Emergence of Omicron FN.1 a descendent of BQ.1.1 in Botswana

This study reports the detection and genetic analysis of a new SARS‑CoV‑2 sublineage called “Omicron FN.1” that was first found in Botswana in late 2022. Omicron FN.1 is a descendant of the global Omicron BQ.1.1 lineage, itself part of the larger Omicron family of variants that dominated COVID‑19 cases worldwide. Using viral genomes from Botswana and other countries, the research team examined the spread and genetic changes of this sublineage.

Out of an analysis of about 16 million global sequences, only 87 belonged to FN.1, with 22 from Botswana, a few from South Africa, and most from the UK. Phylogenetic analysis suggests that FN.1 likely originated in Botswana around October 2022 and then spread locally and to neighbouring regions. It carries two notable changes in the virus’s spike protein—S: K182E and S: T478R—which distinguish it from its closest relatives and could influence how the virus interacts with human immune responses.

FN.1 was rare compared to many other variants and did not cause a major wave of illness in Botswana or elsewhere. This likely reflects that the population had strong pre‑existing immunity from past infections and vaccination, which limited its spread. Nevertheless, the study highlights the importance of ongoing genomic surveillance to quickly identify and monitor new sublineages—and to understand how small genetic changes may affect virus behaviour and immune escape in different settings.

Disclaimer: This lay summary was generated by AI and has not been approved by any of the authors yet.