Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage

Global genomic surveillance of SARS-CoV-2 has identified variants associated with increased transmissibility, neutralization resistance and disease severity. Here we report the emergence of the PANGO lineage C.1.2, detected at low prevalence in South Africa and eleven other countries. The initial C.1.2 detection is associated with a high substitution rate, and includes changes within the spike protein that have been associated with increased transmissibility or reduced neutralization sensitivity in SARS-CoV-2 variants of concern or variants of interest. Like Beta and Delta, C.1.2 shows significantly reduced neutralization sensitivity to plasma from vaccinees and individuals infected with the ancestral D614G virus. In contrast, convalescent donors infected with either Beta or Delta show high plasma neutralization against C.1.2. These functional data suggest that vaccine efficacy against C.1.2 will be equivalent to Beta and Delta, and that prior infection with either Beta or Delta will likely offer protection against C.1.2. The SARS-CoV-2 PANGO lineage C.1.2 has been under monitoring by global health authorities as it has spread worldwide. Here, Bhiman and colleagues characterise the emergence of the lineage, and its neutralisation sensitivity using data from vaccinees and previously infected individuals.

Automated summary

Global genomic surveillance of SARS-CoV-2 has identified a new variant, PANGO lineage C.1.2, which has been detected in low prevalence in South Africa and eleven other countries. It has a high substitution rate and includes changes within the spike protein that have been associated with increased transmissibility or reduced neutralization sensitivity. Similar to the Beta and Delta variants, C.1.2 shows reduced neutralization sensitivity to plasma from vaccinees. However, convalescent donors infected with Beta or Delta show high plasma neutralization against C.1.2. This suggests that the efficacy of vaccines against C.1.2 will be similar to Beta and Delta, and prior infection with Beta or Delta may offer protection against C.1.2. The emergence and neutralization sensitivity of the SARS-CoV-2 PANGO lineage C.1.2 has been monitored by global health authorities.