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Background: Real-life data on the administration of letermovir as cytomegalovirus (CMV) primary prophylaxis after allogeneic hematopoietic cell transplantation (HCT) remain limited. Methods: We conducted a retrospective single-center matched cohort study, comparing consecutive high-risk allogeneic HCT recipients (cases) receiving primary prophylaxis with letermovir and untreated matched historical controls, during a study period of 180 days. The primary outcome was the incidence of clinically significant (cs) CMV infection. Secondary outcomes included duration and costs of CMV-antiviral treatments, hospital resource utilization, hematology and laboratory parameters. Results: Letermovir prophylaxis decreased csCMV infection incidence from 82.7% (controls) to 34.5% (cases; <i>p</i>-value < 0.0001). Controls were more likely to have >1 episode of csCMV infection (59.6%) compared to cases (11.5%; <i>p</i>-value < 0.0001). Letermovir was associated with: shorter overall CMV-associated treatment duration (49 days vs. 77.8 days; <i>p</i>-value: 0.02) and a trend for lower costs of CMV-associated treatments ($4096 vs. $9736; <i>p</i>-value: 0.07) and reduced length of stay (44.8 days vs. 59.8 days; <i>p</i>-value: 0.16). Letermovir administration was associated with significantly shorter duration (27.3 days vs. 57.1 days; <i>p</i>-value: 0.008) and lower costs ($1089 vs. $2281; <i>p</i>-value: 0.008) of valganciclovir treatment. Compared to controls, higher platelet counts were observed in cases (138 G/L vs. 92 G/L; <i>p</i>-value: 0.03) and renal function was improved (94 mL/min/1.73 m² vs. 74 mL/min/1.73 m²; <i>p</i>-value: 0.006). Conclusions: Primary anti-CMV letermovir prophylaxis decreased the incidence of csCMV infection and the administration of CMV-associated treatments and costs, particularly those associated with valganciclovir. An effect of letermovir on platelet reconstitution and renal function of csCMV post-HCT was observed and needs further investigation.