AIDS patient with severe T cell depletion achieved control but not clearance of SARS‐CoV‐2 infection

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Abstract

A late presenter AIDS patient with severe T cell depletion presented non‐severe COVID‐19 symptoms, with prolonged viral shedding. Our case report supports the hypothesis that an effective T cell response may be dispensable for the control of COVID‐19 progression to severe forms, while it may be necessary for SARS‐CoV‐2 clearance.

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Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host

Bina Choi, Manish C. Choudhary, James K. Regan … (2020)

To the Editor: A 45-year-old man with severe antiphospholipid syndrome complicated by diffuse alveolar hemorrhage, 1 who was receiving anticoagulation therapy, glucocorticoids, cyclophosphamide, and intermittent rituximab and eculizumab, was admitted to the hospital with fever (Fig. S1 in the Supplementary Appendix, available with the full text of this letter at NEJM.org). On day 0, Covid-19 was diagnosed by SARS-CoV-2 reverse-transcriptase–polymerase-chain-reaction (RT-PCR) assay of a nasopharyngeal swab specimen, and the patient received a 5-day course of remdesivir (Fig. S2). Glucocorticoid doses were increased because of suspected diffuse alveolar hemorrhage. He was discharged on day 5 without a need for supplemental oxygen. From day 6 through day 68, the patient quarantined alone at home, but during the quarantine period, he was hospitalized three times for abdominal pain and once for fatigue and dyspnea. The admissions were complicated by hypoxemia that caused concern for recurrent diffuse alveolar hemorrhage and was treated with increased doses of glucocorticoids. SARS-CoV-2 RT-PCR cycle threshold (Ct) values increased to 37.8 on day 39, which suggested resolving infection (Table S1). 2,3 On day 72 (4 days into another hospital admission for hypoxemia), RT-PCR assay of a nasopharyngeal swab was positive, with a Ct value of 27.6, causing concern for a recurrence of Covid-19. The patient again received remdesivir (a 10-day course), and subsequent RT-PCR assays were negative. On day 105, the patient was admitted for cellulitis. On day 111, hypoxemia developed, ultimately requiring treatment with high-flow oxygen. Given the concern for recurrent diffuse alveolar hemorrhage, the patient’s immunosuppression was escalated (Figs. S1 through S3). On day 128, the RT-PCR Ct value was 32.7, which caused concern for a second Covid-19 recurrence, and the patient was given another 5-day course of remdesivir. A subsequent RT-PCR assay was negative. Given continued respiratory decline and concern for ongoing diffuse alveolar hemorrhage, the patient was treated with intravenous immunoglobulin, intravenous cyclophosphamide, and daily ruxolitinib, in addition to glucocorticoids. On day 143, the RT-PCR Ct value was 15.6, which caused concern for a third recurrence of Covid-19. The patient received a SARS-CoV-2 antibody cocktail against the SARS-CoV-2 spike protein (Regeneron). 4 On day 150, he underwent endotracheal intubation because of hypoxemia. A bronchoalveolar-lavage specimen on day 151 revealed an RT-PCR Ct value of 15.8 and grew Aspergillus fumigatus. The patient received remdesivir and antifungal agents. On day 154, he died from shock and respiratory failure. We performed quantitative SARS-CoV-2 viral load assays in respiratory samples (nasopharyngeal and sputum) and in plasma, and the results were concordant with RT-PCR Ct values, peaking at 8.9 log10 copies per milliliter (Fig. S2 and Table S1). Tissue studies showed the highest SARS-CoV-2 RNA levels in the lungs and spleen (Figs. S4 and S5). Phylogenetic analysis was consistent with persistent infection and accelerated viral evolution (Figures 1A and S6). Amino acid changes were predominantly in the spike gene and the receptor-binding domain, which make up 13% and 2% of the viral genome, respectively, but harbored 57% and 38% of the observed changes (Figure 1B). Viral infectivity studies confirmed infectious virus in nasopharyngeal samples from days 75 and 143 (Fig. S7). Immunophenotyping and SARS-CoV-2–specific B-cell and T-cell responses are shown in Table S2 and Figures S8 through S11. Although most immunocompromised persons effectively clear SARS-CoV-2 infection, this case highlights the potential for persistent infection 5 and accelerated viral evolution associated with an immunocompromised state.

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SARS-CoV-2 evolution during treatment of chronic infection

Steven A Kemp, Dami A. Collier, Rawlings P Datir … (2021)

Summary SARS-CoV-2 Spike protein is critical for virus infection via engagement of ACE2 1 , and is a major antibody target. Here we report chronic SARS-CoV-2 with reduced sensitivity to neutralising antibodies in an immune suppressed individual treated with convalescent plasma, generating whole genome ultradeep sequences over 23 time points spanning 101 days. Little change was observed in the overall viral population structure following two courses of remdesivir over the first 57 days. However, following convalescent plasma therapy we observed large, dynamic virus population shifts, with the emergence of a dominant viral strain bearing D796H in S2 and ΔH69/ΔV70 in the S1 N-terminal domain NTD of the Spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype diminished in frequency, before returning during a final, unsuccessful course of convalescent plasma. In vitro, the Spike escape double mutant bearing ΔH69/ΔV70 and D796H conferred modestly decreased sensitivity to convalescent plasma, whilst maintaining infectivity similar to wild type. D796H appeared to be the main contributor to decreased susceptibility but incurred an infectivity defect. The ΔH69/ΔV70 single mutant had two-fold higher infectivity compared to wild type, possibly compensating for the reduced infectivity of D796H. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy associated with emergence of viral variants with evidence of reduced susceptibility to neutralising antibodies.

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N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2

Matthew McCallum, Anna De Marco, Florian A. Lempp … (2021)

The SARS-CoV-2 spike (S) glycoprotein contains an immunodominant receptor-binding domain (RBD) targeted by most neutralizing antibodies (Abs) in COVID-19 patient plasma. Little is known about neutralizing Abs binding to epitopes outside the RBD and their contribution to protection. Here, we describe 41 human monoclonal Abs (mAbs) derived from memory B cells, which recognize the SARS-CoV-2 S N-terminal domain (NTD) and show that a subset of them neutralize SARS-CoV-2 ultrapotently. We define an antigenic map of the SARS-CoV-2 NTD and identify a supersite (designated site i) recognized by all known NTD-specific neutralizing mAbs. These mAbs inhibit cell-to-cell fusion, activate effector functions, and protect Syrian hamsters from SARS-CoV-2 challenge, albeit selecting escape mutants in some animals. Indeed, several SARS-CoV-2 variants, including the B.1.1.7, B.1.351 and P1 lineages, harbor frequent mutations within the NTD supersite suggesting ongoing selective pressure and the importance of NTD-specific neutralizing mAbs for protective immunity and vaccine design.

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Author and article information

Contributors

Michele Spinicci: michele.spinicci@unifi.it

Journal

Journal ID (nlm-ta): Eur J Immunol

Journal ID (iso-abbrev): Eur J Immunol

Journal ID (doi): 10.1002/(ISSN)1521-4141

Journal ID (publisher-id): EJI

Title: European Journal of Immunology

Publisher: John Wiley and Sons Inc. (Hoboken )

ISSN (Print): 0014-2980

ISSN (Electronic): 1521-4141

Publication date (Electronic): 04 December 2021

Publication date (Print): February 2022

Publication date PMC-release: 04 December 2021

Volume: 52

Issue: 2 ( doiID: 10.1002/eji.v52.2 )

Pages: 352-355

Affiliations

[ ¹ ] Department of Experimental and Clinical Medicine University of Florence Florence Italy

[ ² ] Infectious and Tropical Diseases Unit Careggi University Hospital Florence Italy

[ ³ ] Intermediate Care Unit, Careggi University Hospital Florence Italy

[ ⁴ ] Microbiology and Virology Unit Careggi University Hospital Florence Italy

[ ⁵ ] Department of Cellular Therapies and Transfusion Medicine Careggi University Hospital Florence Italy

[ ⁶ ] Flow Cytometry Diagnostic Center and Immunotherapy (CDCI) Careggi University Hospital Florence Italy

Author notes

[*] [* ] Full correspondence: Michele Spinicci, MD, Dipartimento di Medicina Sperimentale e Clinica, Largo Brambilla 3, 50134, Firenze, Italia

e‐mail: michele.spinicci@ 123456unifi.it

Article

Publisher ID: EJI5211

DOI: 10.1002/eji.202149574

PMC ID: 9015404

PubMed ID: 34822185

SO-VID: 9bf6dc6c-121e-4053-a424-8f20545ac51f

License:

This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

History

Date revision received : 21 October 2021

Date received : 12 August 2021

Date accepted : 22 November 2021

Page count

Figures: 2, Tables: 0, Pages: 4, Words: 2230

Funding

Funded by: Ministry of Education, University and Research (Italy) Excellence Departments 2018–2022 (Project for the Department of Experimental and Clinical Medicine)

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source-schema-version-number 2.0

cover-date February 2022

details-of-publishers-convertor Converter:WILEY_ML3GV2_TO_JATSPMC version:6.1.4 mode:remove_FC converted:18.04.2022

ScienceOpen disciplines: Immunology

Keywords: covid‐19,hiv,cd4,immunocompromised,monoclonal,convalescent plasma

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ScienceOpen disciplines: Immunology

Keywords: covid‐19, hiv, cd4, immunocompromised, monoclonal, convalescent plasma

AIDS patient with severe T cell depletion achieved control but not clearance of SARS‐CoV‐2 infection

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Abstract

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Wiley: Novel Coronavirus COVID-19

Most cited references 16

Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host

SARS-CoV-2 evolution during treatment of chronic infection

N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2

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