Is Delta+ a new problem? Probably not and too soon to know

There have been several srquenced samples where Delta has acquired a new mutation, K417N. You may be seeing stories about “Delta +” (Pango lineage (B.1.617.2.1) in the news, however the fears outlined in many stories are likely overblown.

It is natural for the idea that this could be a problem to spread. Delta really has hurt a LOT of people and is once again turning our lives even in the mor vaccinated industrialized west upside down. When we hear “Delta” we are primed for fear (and given my experiences on the airline of the same name, some mistrust on top.) Throw in the marketing genius of “plus” and our amygdala really kicks in.

K417N means the amino acid threonine (N) substituting for leucine (K) at location 417 in the spike protein amino acid chain. (Proteins are chains of amino acids). “N” and “K” are used for those two amino acids because “A” and “T” are already spoken for others in the list of the 20 commonly found in human proteins . Another example: the N501Y mutation in the Alpha and several other variants is a tyrosine substitution for arganine at position 501.

Some mutations show up over and over again. Dr. E Hodcroft, (curator of the excellent Covariants.org page from which the figure comes) tells us that it is generally combinations of mutations that result in significant functional changes.

This particular mutation has shown up several times over the past year or so, and so far has not conferred any particular advantage. Several expert soundbites range from unlikely, to probably not nut too soon to tell.

Given the tiny number of strains reported, nothing is known about the transmissibility, immune evasion or lethality of the delta+ strain. Though, given that it has remained at very low frequency everywhere where it has been identified strongly suggest it is not more transmissible than its delta progenitor.
- F Balloux

The K417N mutation has previously occurred on a background of Alpha variant, without significant increased expansion in cases, and now Delta; it likely has little effect on infectiousness of the virus and could have a small effect on antibody binding responses post vaccination.
- R Gupta

We don’t know yet if AY.1 has any extra advantage over Delta, but it would seem unlikely as the difference is only the mutation K417N
- D Robertson

It is too soon to really understand Delta Plus, but this mutation has popped up in many places before and has only become frequent in a few cases.

I am with Dr. Hodcroft on this one: it is hard to extrapolate a significant change from a single mutation. The spike protein is a complex molecule of 1273 amino acids . Proteins’ folded 3D structuresmakes a HUGE difference in function, along with the environment they are functioning in.

Delta has some mutations that are rare or non-existant in other variants of concern and variants of interest, so there is always a chance that N417K is a problem when combined with them, but there is little reason to think that chance is any greater with this mutation than one of many others. F. Balloux’s observation in particular is comforting.

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I have a background in science. I back up nearly everything science I write with peer reviewed research, or at least preprints and pointers to my data sources

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David Theil

David Theil

I have a background in science. I back up nearly everything science I write with peer reviewed research, or at least preprints and pointers to my data sources

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