Molecular Epidemiology of the Norwegian SARS-CoV-2 Delta Lineage AY.63.

ABSTRACT

Extensive genomic surveillance has given great insights into the evolution of the SARS-CoV-2 virus and emerging variants. During the summer months of 2021, Norway was dominated by the Pango lineage AY.63 which is a sub-lineage of the highly transmissible Delta variant. Strikingly, AY.63 did not spread in other countries to any significant extent. AY.63 carried a key mutation, A222V, in the spike protein, as well as the deletion of three residues in nsp1. Although these mutations are close to functionally important areas, we did not find any evidence that they induced higher fitness compared to other Delta lineages. This variant was introduced to Norway at a time when there were low levels of SARS-CoV-2 and contact-reducing measures were relaxed, which probably explains why the lineage rose so quickly. Furthermore, we found that the lack of imports of AY.63 from other countries probably led to the eventual demise of the lineage in Norway.