SARS-CoV-2 infection paralyzes cytotoxic and metabolic functions of immune cells

The SARS-CoV-2 virus is the causative agent of the global COVID-19 infectious disease outbreak, which can lead to acute respiratory distress syndrome (ARDS). However, it is still unclear how the virus interferes with immune cell and metabolic functions in the human body. In this study, we investigated the immune response in 10 acute or convalescent COVID19 patients. We characterized the peripheral blood mononuclear cells (PBMCs) using flow cytometry and found that CD8+ T cells were significantly subsided in moderate COVID-19 and convalescent patients. Furthermore, characterization of CD8+ T cells suggested that patients with a mild and moderate course of the COVID-19 disease and convalescent patients have significantly diminished expression of both perforin and granzyme B in CD8+ T cells. Using 1H-NMR spectroscopy, we characterized the metabolic status of their autologous PBMCs. We found that fructose, lactate and taurine levels were elevated in infected (mild and moderate) patients compared with control and convalescent patients. Glucose, glutamate, formate and acetate levels were attenuated in COVID-19 (mild and moderate) patients. Our findings reveal patients who suffer from an over activation of the immune system, a change of composition in infusion/intravenous fluids during infection with the aim to lower blood levels of glucose, glutamate, acetate and formate could avoid a life-threatening cytokine storm. In summary, our report suggests that SARS-CoV-2 infection leads to disrupted CD8+ T cytotoxic functions and changes the overall metabolic functions of immune cells.

synthesis of lactate intracellularly is crucial for T cells to have an increased glycolytic flux38.

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Peripheral blood mononuclear cells (PBMCs) can be analyzed to measure the health status 147 of an individual and can serve as a health biomarkers42. Therefore, the metabolic status of 148 lymphocytes could help to predict disease severity or to select the optimal therapeutic 149 intervention to boost the immune function during infection. Generally, most of the metabolism-    to the hospital requiring medical care, however, they did not need ventilation or O2 supply.

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Recovered patients were included based on a positive SARS-CoV-2 antibody testing. Study 171 participant characteristics are described in Table 2.

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To compare the number of lymphocytes and monocytes amongst the four study groups,

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PBMCs were stained and analysed by flow cytometry. Both, lymphocytes (p=0.005) and 177 monocytes (p=0.04), were significantly decreased in moderate COVID-19 patients compared 178 with HC (Suppl. Fig. 1a, b). However, mild and convalescent patients also had a reduced, but 179 not significantly reduced, count of lymphocytes/monocytes compared to HC.

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Both T and B cells are indispensable for the immune response against viral infections such as 202 SARS-CoV-2. Firstly, we compared the number of B cells amongst the study groups, which 203 give rise to virus-specific antibodies (see gating strategy in Suppl. Fig. 1c). The CD19+CD3-204 cells (B cells) were significantly increased in mild (p=0.008; 1.7x times) and moderate 205 (p=0.0008; 1.9x times) patients compared with HC (Fig. 2a)

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CD3+ cells were analysed for the CD4+ and CD8+ T cell compartment. There was a tendency 212 of increased CD4+ T cells for outpatients, inpatients and convalescent patients compared to 213 HC, but no significant difference was observed among any of the groups. CD8+ T cells were 214 significantly different between HC compared to moderate (p=0.04) or convalescent (p=0.04) 215 patients (Fig. 2b). Finally, we characterized CD4+Foxp3+CD45R-regulatory T cells (Tregs), 216 however, no significant difference was observed among the different groups (Suppl. Fig. 2).

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Impaired activation and defective cytotoxic functions of CD8+ T cells

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We found that the percentage of CD8+ T cells was decreased in mild and convalescent 221 patients compared to HC. Thus, we explored the activation status of CD8+ T cells based on 222 HLA-DR expression. We found that CD8+ T cell activation status in all three groups of infected 223 patients were significantly different from HC (mild p=0.01, moderate p=0.009, and 224 convalescent p=0.008, Fig. 3a). We characterized the cytotoxic potential of CD8+ T cells based 225 on granzyme B and perforin levels and found that there was a tendency of decreased 226 granzyme B expression in mild, moderate and convalescent patients compared with HC ( Fig.   227 3b), however it did not reach significance. Perforin was significantly decreased in convalescent 228 (p=0.03) patients compared with HC ( Fig. 3b), although mild patients also had borderline 229 significantly reduced levels (p=0.06). Furthermore, we studied the expression of CD38, a 230 marker of cell activation, which was significantly upregulated in convalescent patients 231 compared with HC (p=0.01), mild (p=0.03) and moderate (p=0.02) patients (Fig. 4a). Similarly, 232 convalescent patients had significantly increased numbers of CD38+PD-1+ cytotoxic CD8+ T 233 cells compared with HC (p=0.005), moderate (p=0.002) and mild (p=0.002), which reflects the 234 exhaustion and non-responsiveness (anergy) of CD8+ T cells (Fig. 4b). Overall, our data suggested that CD8+ T cells have reduced activation, diminished expression of cytotoxic 236 molecules such as perforin and granzyme B and severely exhausted phenotype.

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Dynamics of metabolites production in mild, moderate and convalescent patient that spectral data from mild and moderate patients formed overlapping clusters clearly distinct 242 from a cluster formed by HC and convalescent patients (Fig. 5b), indicating a strong difference 243 in metabolite levels between infectious state compared to healthy or recovered state.

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Statistical analysis of the four different groups, revealed that 15 metabolites showed p-values 245 < 0.05, with highest significance for metabolites from the energy metabolism (Fig. 5c Table 1). The data indicate a strong consumption of glucose, acetate, formate during 247 infection, while with lactate levels are increased. Furthermore, we also found very high levels 248 of fructose in PBMCs from mild patients, medium concentrations in moderate and, low levels 249 in HC and convalescent patients (Fig. 5c). Furthermore, glutamate was almost abolished in 250 mild and moderate patients, potentially as a consequence of enhanced production of α-251 ketoglutarate in the TCA cycle in PBMCs via glutamate dehydrogenase (Fig. 5c).

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To find an association between different metabolites, we applied the variable importance of 254 projection (VIP) score. We found that formate and glucose had the highest score compared to

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To find an association between different metabolites, we applied the variable importance of 269 projection (VIP) score. We found that formate and glucose had the highest score compared to 270 other metabolites (Fig. 6A). In order to determine if additional metabolites are positively 271 associated with changes in glucose, lactate and fructose, we performed a pattern hunter 272 analysis for all metabolites. We found that high glucose levels correlated with high formate, dihydroxy acetone phosphate (DAP) into the glycolysis, is correlated positively with lactate glucose (Fig. 6).

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Statistical analysis

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Bar diagrams were prepared using GraphPad Prism 6.0. FACS data were analysed using one-

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One exemplary dot plot is shown per study group. There was statistically significant 498 difference among HC, mild, moderate and convalescent (upper FACS panel).

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However, CD8+ T cells were significantly reduced in outpatient and convalescent 500 patients. *P value <0.05.

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All the authors have seen the manuscript, substantially contributed and agreed to be co-588 author.

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We thank you all the patients who participated in this study and FACS core facility (Klinikum-