Intrahost viral evolution of SARS-CoV-2 infections in rheumatic versus hematological patients with severe iatrogenic immunosuppression

ObjectivesImmunocompromised patients with B-cell depletion are at risk of ongoing SARS-CoV-2 replication that can lead to intra-host genomic divergence, immune escape during treatment and potentially emergence of novel variants.MethodsWe conducted a prospective observational study including severely immunocompromised rheumatic and hematologic patients with laboratory-confirmed COVID-19. SARS-CoV-2 virome sequencing was performed on respiratory samples, followed by phylogenetic and intrahost single nucleotide variants (iSNVs) analysis. In a subset of patients, lymphocyte subpopulations were assessed by flow cytometry.ResultsTwenty-six patients were included (median age: 71 years, rheumatic disease: 50%, treated with B-cell depleting agent: 88%, prior COVID-19 infection: 68%, relapsing COVID-19: 65%, ≥ 3 vaccine doses: 68%). Twenty-two patients (85%) were hospitalized with 23% mortality. Three unique RdRP and 3CLPro gene mutations were identified with a prevalence < 0.1%, not known to confer antiviral resistance. We identified 30 mutations in the spike gene with prevalence < 0.1% or leading to a new N-glycosylation site. In patients with paired samples, we noticed a statistically significant iSNVs accumulation with an average substitution rate per site per day of 7 × 10–6 (p < 0.001). We did not observe statistically significant difference in the substitution rates between rheumatic and hematologic patients.ConclusionIn our cohort, a significant proportion of patients had relapsing COVID-19. Unique and rare mutations were detected mainly in the spike gene, whereas those in the polymerase and protease genes were not of known significance. We found a positive correlation of iSNVs accumulation with infection duration, without difference in substitution rates between rheumatic and hematologic patients.