Genomic epidemiology and immune escape of SARS-CoV-2 recombinant strains circulating in Botswana

AI Summary

This study analysed the genetic make‑up and changes of SARS‑CoV‑2 (the virus that causes COVID‑19) in Botswana from 2020 to 2023 to understand how recombinant strains—viruses formed when different virus lineages mix—are evolving and whether they might evade immune responses. The researchers looked at more than 5,200 near‑complete viral genomes collected across the country.  

They found a small number of recombinant strains circulating in Botswana, with most being descended from the Omicron group of variants. A few lineages not directly from Omicron were also detected. These recombinant viruses tended to group into transmission clusters, showing that they spread locally. Most recombination events occurred in a key part of the virus’s spike protein, which is the part that helps the virus enter human cells.  

The team identified 16 mutations of interest across different viral proteins. Most of these mutations are rare globally, but one in the spike protein (called S:Q474K) was predicted by computer analysis to help the virus avoid recognition by certain immune cells. This kind of change could, in theory, make it easier for the virus to bypass immune defenses triggered by past infection or vaccination.  

Overall, the findings highlight that recombinant SARS‑CoV‑2 strains are present but uncommon in Botswana and that close monitoring of these genetic changes remains important to detect any variants that may spread more easily or reduce vaccine effectiveness.