Publication date: Oct 24, 2024

CDC continues to track the evolution of SARS-CoV-2, including the Omicron variant and its descendants, using national genomic surveillance. This report summarizes U. S. trends in variant proportion estimates during May 2023-September 2024, a period when SARS-CoV-2 lineages primarily comprised descendants of Omicron variants XBB and JN. 1. During summer and fall 2023, multiple descendants of XBB with immune escape substitutions emerged and reached >10% prevalence, including EG. 5-like lineages by June 24, FL. 1.5. 1-like lineages by August 5, HV. 1 lineage by September 30, and HK. 3-like lineages by November 11. In winter 2023, the JN. 1 variant emerged in the United States and rapidly attained predominance nationwide, representing a substantial genetic shift (>30 spike protein amino acid differences) from XBB lineages. Descendants of JN. 1 subsequently circulated and reached >10% prevalence, including KQ. 1-like and KP. 2-like lineages by April 13, KP. 3 and LB. 1-like lineages by May 25, and KP. 3.1. 1 by July 20. Surges in COVID-19 cases occurred in winter 2024 during the shift to JN. 1 predominance, as well as in summer 2023 and 2024 during circulation of multiple XBB and JN. 1 descendants, respectively. The ongoing evolution of the Omicron variant highlights the importance of continued genomic surveillance to guide medical countermeasure development, including the selection of antigens for updated COVID-19 vaccines.

Semantics

Original Article