SARS-CoV-2 evolution in hospitalized and immunosuppressed patients

We investigated SARS-CoV-2 evolution in hospitalized and immunosuppressed patients between November 2021 and November 2022 in the Chicago area. A total of 210 nasopharyngeal swab RNA samples from 192 positive patients (64% hospitalized, 39% immunosuppressed) were collected and sequenced. Sequencing library preparation was performed using the NEBNext ARTIC SARS-CoV-2 FS Library Prep Kit for Illumina according to the standard protocol, with the modification that the ARTIC V4.1 primer panel was used. Sequencing runs were performed at the Loyola Genomics Facility on an Illumina Miseq with 300-cycle V2 reagent kits.