Emergence of the BA.2.87.1 lineage of SARS-CoV-2 in South Africa

The emergence of various SARS-CoV-2 lineages with adaptive mutations is of significant concern worldwide; especially when these mutations enhance the virus's ability to either evade immune responses or transmit more efficiently. Between September and December 2023, a highly diverged BA.2 related lineages, designated BA.2.87.1, was detected through diagnostic testing, syndromic surveillance and wastewater surveillance in the Limpopo, Mpumalanga, Westen cape, Eastern Cape and Gauteng provinces of South Africa. This lineage harbours 20 amino acid substitutions in Spike protein relative to baseline BA.2, including at antigenic sites of the receptor-binding domain (including N417T, K444N, V445G, L452M, N460K, K478T, N481K and R493Q), and, most strikingly, large deletions of the N-terminal domain (NTD) residues 15-26 and 136-146. Such large NTD deletions have never been observed in circulating lineages but do sometimes occur in highly mutated sequences originating in chronic infections. Phylodynamic analysis supports the possibility that the BA.2.87.1 lineage originated in a chronic infection in that the nearest known relative of this lineage last circulated at least 18 months prior to its first detection. Although BA.2.87.1 had immune evasion and/or transmission potential, its detection was not associated with a surge of infections and it appears to have been rapidly displaced by the globally dominant BA.2.86 lineage, JN.1, in the last few weeks of 2023. Our findings further strengthen the case for genomic surveillance through clinical and wastewater surveillance systems.