.
However the detection of the new delta sub-variant ie Delta+E484Q shows that there is a transmission advantage driven by an undocumented superspreading event in the area of Paris in August that would leave traces in virus genomes. This could be consistent with the fact that the number of sequences from Delta+E484Q in the GISAID database is currently very low (935 of the 937,570 Delta sequences in GISAID).
Furthermore, combining these new sequences with 8 Delta sequences per month (April to September) from Italy, Spain, France, UK, Belgium, and Germany did not identify a clear link with the phylogenetic cluster of interest.
In vitro studies using viral culture assays could be instrumental to understand this phenomenon. SARS-CoV-2 prevalence remains high and the beginning of the school term in France is likely to increase virus spread. Therefore, the alternative, more worrying, interpretation of these results, which is an
adaptive advantage of a combination of the S:E484Q and S:T95I mutations, warrants close monitoring of these genomic pattern
The study team says that further monitoring is needed to determine if this trend is driven by undocumented super-spreading events or an early signal of future viral evolutionary dynamics.
The SARS-CoV-2 Variants
study findings have already been reported to the WHO and also to the US.CDC. in the last 24 hours.
It must be noted that the Delta variant is mutating rapidly due to pressure from vaccinations and also the use of various monoclonal and polyclonal antibody therapeutics. Coupled with the fact that more infections are rampant and also the dynamics of the populations of those vaccinated versus those unvaccinated are all contributing factors to the virus mutations rates.
To date there are more than 130 Delta sub-variants with unique mutations and deletions found on them that have emerged in this short time and scientists have only classified about less than 25 % of them!
The coming weeks as we have always been saying are going to be real interesting times as those living in the illusion that the COVID-19 pandemic is going to be tamed and that things will return to normal soon or that the mass vaccination programs are going to solve everything are going to be in for rude shock. The SARS-CoV-2 virus still has a lot in its sleeve to meet its goal of eradicating a sizeable amount of the human population. It has yet to even start what it was created for and to date as only being going through its ‘dry-run’ phases only.
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