Longitudinal study of a SARS-CoV-2 infection in an immunocompromised patient with X-linked agammaglobulinemia.

Abstract We describe the case of a 23-year-old immunocompromised male patient with clinically diagnosed X-linked agammaglobulinemia who was admitted to the hospital on the 14th April 2020 due to coronavirus disease of 2019 (COVID-19). Despite COVID-19 test negativizations, the patient was hospitalized most of the time and finally admitted to the intensive care unit where he died from multiorgan failure and shock. Over 149 days, 26 respiratory samples were collected, subjected to viral genome sequencing, and all assigned to the same lineage, supporting a single viral infection event. The accumulation of mutations throughout the course of the infection was accelerated and suggested the presence of compartmentalized viral subpopulations that evolved independently in the upper and lower respiratory airways. These results support that long-term viral shedding in immunocompromised patients is one possible mechanism for the emergence of variants of concern and provide evidence towards the infection control guidelines in these patients.