Abstract
•Immunocompromised patients may acquire different clades of SARS-CoV-2 infection.•Infection with different SARS-CoV-2 clades poses significant management challenges.•Prolonged secretion of SARS-CoV-2 occurs in immunocompromised patients.•The impact of rituximab and B cell-depleting agents requires definition.•The responses to COVID-19 vaccines need further study.
Immunocompromised patients who have a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection pose many clinical and public health challenges. We describe the case of a hematopoietic stem cell transplantation patient with lymphoma who had a protracted illness requiring three consecutive hospital admissions. Whole genome sequencing confirmed two different SARS-CoV-2 clades. Clinical management issues and the unanswered questions arising from this case are discussed.