Evolution of SARS-CoV-2 and antigenic escape in immunocompromised patients

To the editor:

Peplomer mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that result in escape from neutralizing antibodies can occur in immunocompromised patients with prolonged infection.^1,2 It is hypothesized that such virus avoidance contributes to the emergence of mutant strains of global concern.³ In the absence of an effective immune response, selective pressure, such as monoclonal antibody therapy, can result in immunologically significant mutations.

To understand the selective pressures that drive the evolution of SARS-CoV-2 in the host, such evolution and intrinsic immune response and extrinsic factors in a convenient sample obtained from 5 patients with B cell deficiency. We investigated the relationship with sex antibody treatment. (For more information on each patient’s medical history, see Supplementary appendixAvailable at NEJM.org with the full text of this letter. All patients had SARS-CoV-2 infection lasting 42 to 302 days after the first positive test (day 0) (Figure S1 and Table S1). Supplementary appendix). This study was approved by the Emory University Institutional Review Board. Informed consent was obtained from patients (patients 2, 4, and 5) who provided whole blood samples for the study.

Figure 1. Figure 1. Neutralizing antibody titers, effector T cell responses, and spike mutations in 5 immunocompromised patients.

Panel A shows the neutralizing antibody titers in patient sera against the reference SARS-CoV-2 pseudovirus Wuhan-Hu-1 at various time points after infection. These titers represent the reciprocal of serum dilution in which up to half of the pseudovirus neutralization was observed. The data show the geometric mean of 2-5 independent experiments. The ? bar shows the standard deviation. The dotted line represents the lower limit of detection. Panels B and C respond to the frequency of CD154, interferon-γ, tumor necrosis factor (TNF), or CD4 + or CD8 + T cells expressing interleukin-2 minus the background, non-naive (ie, effector or). Memory) Shown as a percentage of cells. Stimulation of peripheral blood mononuclear cells with peptide megapools containing 15-mer from the spike open reading frame (ORF) and peptide megapools containing predicted CD8 + T cell epitopes from the ORF containing spikes, respectively. Frequency was determined by flow cytometry in patients 4 and 5, healthy control donors (HC2), and two age-matched patients admitted with Covid-19 (Covid 1 and 2). Panel D shows mutations in the gene encoding the SARS-CoV-2 peplomer compared to the Wuhan-Hu-1 strain, depending on patient ID and time point. Shading indicates the frequency of mutations. For each mutation, the observed mutant nucleotides are listed above the plot and the amino acid mutations are listed below the plot.

Patient 1 had not received antibody treatment and was negative for neutralizing antibodies on day 37. Patients 2 and 3 were treated with the monoclonal antibody bumlanivimab on days 4 and 8, respectively. Their sera strongly neutralized the reference pseudovirus (Wuhan-Hu-1) on days 33 (patient 2) and 55 (patient 3), neutralizing antibodies until days 77 and 83, respectively. Maintained a rise in prices (Figure 1A). Patient 4 received convalescent plasma on days 0 and 104 and failed to detect neutralizing antibodies on days 82 and 101. Patient 5 received convalescent plasma on day 200 and had low neutralizing antibody titers on day 204. Binding of IgG titers to peplomer reflected serum neutralization. Titer (Fig. S2). All but one patient (Patient 2) eventually recovered. Patients 2, 4, and 5 provided peripheral blood samples for immunophenotypic testing. All three of these patients had lower lymphocyte counts and lower frequency of CD19 + B cells (0.19% in patient 2 and 0.01 in patient 4) compared to healthy controls and age-matched inpatients. %, 0.01% for patient 5). 2019 Coronavirus disease patient (Covid-19) (Fig. S3). Patient 3 had clinically low levels of T and B cells. Therefore, the antibody response to reference SARS-CoV-2 in patients 2, 3, and 5 was probably due to extrinsic treatment. SARS-CoV-2 specific effector T cell responses were detectable in patients 4 and 5, and CD8 + T cells secreted antiviral interferon-γ and tumor necrosis factor, but at background levels in patient 2. Was only detectable (Figures 1B and 1C And figs. S4, S5, and S6).

SARS-CoV-2 sequencing (Tables S2 and Figures S7 and S8) revealed the evolution of peaplomers in patients 2 and 3 (Table S2 and Figures S7 and S8).Figure 1D And Figure S9); Both of these patients treated with bumlanivimab were deficient in T cells and B cells. Consensus-level mutations and single nucleotide polymorphisms in the sample were found in the spike receptor binding domain (RBD) and N-terminal domain (NTD), which are regions associated with antigenic escape.^Four In contrast, no RBD or NTD mutations were found in patients 1 who did not receive the antibody, or patients 4 and 5 who received convalescent plasma and showed an intact T cell response to SARS-CoV-2. It was.

To assess whether the viruses obtained from patients 1, 2, and 3 were neutralized by autologous serum, we constructed an infectious pseudovirus expressing variant spikes (Figure S10). The sera of patients 1, 2, and 3 did not neutralize the pseudovirus with mutation spikes, even though the sera of patients 2 and 3 neutralized the reference pseudovirus (Fig. S11). Therefore, the spike mutations in patients 2 and 3 conferred neutralization resistance to bumlanivimab.

Our results underscore the potential importance of selective pressure, such as the use of monoclonal antibodies, in promoting the emergence of SARS-CoV-2 escape mutations. These findings highlight the need for a better understanding of the impact of different treatments on immunocompromised patients. Our results also support the findings of previous studies in which patients with B cell deficiency were found to induce effector T cells.^Five Results that may indicate an important role for T cells in controlling infection.

Erin M. Scherer, Ph.D., D.Phil.
Ahmed Babi Car, MB, BS
Max W. Adelman, MD
Brent Allman, BA
Autumn key, MS
Jennifer M. Kleingenz, BS
Dr. Rose M. Langschjoen
Phuong-Vi Nguyen, BS
Ivy Oniechi, MS
Jacob D. Sherman, BS
Trevor W. Simon, MS
Hannah Solov
Emory University, Atlanta, Georgia
[email protected]

Jessica Guide, MPH
Emory Healthcare, Atlanta, GA

Jay Barkey, MD
Andrew S. Webster, MD
Emory University, Atlanta, Georgia

Dr. Daniela Weiskov
Institute of Immunology, La Jolla, La Jolla, CA

Dr. Daniel B. Weissman
Yongxian Xu, MD
Jessie J. Wagoner, MD
Katia Koelle, Ph.D.
Nadine Rouphael, MD
Stephanie M. Pouch, MD
Ann Piantadosi, MD, Ph.D.
Emory University, Atlanta, Georgia
[email protected]

The views expressed in this letter are those of the author and do not necessarily represent the official views of the National Institutes of Health.

This letter was published on June 8, 2022 at NEJM.org.