Phenotype of SARS-CoV-2-specific T-cells in COVID-19 patients with acute respiratory distress syndrome

COVID-19 is associated with lymphopenia and cytokine storm, but no information is available on specific cellular immune responses to SARS-CoV-2. Here, we characterized SARS-CoV-2-specific CD4+ and CD8+ T-cells in patients with acute respiratory distress syndrome. The spike protein (S) proved a potent T-cell antigen and specific T-cells predominantly produced Th1 cytokines. These novel data are important in vaccine design and will facilitate evaluation of vaccine candidate immunogenicity.


Introduction
A novel coronavirus, named SARS-CoV-2, has been identified as the causative agent of a global outbreak of respiratory tract disease (COVID-19) 1,2 . On April 9 th , over 1.5 million cases and more than 90,000 deaths were reported globally. COVID-19 is characterized by fever, cough, dyspnea and myalgia 2 , but in some patients the infection results in moderate to severe acute respiratory distress syndrome (ARDS), requiring invasive mechanical ventilation for a period of several weeks. COVID-19 patients may present with lymphopenia 2,3 , but the disease has also been associated with immune hyperresponsiveness referred to as 'cytokine storm' 4 . A transient increase in co-expression of CD38 and HLA-DR by T-cells, a phenotype of CD8 + Tcell activation in response to viral infection, was observed concomitantly 5 . This increase in both CD4 + and CD8 + CD38 + HLA-DR + T-cells preceded resolution of clinical symptoms in a non-severe, recovered, COVID-19 patient 6 .
Despite the large numbers of cases and deaths, no information is available on the phenotype of SARS-CoV-2-specific T-cells. Here, we stimulated peripheral blood mononuclear cells (PBMC) from eight COVID-19 patients with ARDS, collected up to three weeks after admission to the intensive care unit (ICU), with MegaPools (MP) of overlapping or prediction-based peptides covering the SARS-CoV-2 proteome 7 . We detected SARS-CoV-2-specific CD4 + and CD8 + T-cells in all COVID-19 patients, whereas peptide stimulation of healthy control PBMC samples collected before the outbreak showed no response. SARS-CoV-2-specific T-cells predominantly produced Th1 cytokines, although Th2 cytokines were also detected.
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Results
We included eight COVID-19 patients with moderate to severe ARDS in this study (Figure 1a). Patients were between 49 and 72 years old (average 59 ± 7 years) and of mixed gender (4 female, 4 male). All patients tested SARS-CoV-2 positive by RT-PCR and were ventilated during their stay at the ICU. At the time of writing, 3 patients were transferred out of the ICU, 1 patient was deceased, and 4 patients were still in follow-up. Patients were treated with lung protective ventilation using the higher PEEP/lower FiO2 table of the ARDSnet and restrictive volume resuscitation.
They received antibiotics as a part of a treatment regime aimed at selective decontamination of the digestive tract. No antiviral or immunomodulatory drugs were used. All patients were at the ICU and included shortly after ICU admission; selfreported illness varied between 5 and 14 days before inclusion (Figure 1a CD4:CD8 ratios were increased in COVID-19 patients when compared to HC (6.2 ± 3.0 in COVID-19 vs 2.4 ± 1.0 in HC, p=0.0037, Figure 1c). This may reflect migration of CD8 + T-cells to the respiratory tract. PBMC were stimulated with three different peptide MPs: MP_S, MP_CD4_R and two MP_CD8 pools. MP_S contained 221 overlapping peptides (15-mers overlapping by 10 amino acids) covering the entire surface glycoprotein (spike, S) and can stimulate both CD4 + and CD8 + T-cells. MP_CD4_R contained 246 HLA class II predicted All rights reserved. No reuse allowed without permission. the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2020.04.11.20062349 doi: medRxiv preprint epitopes covering all viral proteins except S, specifically designed to activate CD4 + T-cells. The two MP_CD8 pools combined contained 628 HLA class I predicted epitopes covering all SARS-CoV-2 proteins, specifically designed to activate CD8 + T- the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.
The majority of virus-specific CD8 + T-cells was identified as CCR7effector memory (T EM ) or terminally differentiated effector (T EMRA ) 9 . Both these CD8 + effector subsets are potent producers of IFNg, contain preformed perforin granules for immediate antigen-specific cytotoxicity and home efficiently to peripheral lymphoid tissues 8 .
As production of pro-inflammatory cytokines can be predictive of severe clinical outcome for other viral diseases 10 , we measured antigen-specific production of 13 cytokines in cell culture supernatants from PBMC stimulated with MP_S ( Figure 1f, IL-21 data not shown), MP_CD4_R and MP_CD8 (data not shown). Activation of PBMC by the overlapping S peptide pool led to a strong significant production of the Th1 cytokines IFNg, TNFa and IL-2 in COVID-19 patients when compared to HC.
More characteristic Th2 cytokines (IL-5, IL-13, IL-9 and IL-10) were also consistently detected, albeit at low levels. IL-6 levels were not different between COVID-19 patients and HC, while IL-4 and IL-21 could not be detected at all. Antigen-specific production of cytokines related to a Th17 response was mixed; IL-17 production was not different between patients and HC, whereas IL-22 could be detected. Thus, stimulation of PBMC from COVID-19 patients with MP led to a balanced production of IFNg, TNFa, IL-2, IL-5, IL-13, IL-9, IL-10 and IL-22. the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.
SARS-CoV-2-specific CD4 + T-cells were detected in all patients, and frequencies of virus-specific responder cells increased significantly over time (ANOVA repeated measures, p<0.001).
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Discussion
Collectively, these data provide information on the breadth, kinetics and phenotype of virus-specific cellular immune responses in COVID-19 ARDS patients. We provide evidence that SARS-CoV-2-specific CD4 + and CD8 + T-cells appear in blood of ARDS patients in the first two weeks post onset of symptoms, and their frequency increases over time. The phenotype of the antigen-specific cellular immune response is balanced; SARS-CoV-2-specific CD4 + T-cells in blood were typically central memory, CD8 + T-cells typically had a more effector phenotype. It is tempting to speculate that the CD8 + cytotoxic T-cells are predominantly responsible for the production of IFNg, whereas virus-specific CD4 + T-cells could be responsible for the production of typical Th1 and Th2 cytokines. Elevated levels of IL-6 in patient plasma have previously been correlated to respiratory failure in COVID-19 patients 11 . Here, we could not detect increased specific production of IL-6 in PBMC stimulated with peptide pools, suggesting that virus-specific T-cells are not to blame for the production of IL-6 and the concomitant 'cytokine storm', but that these are predominantly mediated by innate immune cells.
Novel SARS-CoV-2 vaccines are currently in development and mainly focus on the surface glycoprotein S as an antigen for efficient induction of virus-specific neutralizing antibodies. We now show that S can also be a potent immunogen for inducing virus-specific CD4 + and CD8 + T-cells, and our data combined with a previous study in a non-severe, recovered, COVID-19 patient 6 , indicate that virusspecific T-cells could be beneficial for a good clinical outcome. Collectively, these novel data are important for vaccine design and will facilitate the evaluation of future vaccine immunogenicity. All rights reserved. No reuse allowed without permission. the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.
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Competing interest statement
The authors declare no competing interests.
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Epitope MegaPool (MP) design and preparation. SARS-CoV-2 virus-specific CD4
and CD8 peptides were synthesized as crude material (A&A, San Diego, CA), resuspended in DMSO, pooled and sequentially lyophilized as previously reported 13 . SARS-CoV-2 epitopes were predicted using the protein sequences derived from the SARS-CoV-2 reference (GenBank: MN908947) and IEDB analysis-resource as previously described 7,14 . Specifically, CD4 SARS-CoV-2 epitope prediction was carried out using a previously described approach in Tepitool resource in IEDB 15,16 similarly to what was previously described 7 , but removing the resulting Spike the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint (which was not peer-reviewed) is Briefly, ELISA plates were coated with recombinant SARS-CoV-2 RBD protein.
Following blocking, samples were added and incubated for 1 hour, after which the plates were washed and a secondary HRP-labelled rabbit anti-human IgG (DAKO) was added. Following a 1 hour incubation, the plates were washed, the signal was developed using TMB, and the OD450 was measured for each well. All rights reserved. No reuse allowed without permission. the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2020.04.11.20062349 doi: medRxiv preprint Analysis was performed using the LEGENDplex analysis software v8.0, which distinguishes between the 13 different analytes on basis of bead size and internal All rights reserved. No reuse allowed without permission. the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2020.04.11.20062349 doi: medRxiv preprint 16 dye. Quantity of each respective cytokine is calculated on basis of intensity of the streptavidin PE signal and a freshly prepared standard curve.
Statistical analysis. For comparison of CD3 + T-cell percentages, CD4:CD8 ratios, CD69 + CD137 + stimulated T-cells and cytokine levels between HC and COVID-19 patients all log transformed data was tested for normal distribution. If distributed normally, groups were compared via an unpaired T test. If not distributed normally, groups were compared via a Mann-Whitney test. Two-tailed p values are reported throughout the manuscript. One way ANOVA repeated measures was used to test for linear trend over sequential time points (0, 7 and 14 days post inclusion).
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(j) Activation after stimulation could be observed in almost all PBMC samples from COVID-19 patients, whereas this activation was not observed in healthy controls (HC).
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