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Li Y, Choudhary MC, Regan J, Boucau J, Nathan A, Speidel T, Liew MY, Edelstein GE, Kawano Y, Uddin R, Deo R, Marino C, Getz MA, Reynold Z, Barry M, Gilbert RF, Tien D, Sagar S, Vyas TD, Flynn JP, Hammond SP, Novack LA, Choi B, Cernadas M, Wallace ZS, Sparks JA, Vyas JM, Seaman MS, Gaiha GD, Siedner MJ, Barczak AK, Lemieux JE, Li JZ. SARS-CoV-2 Viral Clearance and Evolution Varies by Extent of Immunodeficiency. medRxiv 2023:2023.07.31.23293441. [PMID: 37577493 PMCID: PMC10418302 DOI: 10.1101/2023.07.31.23293441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Despite vaccination and antiviral therapies, immunocompromised individuals are at risk for prolonged SARS-CoV-2 infection, but the immune defects that predispose to persistent COVID-19 remain incompletely understood. In this study, we performed detailed viro-immunologic analyses of a prospective cohort of participants with COVID-19. The median time to nasal viral RNA and culture clearance in the severe hematologic malignancy/transplant group (S-HT) were 72 and 40 days, respectively, which were significantly longer than clearance rates in the severe autoimmune/B-cell deficient (S-A), non-severe, and non-immunocompromised groups (P<0.001). Participants who were severely immunocompromised had greater SARS-CoV-2 evolution and a higher risk of developing antiviral treatment resistance. Both S-HT and S-A participants had diminished SARS-CoV-2-specific humoral, while only the S-HT group had reduced T cell-mediated responses. This highlights the varied risk of persistent COVID-19 across immunosuppressive conditions and suggests that suppression of both B and T cell responses results in the highest contributing risk of persistent infection.
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Affiliation(s)
- Yijia Li
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Manish C Choudhary
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - James Regan
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Julie Boucau
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Anusha Nathan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Program in Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Boston, MA 02115, USA
| | - Tessa Speidel
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - May Yee Liew
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gregory E Edelstein
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yumeko Kawano
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rockib Uddin
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rinki Deo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Caitlin Marino
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Matthew A Getz
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Zahra Reynold
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Mamadou Barry
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Rebecca F Gilbert
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Dessie Tien
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Shruti Sagar
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tammy D Vyas
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - James P Flynn
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sarah P Hammond
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lewis A Novack
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Bina Choi
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Manuela Cernadas
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zachary S Wallace
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jeffrey A Sparks
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jatin M Vyas
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Gaurav D Gaiha
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Mark J Siedner
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Amy K Barczak
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Jacob E Lemieux
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan Z Li
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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