Initial introduction and spread of the SARS-CoV-2 AY.4.2.1 Delta variant in Bulgaria, a genomic insight

Abstract

The evolution of the emerging SARS-CoV-2 variants carrying mutations in the spike protein raises concerns about the possibility of accelerated transmission in the ever-evolving COVID-19 pandemic worldwide. AY.4.2, a sublineage of the Delta variant, was considered a variant under investigation (VUI) and also gained the nickname "Delta Plus," due to its extra mutations, Y145H and A222V. In this study, using genomic epidemiology, we provide the first insights into the introduction of AY.4.2 in Bulgaria and the AY.4.2.1 sublineage that found larger dissemination only in Bulgaria and the United Kingdom.

Keywords: SARS coronavirus; epidemiology; mutation/mutation rate.

Figure 1

Genomic epidemiology of the SARS‐CoV‐2 AY.4.2 variant in Bulgaria. (A) Time‐stamped phylogenetic tree including the n = 40 AY.4.2 isolates obtained in this study plus n = 13 434 representative SARS‐CoV‐2 genomes collected up to November 20, 2021. The genomes generated in this study have been highlighted in the tree (gray circles). (B) Genome map of the AY.4.2 sublineage, where the spike region is shown in detail and in color, and the rest of the genome is shown in gray. NTD, N‐terminal domain; ORF, open reading frame; RBD, receptor binding domain; RBM, receptor binding motif; SD1, subdomain 1; SD2, subdomain 2. AY.4.2 characterizing mutations highlighted included the additional ones identified within the Bulgarian strains (V36F and R158G in bold).