Viral Population Heterogeneity and Fluctuating Mutational Pattern during a Persistent SARS-CoV-2 Infection in an Immunocompromised Patient

• Published in: Viruses Vol. 15; no. 2; p. 291
• Main Authors: Brandolini, Martina, Zannoli, Silvia, Gatti, Giulia, Arfilli, Valentina, Cricca, Monica, Dirani, Giorgio, Denicolò, Agnese, Semprini, Simona, Grumiro, Laura, Imola, Manuela, Larne, Damiano, Marino, Maria Michela, Manera, Martina, Mancini, Andrea, Taddei, Francesca, Zagarrigo, Manuel, Biagetti, Carlo, Sambri, Vittorio
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 19.01.2023; MDPI
• Subjects: Case Report; chronic diseases; COVID-19; Cytomegalovirus; Evaluation; Evolution; genetic similarity; Hematology; Humans; Immunocompromised Host; Immunocompromised hosts; immunocompromised patients; Infections; intra-host evolution; Laboratories; Lymphoma; Monoclonal antibodies; Mutation; NGS whole-genome sequencing; patients; Persistent infection; Polymerase chain reaction; SARS-CoV-2; SARS-CoV-2 - genetics; Sequence analysis; Serology; Severe acute respiratory syndrome coronavirus 2; viruses; Whole genome sequencing; Italy; United States > US; Taiwan; COVID-19; NGS whole-genome sequencing; immunocompromised patients; intra-host evolution; SARS-CoV-2
• ISSN: 1999-4915; 1999-4915
• DOI: 10.3390/v15020291

Literature offers plenty of cases of immunocompromised patients, who develop chronic and severe SARS-CoV-2 infections. The aim of this study is to provide further insight into SARS-CoV-2 evolutionary dynamic taking into exam a subject suffering from follicular lymphoma, who developed a persistent infection for over 7 months. Eight nasopharyngeal swabs were obtained, and were analyses by qRT-PCR for diagnostic purposes. All of them were considered eligible (Ct < 30) for NGS sequencing. Sequence analysis showed that all sequences matched the B.1.617.2 AY.122 lineage, but they differed by few mutations identifying three genetically similar subpopulations, which evolved during the course of infection, demonstrating that prolonged replication is paralleled with intra-host virus evolution. These evidences support the hypothesis that SARS-CoV-2 adaptive capacities are able to shape a heterogeneous viral population in the context of immunocompromised patients. Spill-over of viral variants with enhanced transmissibility or immune escape capacities from these subjects is plausible.