T-Cell Phenotypes and Systemic Cytokine Profiles of People Living with HIV Admitted to Hospital with COVID-19

Abstract

Whether SARS-CoV-2 infection leads to a higher mortality and morbidity in people living with HIV (PLWH) in Africa remains inconclusive. In this study, we explored the differences in the T-cell phenotypes between people with and without HIV on the day of admission (V1) and ±7 days later (V2), as well as their cytokine/chemokine profiles on V1. Patients admitted with COVID-19 were recruited between May 2020 and December 2021 from the Steve Biko Academic and Tshwane District Hospitals in Pretoria, South Africa. Of 174 patients, 37 (21%) were PLWH. T-cell profiles were determined by flow cytometry, and cytokine levels were determined using a multiplex suspension bead array. PLWH were significantly younger than those without HIV, and were more likely to be female. In an adjusted analysis, PLWH had higher percentages of CD4+ central memory (CM) programmed cell death protein 1 (PD-1)+, CD8+ effector memory (EM)2, and CD8+ EM4 CD57+ cells, as well as higher concentrations of interleukin (IL)-35 at admission. PLWH with CD4+ T-cell counts of >200 cells/mm³ had altered CD4+ and CD8+ T-cell profiles, lower levels of systemic inflammation measured by plasma ferritin and PCT levels, and less severe disease. PLWH with CD4+ T-cell counts of <200 cells/mm³ on admission had higher concentrations of IL-6 and lower levels of IL-29. At V2, the percentages of CD4+ CM PD-1+ T-cells and CD8+ EM4 T-cells co-expressing CD57 and PD-1 remained higher in PLWH, while all other CD8+ EM populations were lower. Fewer CD8+ EM T-cells after ±7 days of admission may be indicative of mechanisms inhibiting EM T-cell survival, as indicated by the higher expression of IL-35 and the T-cell maturation arrest observed in PLWH. This profile was not observed in PLWH with severe immunodeficiency, highlighting the need for differentiated care in the broader PLWH population.

Keywords: COVID-19; HIV; SARS-CoV-2; T-cells; cytokines.

Figure 1

Visit 1 differences in T-cell populations between people living with and without HIV hospitalized with COVID-19. (A) Representative UMAP plots of people living with and without HIV at admission with COVID-19. (B) Representative dot plots of people living with and without HIV showing differences in CD4+ T-cell subsets, CD4+ EM subsets, and CM PD-1+ expression. (C) Representative dot plots of people living with and without HIV showing differences in CD8+ EM subsets and PD-1 expression in CD8+ EM2 and EM3 populations, as well as TEMRA end-stage effectors expressing CD57. (D) COVID+ PLWH had a higher percentage of CD4+ and CD8+ CM T-cells expressing PD-1. Abbreviations: central memory (CM), control PLWH without COVID-19 (Control PLWH), control people living without HIV without COVID-19 (Control PLWOH), double negative (DN), double positive (DP), end-stage effector (E), effector memory (EM), not significant (ns), pre-effector 1 (pE1), PLWH hospitalized with COVID-19 (COVID+ PLWH), people living without HIV hospitalized with COVID-19 (COVID+ PLWOH), programmed cell death protein 1 (PD-1), and terminally differentiated T-cells re-expressing CD45RA (TEMRA). The Kruskal–Wallis test with post hoc Dunn’s test was used to compare continuous variables between groups. p-value: ***: <0.001.

Figure 2

T-cell subsets comparing PLWH with undetectable and detectable HIV viral loads upon hospitalization with COVID-19, as well as their respective controls. (A) Representative UMAP plots of the T-cell populations of PLWH with undetectable and detectable VLs at admission with COVID-19. (B) PLWH with a detectable VL with COVID-19 had significantly higher percentages of CD4+ EM T-cells compared to PLWH with an undetectable VL at admission. (C) PLWH with a detectable VL with COVID-19 had significantly higher percentages of CD8+ EM T-cells compared to PLWH with an undetectable VL. PLWH with a detectable VL admitted with COVID-19 had significantly lower percentages of CD8+ EM T-cells compared to PLWH with undetectable VL controls. (D) PLWH with a detectable VL with COVID-19 had significantly higher percentages of CD8+ PD-1+ T-cells than PLWH with an undetectable VL at admission. (E) PLWH with a detectable VL with COVID-19 had significantly lower percentages of CD8+ EM4 CD57+ T-cells compared to PLWH with an undetectable VL at admission. Abbreviations: central memory (CM), double negative (DN), effector memory (EM), not significant (ns), programmed cell death protein 1 (PD-1), pre-effector (pE), terminally differentiated effector memory T-cells re-expressing CD45RA (TEMRA), and viral load (VL). The Kruskal–Wallis test with post hoc Dunn’s test was used to compare continuous variables between groups. p-value: *: <0.05, **: <0.01, ***: <0.001.

Figure 3

Comparison of cytokine concentrations in PLWH hospitalized with COVID-19 with detectable and undetectable HIV VLs and their respective controls. (A) IL-2 concentrations were significantly higher in PLWH with an undetectable VL than in both PLWH with a detectable VL at admission and PLWH with undetectable VL controls. (B) IL-4 concentrations were significantly higher in PLWH with an undetectable VL than in both PLWH with a detectable VL at admission and PLWH with undetectable VL controls. (C) IL-6 concentrations were higher in both patient groups compared to their respective controls. (D) IFN-γ concentrations were significantly higher in PLWH with an undetectable VL than in both PLWH with a detectable VL at admission and PLWH with undetectable VL controls. (E–H) Concentrations of IL-20, IL-22, IL-35, and IL-12p40 were significantly higher in PLWH admitted with COVID-19 with an undetectable VL than in PLWH with a detectable VL. No significant differences were found between the patient groups and the respective control groups. Abbreviations: interleukin (IL), interferon (IFN), not significant (ns). The Kruskal–Wallis test with post hoc Dunn’s test was used to compare continuous variables between groups. Results are presented as median and interquartile range (IQR). p-value: *: <0.05, **: <0.01.

Figure 4

T-cell phenotypes of PLWH hospitalized with COVID-19 with CD4+ T-cell counts < or ≥200 cells/mm³. (A) PLWH with a CD4+ T-cell count < 200 cells/mm³ had significantly lower percentages of CD4+ T-cells than PLWH with a CD4+ T-cell count ≥ 200 cells/mm³. (B) PLWH with a CD4+ T-cell count < 200 cells/mm³ had significantly lower percentages of CD4+ N T-cells than PLWH with a CD4+ T-cell count ≥ 200 cells/mm³. PLWH with a CD4+ T-cell count ≥ 200 cells/mm³ also had a significantly higher percentage of CD4+ N T-cells than PLWH controls with a CD4+ T-cell count ≥ 200 cells/mm³. (C) PLWH with a CD4+ T-cell count ≥ 200 cells/mm³ had significantly lower percentages of CD4+ EM T-cells than both PLWH with a CD4+ T-cell count < 200 cells/mm³ and the respective PLWH controls without COVID-19. (D) PLWH with a CD4+ T-cell count < 200 cells/mm³ had significantly lower percentages of CD8+ T-cells than PLWH with a CD4+ T-cell count ≥ 200 cells/mm³. (E) PLWH with a CD4+ T-cell count of <200 cells/mm³ with COVID-19 had significantly lower percentages of CD8+ CM T-cells than both PLWH with a CD4+ T-cell count of ≥200 cells/mm³ and control PLWH with a CD4+ T-cell count of <200 cells/mm³. Abbreviations: central memory (CM), effector memory (EM), naïve (N), and not significant (ns). The Kruskal–Wallis test with post hoc Dunn’s test was used to compare continuous variables between groups. p-value: *: <0.05, **: <0.01.

Figure 5

Comparison of CD4+ T-cell phenotypes at Visit 2 between people living with and without HIV hospitalized with COVID-19 and their respective controls. (A) Representative UMAP plots of CD4+ T-cell populations in people living with and without HIV at Visit 2. (B) COVID+ PLWH had significantly higher percentages of CD4+ CM PD-1+ T-cells when compared to COVID+ PLWOH at V2. Both patient groups (COVID+ PLWH and COVID+ PLWOH) had lower percentages of CD4+ CM PD-1+ T-cells when compared to their respective controls not admitted with COVID-19. (C) COVID+ PLWH had significantly lower percentages of CD4+ CM T-cells overall compared to COVID+ PLWOH at Visit 2. No significant difference was found between the patient groups and respective control groups in terms of the percentage of CD4+ CM T-cells. Abbreviations: central memory (CM), control people living without HIV (PLWOH) without COVID-19 (Control PLWOH), control PLWH without COVID-19 (Control PLWH), effector memory (EM), not significant (ns), PLWH hospitalized with COVID-19 (COVID+ PLWH), PLWOH hospitalized with COVID-19 (COVID+ PLWOH), and programmed cell death protein 1 (PD-1). The Kruskal–Wallis test with post hoc Dunn’s test was used to compare continuous variables between groups. p-value: *: <0.05, **: <0.01, ***: <0.001.

Figure 6

Comparison of CD8+ T-cell phenotypes at Visit 2 between people living with and without HIV hospitalized with COVID-19 and their respective controls. (A) Representative UMAP plots of CD8+ T-cell populations of people living with and without HIV at Visit 2. (B) COVID+ PLWH had significantly higher percentages of CD8+ CM PD-1+ T-cells than COVID+ PLWOH. No significant differences were found between patient groups and the respective controls in terms of the percentage of CD8+ CM PD-1+ T-cell population. (C) COVID+ PLWH admitted with COVID-19 had significantly higher percentages of CD8+ EM3 PD-1+ T-cells than COVID+ PLWOH admitted with COVID-19. The same difference was found between control participants; Control PLWH had higher percentages of CD8+ EM3 PD-1+ T-cells than Control PLWOH. (D) COVID+ PLWOH had significantly lower percentages of CD8+ EM4 PD-1+ when compared to both COVID+ PLWH and their respective control group without COVID-19. (E) COVID+ PLWH admitted with COVID-19 had significantly higher percentages of CD8+ EM4 PD-1+ CD57+ T-cells when compared to COVID+ PLWOH. The same difference was found between control participants: Control PLWH had higher percentages of CD8+ EM4 PD-1+ CD57+ T-cells than Control PLWOH. Abbreviations: central memory (CM), control PLWH without COVID-19 (Control PLWH), control people living without HIV without COVID-19 (Control PLWOH), effector memory (EM), not significant (ns), people living without HIV (PLWOH) hospitalized with COVID-19 (COVID+ PLWOH), PLWH hospitalized with COVID-19 (COVID+ PLWH), and programmed cell death protein 1 (PD-1). The Kruskal–Wallis test with post hoc Dunn’s test was used to compare continuous variables between groups. p-value: *: <0.05, **: <0.01, ***: <0.001.