FIGURE 1.

Whole genome sequencing lineage determination among adults hospitalized with COVID-19 — 21 academic medical centers in 18 states,*^,† March–July 2021

* Specimens with SARS-CoV-2 detected by reverse transcription–polymerase chain reaction and with a cycle threshold <32 for at least one of two nucleocapsid gene targets tested underwent whole genome sequencing. SARS-CoV-2 lineages were assigned with >80% coverage using Pangolin genomes. Results are presented for B.1.1.7 (Alpha) variants, B.1.617.2 (Delta) variants, and other (neither B.1.1.7 or B.1.617.2) variant with lineage determined by whole genome sequencing. Of 74 Delta variants sequenced, four belonged to the AY.3 Delta sublineage. The histogram provides the number of viruses sequenced by week of hospital admission.

^† Hospitals by region included Northeast: Baystate Medical Center (Springfield, Massachusetts), Beth Israel Deaconess Medical Center (Boston, Massachusetts), Montefiore Medical Center (Bronx, New York); South: Vanderbilt University Medical Center (Nashville, Tennessee), University of Miami Medical Center (Miami, Florida), Emory University Medical Center (Atlanta, Georgia), Johns Hopkins Hospital (Baltimore, Maryland), Wake Forest University Baptist Medical Center (Winston-Salem, North Carolina), Baylor Scott and White Health (Temple, Texas); Midwest: University of Iowa Hospitals (Iowa City, Iowa), University of Michigan Hospital (Ann Arbor, Michigan), Hennepin County Medical Center (Minneapolis, Minnesota), Barnes-Jewish Hospital (St. Louis, Missouri), Cleveland Clinic (Cleveland, Ohio), Ohio State University Wexner Medical Center (Columbus, Ohio); West: Stanford University Medical Center (Stanford, California), UCLA Medical Center (Los Angeles, California), UCHealth University of Colorado Hospital (Aurora, Colorado), Oregon Health & Science University Hospital (Portland, Oregon), Intermountain Medical Center (Murray, Utah), University of Washington (Seattle, Washington).