Case Report: Discovery a Novel SARS-CoV-2 Variant in a Six-Months Long-Term Swab Positive Female Suffering From Non-Hodgkin Lymphoma

• Published in: Frontiers in oncology Vol. 11; p. 705948
• Main Authors: Capoluongo, Ettore, Nardelli, Carmela, Esposito, Maria Valeria, Buonomo, Antonio Riccardo, Gelzo, Monica, Pinchera, Biagio, Zappulo, Emanuela, Viceconte, Giulio, Portella, Giuseppe, Setaro, Mario, Gentile, Ivan, Castaldo, Giuseppe
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 20-07-2021
• Subjects: long-term infection; non-Hodgkin lymphoma; novel variant; Oncology; ORF3a; SARS-CoV-2; whole genome sequencing; whole genome sequencing; novel variant; SARS-CoV-2; non-Hodgkin lymphoma; long-term infection; ORF3a
• ISSN: 2234-943X; 2234-943X
• DOI: 10.3389/fonc.2021.705948

We report the case of a woman with non-Hodgkin lymphoma who remained positive on the molecular assay for SARS-CoV-2 for six months: she has never experienced a severe form of COVID-19 although in absence of seroconversion.
The whole SARS-CoV-2 genome analysis was performed by the CleanPlex SARS-CoV-2 Research and Surveillance NGS Panel (PARAGON GENOMICS, Hayward, USA).
We found twenty-two mutations in SARS-CoV-2 genome and a novel deleterious ORF3a frameshift c.766_769del corresponding to a unique and novel lineage. The region affected by this frameshift variant is reported as being important in determining SARS-CoV-2 immunogenicity. Patient's immunophenotype showed the absence of B lymphocytes and significantly reduced T-cell count. Only after the treatment with hyperimmune plasma she finally became negative on the swab.
Our findings could be helpful in the management of patients with immunodeficiency, particularly when novel variants, potentially altering the virus immune response, are present.