Genomic Surveillance for SARS-CoV-2 Variants: Circulation of Omicron XBB and JN.1 Lineages - United States, May 2023-September 2024

Abstract

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.

FIGURE 1

National estimates of biweekly proportions of SARS-CoV-2 variants (A) and estimated normalized frequency of variant-attributed COVID-19 cases (B) — United States, May 14, 2023–September 14, 2024 Abbreviations: NREVSS = National Respiratory and Enteric Virus Surveillance System; NS3 = National SARS-CoV-2 Strain Surveillance. * Sequences are reported to CDC through NS3, contract laboratories, public health laboratories, and other U.S. institutions. Variant proportion estimation methods use a complex survey design and statistical weights to account for the probability that a specimen is sequenced. https://covid.cdc.gov/covid-data-tracker/#variant-proportions ^† Lineages reaching a prevalence of ≥1% with spike protein substitutions of potential therapeutic relevance and separated out on the COVID Data Tracker website (https://covid.cdc.gov/covid-data-tracker/#variant-proportions). Lineages were ordered by date of first appearance on the COVID Data Tracker. Lineages with identical spike residue 31 and receptor binding domain amino acid sequences (residues 332–527) were grouped with a representative lineage and denoted as “representative lineage-like.” “Other” represents aggregated lineages circulating at <1% prevalence nationally during all 2-week periods displayed. ^§ Normalized frequency of COVID-19 cases attributable to variants was estimated by multiplying biweekly counts of positive test results from NREVSS with variant proportions and scaling by the maximum NREVSS case count, which occurred in the 2-week period ending January 6, 2024.

FIGURE 2

Subsampled SARS-CoV-2 sequences, by lineage group, date of specimen collection, and number of spike protein amino acid differences (including substitutions, insertions, and deletions) relative to Wuhan-Hu-1 reference — United States, January 1, 2021–September 14, 2024 * Sequences were subsampled (5,000) for analysis from an initial dataset of 1 million sequences spanning January 1, 2021–September 14, 2024. Each year within the study period was proportionately represented, and subsampling accounted for geographic representation by ensuring that sequences from each state were included. ^† Sequences are reported to CDC through the National SARS-CoV-2 Strain Surveillance program, contract laboratories, public health laboratories, and other U.S. institutions. ^§ Lineages reaching a prevalence of ≥1% with spike protein substitutions of potential therapeutic relevance and separated out on the COVID Data Tracker website (https://covid.cdc.gov/covid-data-tracker/#variant-proportions). Lineages were ordered by date of first appearance on the COVID Data Tracker. Lineages with identical spike residue 31 and receptor binding domain amino acid sequences (residues 332–527) were grouped with a representative lineage and denoted as “representative lineage-like.” “Other” represents aggregated lineages circulating at <1% prevalence nationally during all 2-week periods displayed.