Persistent Severe Acute Respiratory Syndrome Coronavirus 2 Infection in Immunocompromised Host Displaying Treatment Induced Viral Evolution

Abstract

We report a coronavirus disease 2019 case with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) persisting beyond 333 days in an immunocompromised patient with chronic lymphocytic leukemia, asymptomatically carrying infectious SARS-CoV-2 at day 197 postdiagnosis. In addition, viral sequencing indicates major changes in the spike protein over time, temporally associated with convalescent plasma treatment.

Keywords: CLL; SARS-CoV-2; persistent infection; viral evolution.

Figure 1.

(A) Timeline depicting the clinical parameters from time of diagnosis (day 0) until day 200. Fluctuations in total lymphocyte counts (×10⁹/L) and C-reactive protein (mg/L) are shown as dotted red and blue lines, respectively. Hospital admissions are shown with gray shaded areas. Initiation of treatment administration is indicated by vertical lines in black for remdesivir (R) and dexamethasone (D) and in green for convalescent plasma (CP). Pharyngeal swabs for viral outgrowth was sampled on day 126 and 197 postdiagnosis (black arrows), whereas blood samples for immunologic and serological assessments were sampled on day 126 (orange arrow). (B) Pharyngeal swab samples taken on day 126 and 197 postdiagnosis was used for ribonucleic acid (RNA) extraction and subsequent droplet digital polymerase chain reaction (ddPCR) for quantification of viral load. (C) Vero E6/TMPRSS2 cells were inoculated with swab transport media and subsequently assessed for viral outgrowth. Input swab material was washed away after 24 hours of inoculation, after which cell supernatant containing viral outgrowth was collected and used for RNA extraction and subsequent ddPCR, with viral copies increasing over a 5-day time period. (D) Meso Scale analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific immunoglobulin G (IgG) towards full-length spike, the spike receptor-binding domain (RBD), N-terminal domain (NTD), and nucleocapsid. “P”: The case patient antibody titers (large red dot) in the context of a cohort of 203 recovered SARS-CoV-2-infected individuals. “C”: Antibody levels of 10 prepandemic controls for comparison. (E) Plasma antibody SARS-CoV-2 neutralizing capacity was analyzed by a SARS-CoV-2 spike pseudovirus neutralization assay. Case patient plasma (red) is shown in the context of the 95% confidence interval (gray shaded area) of 10 prepandemic controls (Controls). (F) Illumina sequencing of SARS-CoV-2 RNA from clinical samples taken at day 24 (tracheal secretion), day 59 (bronchoalveolar lavage), day 80 (pharyngeal swab), day 126 (pharyngeal swab), day 142 (pharyngeal swab), day 155 (pharyngeal swab), and day 197 (pharyngeal swab). Red lines indicate timepoints between sampling days with administration of convalescent plasma (CP) (day 70, 127, and 128).