Evolution and neutralization escape of the SARS-CoV-2 BA.2.86 subvariant.

Omicron BA.2.86 subvariant differs from Omicron BA.2 as well as recently circulating variants by over 30 mutations in the spike protein alone. Here we report on the isolation of the live BA.2.86 subvariant from a diagnostic swab collected in South Africa which we tested for escape from neutralizing antibodies and viral replication properties in cell culture. We found that BA.2.86 does not have significantly more escape relative to Omicron XBB.1.5 from neutralizing immunity elicited by either Omicron XBB-family subvariant infection or from residual neutralizing immunity of recently collected sera from the South African population. BA.2.86 does have extensive escape relative to ancestral virus with the D614G substitution (B.1 lineage) when neutralized by sera from pre-Omicron vaccinated individuals and relative to Omicron BA.1 when neutralized by sera from Omicron BA.1 infected individuals. BA.2.86 and XBB.1.5 show similar viral infection dynamics in the VeroE6-TMPRSS2 and H1299-ACE2 cell lines. We also investigate the relationship of BA.2.86 to BA.2 sequences. The closest BA.2 sequences are BA.2 samples from Southern Africa circulating in early 2022. Similarly, many basal BA.2.86 sequences were sampled in Southern Africa. This suggests that BA.2.86 potentially evolved in this region, and that unobserved evolution led to escape from neutralizing antibodies similar in scale to recently circulating strains of SARS-CoV-2.

Macroinvertebrate Assemblages along the Longitudinal Gradient of an Urban Palmiet River in Durban, South Africa.

Urban rivers are regarded as unnatural because they drain catchments characterized by impervious surfaces. The present study explored macroinvertebrate communities in relation to water and habitat quality along the longitudinal gradient of an urban Palmiet River in Durban, South Africa. Sampling was conducted across six sites along the river. The water quality has shown a significant variation (ANOVA, p < 0.05) across six sites. Good-quality water was observed at Site 6, whereas Site 5 exhibiting hypertrophic condition. Sites 4 to 1 were all eutrophic; however, nutrient levels showed to decrease from Site 4 down to Site 2 and increased again at Site 1. A similar trend was observed for habitat quality, with Site 6 showing excellent and Site 5 exhibited poor habitat. Coinciding with water and habitat quality, macroinvertebrate diversity and abundance showed significant differences across six sites. Sensitive palaemonids, notonemourids, and amphipods were only observed in the headwaters and have contributed over 50% of the variation in abundance between Site 6 and other sites. The non-metric multidimensional scaling (NMDS) plot has also shown clear discrimination (MANOVA, p < 0.001) for the Average Score Per Taxon (ASPT) across the six sites. Macroinvertebrate communities have shown a clear association between water and habitat quality. These findings affirm the ecological importance of urban rivers as they provide refuge to aquatic biodiversity, with anthropogenic litter providing additional habitats for other taxa. Despite the current conditions supporting biodiversity and the functioning of the river, it is unclear if the system could endure further disturbance.

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.