Emergence of novel combinations of SARS-CoV-2 spike receptor binding domain variants in Senegal

Abstract

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages that carry mutations in the spike gene are of concern for potential impact to treatment and prevention efforts. To monitor for new SARS-CoV-2 mutations, a panel of specimens were sequenced from both wave one (N = 96), and wave two (N = 117) of the pandemic in Senegal by whole genome next generation sequencing. Amongst these genomes, new combinations of SARS-CoV-2 spike mutations were identified, with E484K + N501T, L452R + N501Y, and L452M + S477N exclusively found in second wave specimens. These sequences are evidence of local diversification over the course of the pandemic and parallel evolution of escape mutations in different lineages.

Figure 1

Molecular surveillance of SARS-CoV-2 in Senegal. In panel (A), the number of sequences classified in the indicated lineages present in waves one and two are shown proportionally to the total number of sequences generated with > 60% genome coverage from each wave as designated in the total numbers below each plot. An * indicates lineages that were present in both waves. In panel (B), the sequence and specimen metadata are listed for each strain carrying spike mutation of concern at position 501, 484, or 452. All sequences in this panel are from wave two. In panel (C), the lineage defining amino acid mutations (in comparison to the reference genome NC_045512) for the new strains identified in this study are shown. (A) Lineages identified, (B) Variant specimen summary, (C) Escape variant lineages.