New SARS-CoV-2 Omicron Variant with Spike Protein Mutation Y451H, Kilifi, Kenya, March-May 2023

Abstract

We report a newly emerged SARS-CoV-2 Omicron subvariant FY.4 that has mutations Y451H in spike and P42L in open reading frame 3a proteins. FY.4 emergence coincided with increased SARS-CoV-2 cases in coastal Kenya during April-May 2023. Continued SARS-CoV-2 genomic surveillance is needed to identify new lineages to inform COVID-19 outbreak prevention.

Keywords: COVID-19; FY.4; Kenya; Kilifi; Omicron; SARS; SARS-CoV-2; coronavirus; coronavirus disease; respiratory infections; severe acute respiratory syndrome coronavirus 2; viruses; zoonoses.

Figure

Number of positive samples, distribution, and growth rate for new SARS-CoV-2 Omicron variant with spike protein mutation Y451H, Kilifi, Kenya, March–May 2023. The x axes indicate calendar weeks beginning on January 1, 2023. A) Weekly number of collected samples (black data line) and positive SARS-CoV-2 cases (data bars) in health facilities within the KHDSS during January–May 2023. Vertical dotted lines indicate the weeks when the FY.4 lineage was first detected in Kenya (red) and Kilifi (black). B) Weekly distribution of SARS-CoV-2 lineages observed in samples processed at the Kenya Medical Research Institute Wellcome Trust Research Programme from KHDSS (red dots) and non-KHDSS (blue dots) health facilities during January–May 2023. C) Growth rate estimates for the Omicron FY.4 variant in Kenya relative to those in the United States and Germany. KHDSS, Kilifi Health Demographic Surveillance System.