Within-host evolution of SARS-CoV-2 in an immunosuppressed COVID-19 patient: a source of immune escape variants

The recent emergence of SARS-CoV-2 variants showing increased transmissibility and immune escape is a matter of global concern. Their origin remains unclear, but intra-host virus evolution during persistent infections could be a contributing factor. Here, we studied the long-term SARS-CoV-2 infection in an immunosuppressed kidney transplant recipient. Frequent respiratory specimens were tested by RT-qPCR and analyzed for changes in the viral genome by next-generation sequencing (NGS) and virus isolation. Late in infection, several mutations in the viral genome emerged.