Yearlong COVID-19 Infection Reveals Within-Host Evolution of SARS-CoV-2 in a Patient With B-Cell Depletion

B-cell-depleting therapies may lead to prolonged disease and viral shedding in individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and this viral persistence raises concern for viral evolution. We report sequencing of early and late samples from a 335-day infection in an immunocompromised patient. The virus accumulated a unique deletion in the amino-terminal domain of the spike protein, and complete deletion of ORF7b and ORF8, the first report of its kind in an immunocompromised patient. Unique viral mutations found in this study highlight the importance of analyzing viral evolution in protracted SARS-CoV-2 infection, especially in immunosuppressed hosts.

Automated summary

B-cell-depleting therapies can result in prolonged disease and viral shedding in SARS-CoV-2-infected individuals, raising concerns for viral evolution. This study sequenced early and late samples from a 335-day infection in an immunocompromised patient and identified unique viral mutations, highlighting the importance of analyzing viral evolution in prolonged infections, especially in immunosuppressed hosts.