Evolution and viral properties of the SARS-CoV-2 BA.3.2 subvariant

Abstract The SARS-CoV-2 Omicron subvariant BA.3.2 descends from BA.3. It emerged two years after BA.3 ceased to circulate and differs by 39 spike mutations from BA.3. Similar to BA.2.86, which circulated at low levels before giving rise to JN.1, BA.3.2 shows a low but persistent circulation globally. Here, we characterize the phylogenetic origin, infection in cell culture, and neutralization of BA.3.2 using live virus and blood plasma samples collected in South Africa at different stages of the Covid-19 pandemic. Like the Omicron BA.2.86 subvariant, we find that BA.3.2 likely emerged in Southern Africa. We also find that an 871 bp deletion removed ORF7 and ORF8. In H1299-ACE2 cells, BA.3.2 has lower cytotoxicity measured as plaque area compared to ancestral SARS-CoV-2 but similar to the co-circulating LP.8.1 Omicron subvariant with which it also shares similar replication and infection focus size. BA.3.2 and LP.8.1 exhibit complete escape from neutralization from pre-Omicron collected plasma samples, have low levels of neutralization by plasma collected in 2024, and higher neutralization by plasma collected in 2025, with BA.3.2 showing moderately lower neutralization than LP.8.1. The emergence of long branch subvariants like BA.3.2 without intermediates likely indicates that unmonitored persistent infections continue to drive large evolutionary shifts in this virus.