A relatively new emergent #SARSCoV2 lineage/variant from India, bearing the combination of Spike mutations L452R+E484Q, has been making rounds in the news recently. Here's a quick phylogenetic analysis of all genomes with L452R+E484Q from GISAID.

L452R+E484Q seems to be recurrently emerging in 3 different lineages. While the Indian genomes fall under Nextstrain clade 20A, the USA and Sweden genomes form separate clusters under 20C and 20B respectively
@trvrb @nextstrain

In USA, E484Q was found in some California VOC genomes (PANGO Lineages B.1.427-B.1.429), which already contain L452R

A zoomed-in view of the USA B.1.427-B.1.429 cluster:
While in Sweden, L452R+E484Q was found in genomes belonging to the lineage L.3 and was detected as early as December 2020 (EPI_ISL_766714)

A zoomed-in view of the Sweden L.3 cluster:

In India, as already previously reported, the variant has shown a particularly increased prevalence in Maharashtra, where the variant is seen to been present at a very low frequency since October 2020

And the variant has recently been designated as the PANGO Lineage B.1.617
@arambaut @AineToole
Apart from L452R+E484Q, the genomes also have the spike mutation P681R.

Both mutations are associated with antibody escape while L452R has also been associated with a modest increase in infectivity https://covariants.org/variants/S.L452Rhttps://twitter.com/vinodscaria/status/1374778715339509766
Moving forward, further sequencing and experimental assays will be needed to establish how concerning the combination is!

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