Thread by @vinodscaria

Closely tracking the delta+ lineages now across the world, one of the lineages AY.3 seems to be emerging in the United States of America. This tweetorial is to summarise the observations. I will be updating this thread as new evidence emerges.
Thanks

The interest in looking at this lineage closely comes from the fact that this lineage has been on the rise in USA in recent weeks.
Thanks @Unusual_Times for pointing this.

AY.3 seems to be localized to some states, like #Mississippi and #Missouri with nearby states slowly picking up.

While the epi-trends are not very clear, the number of genomes of AY.3 seem to be increasing faster than Delta B.1.617.2 . This could be potentially due to cluster testing also, but surely needs epi data to confirm.

AY.3 does not have the K417N mutation in the spike protein unlike their delta+ counterparts AY.1 and AY.2

And is largely charecterised by non-spike mutations. Specifically ORF1a mutation I3731V . This is clearly of interest since nothing is pretty much known about ORF1a and role in viral transmission or fitness.

A dedicated build for AY.3 phylogeny has been made available by @firefoxx66 . The tree can be browsed here nextstrain.org/groups/neherla…

Continued evolution is observed in this lineage with a new sublineage AY.3.1 now assigned github.com/cov-lineages/p… and charecterised by additional mutations ORF1a:D1127Y and ORF1b:H1550Y

Interesting clues on what is really happening can come from the fact that the nonstructural proteins NSP6 and NSP14 both are involved in #autophagy
sciencedirect.com/science/articl…
tandfonline.com/doi/abs/10.108…
and NSP6 is also involved in IFN antagonism
sciencedirect.com/science/articl…

The estimated current advantage of AY.3 wrt delta in US is ~40%
cov-spectrum.ethz.ch/explore/United…

And now growing in proportions in the USA

@TWenseleers suggest possible founder effect and insignificant advantage compared to delta B.1.617.2

Updated analysis from @TWenseleers

Spread of AY.3 in #SouthAfrica.
At least this does not look like a founder effect to me.
@alchemytoday @TWenseleers

With the new sub-lineage AY.3.1 now a significant number of #Mississippi, #UnitedStates genomes are reclassified.
Thanks @alchemytoday for adding this sublineage