Different Within-Host Viral Evolution Dynamics in Severely Immunosuppressed Cases with Persistent SARS-CoV-2

A successful Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variant, B.1.1.7, has recently been reported in the UK, causing global alarm. Most likely, new variant emerged a persistently infected patient, justifying special focus on these cases. Our aim this study was to explore certain clinical profiles involving severe immunosuppression that may help explain prolonged persistence of viable viruses. We present three severely immunosuppressed cases (A, B, and C) with history lymphoma SARS-CoV-2 shedding (2, 4, 6 months), two whom finally died. Whole-genome sequencing 9 10 specimens from Cases B revealed extensive within-patient acquisition diversity, 12 28 single nucleotide polymorphisms, respectively, which suggests ongoing replication. This diversity not observed for Case C after analysing 5 sequential nasopharyngeal one plasma specimen, only bronchoaspirate although viral viability still considered based constant low Ct values throughout disease recovery virus cell cultures. The acquired followed different dynamics. For A, polymorphisms were quickly fixed (13–15 days) emerging as minority variants, while higher at slower emergence: fixation pace (1–2 months). Slower evolutionary following administration hyperimmune plasma. work adds knowledge immunocompromised patients demonstrates viability, noteworthy intra-patient dynamics persistent