New genomic surveillance data published today in Morbidity and Mortality Weekly Report show that JN.1 and its descendants have been the most common SARS-CoV-2 variants in 2024, and they're still evolving.
The genomic surveillance was conducted by the Centers for Disease Control and Prevention's national SARS-CoV-2 genomic surveillance program, which previously detected both the Delta and Omicron variants.
The new report covers detections from May 2023 through September 2024, from which researchers analyzed 208,357 SARS-CoV-2 sequences from 56 US jurisdictions.
In the summer of 2023, the authors write, multiple Omicron XBB descendants, including EG.5-like lineages, FL.1.5.1-like lineages, and HV.1 lineages reached more than 10% prevalence in the United States.
JN.1 increased in winter of 2023
By the winter of 2023, however, JN.1 increasingly took hold.
The JN.1 variant emerged in the United States and rapidly attained predominance nationwide.
"The JN.1 variant emerged in the United States and rapidly attained predominance nationwide, representing a substantial genetic shift," the authors write. "Surges in COVID-19 cases occurred in winter 2024 during the shift to JN.1 predominance.”
More surges were seen in the summer of 2024, the authors write, when cocirculation of JN.1 descendant lineages with identical substitutions, including the S31 deletion, R346T, and F456L emerged. These substitutions cause immune escape and increased transmissibility.
"Continued monitoring to determine whether this pattern of divergent variant emergence followed by subsequent stepwise evolutionary changes continues will be important for updating COVID-19 vaccines and anticipating surges in COVID-19 activity," the authors conclude.