Effects of tuberculosis and/or HIV-1 infection on COVID-19 presentation and immune response in Africa

Abstract

Few studies from Africa have described the clinical impact of co-infections on SARS-CoV-2 infection. Here, we investigate the presentation and outcome of SARS-CoV-2 infection in an African setting of high HIV-1 and tuberculosis prevalence by an observational case cohort of SARS-CoV-2 patients. A comparator group of non SARS-CoV-2 participants is included. The study includes 104 adults with SARS-CoV-2 infection of whom 29.8% are HIV-1 co-infected. Two or more co-morbidities are present in 57.7% of participants, including HIV-1 (30%) and active tuberculosis (14%). Amongst patients dually infected by tuberculosis and SARS-CoV-2, clinical features can be typical of either SARS-CoV-2 or tuberculosis: lymphopenia is exacerbated, and some markers of inflammation (D-dimer and ferritin) are further elevated (p < 0.05). Amongst HIV-1 co-infected participants those with low CD4 percentage strata exhibit reduced total, but not neutralising, anti-SARS-CoV-2 antibodies. SARS-CoV-2 specific CD8 T cell responses are present in 35.8% participants overall but undetectable in combined HIV-1 and tuberculosis. Death occurred in 30/104 (29%) of all COVID-19 patients and in 6/15 (40%) of patients with coincident SARS-CoV-2 and tuberculosis. This shows that in a high incidence setting, tuberculosis is a common co-morbidity in patients admitted to hospital with COVID-19. The immune response to SARS-CoV-2 is adversely affected by co-existent HIV-1 and tuberculosis.

Fig. 1. Radiographic appearances of combined SARS-CoV-2 and M. tuberculosis infection and relationship between radiographic (Brixia and British Society for Thoracic Imaging (BSTI)) score and clinical severity assessed by WHO COVID-19 ordinal scale.

A, B Chest radiographs and computed tomographic pulmonary angiography (CTPA) of two COVID-19 patients. A1: 43-year-old HIV-1 uninfected male (patient number 58) presenting with consolidation and cavitation in the right upper lobe (red arrow), 3+ sputum smear positive and also SARS-CoV-2 RT-PCR positive (threshold cycle: 32.45). A2: Because of persistent hypoxia and tachypnoea he underwent CTPA which showed bi-basal wedge-shaped opacities in keeping with pulmonary embolism (PE) and/or consolidation related to COVID-19. Discharged after 22 days. B1: 43-year-old HIV-1 uninfected female (patient number 36) presenting with SARS-CoV-2 positive RT-PCR (threshold cycle: 21.2) with diffuse bilateral pulmonary opacification with ground glass and consolidation on the chest radiograph who deteriorated necessitating intubation and ventilation for 36 days. The patient remained O2 dependent after extubation and a CTPA (B2) for suspected PE instead revealed cavitation associated with opacification and air bronchograms in the superior segment of the right lower lobe (arrow) together with subcarinal and pretracheal lymphadenopathy. The patient was found Gene Xpert MTB/Rif positive. C BSTI classification of RT-PCR proven SARS-CoV-2 cases in the absence or presence of HIV-1 and/or tuberculosis. The increase in the proportion of radiographs classified as Non-COVID like tended to increase in those with coincident tuberculosis. Comparisons were performed by Chi-square test. D Brixia radiographic and, E BSTI, severity scores in relation to WHO clinical severity scale in N = 104 SARS-CoV-2 participants. Comparisons were performed using a Kruskal-Wallis test. F Brixia score in relation to the presence or absence of HIV-1 and/or tuberculosis co-infection in N = 104 SARS-CoV-2 participants. The extent of changes related COVID-19 was decreased amongst those with coincident HIV-1 associated tuberculosis. Comparisons were performed using a Kruskal-Wallis test with Dunn’s correction. G WHO ordinal scale at presentation in N = 104 SARS-CoV-2 participants in relation to the presence or absence of HIV-1 and/or tuberculosis co-infection. Comparisons were performed using a Kruskal-Wallis test with Dunn’s correction.

Fig. 2. Total white cell and differential count in healthy persons (HC), non-COVID-19 hospitalized participants (NC), and COVID-19 participants.

A The total white cell count was raised in both COVID-19 and NC patients with no differences between the groups. The count increased with increasing COVID-19 severity. Amongst COVID-19 patients the total white cell count was highest in HIV-1 uninfected patients with coincident tuberculosis. B The lymphocyte count was lower in both COVID-19 and NC patients with no differences between these groups. The count tended to decrease with increasing COVID-19 severity. Amongst COVID-19 patients the lymphocyte count was lowest in triply infected patients with HIV-1 and coincident tuberculosis. C The neutrophil count was raised in both NC and COVID-19 patients with no differences between the groups. The count increased with increasing COVID-19 severity. Amongst COVID-19 patients there were no differences in count in the presence of HIV-1 and/or tuberculosis. D The monocyte count was raised in both NC and COVID-19 patients with no differences between these groups. No trend in relation to COVID-19 severity was observed. Amongst COVID-19 patients, those with coincident tuberculosis had higher counts than those with combined HIV-1 and COVID-19 infections without tuberculosis. E Eosinophil counts were lower in both COVID-19 and NC patients being lowest in those with COVID-19 infection with a trend in this decrease observed in relation to disease severity. Amongst COVID-19 patients, no significant effect of HIV-1 and/or tuberculosis infection was observed. Line indicates the median value and shaded area the normal range. All comparisons were performed using a Kruskal-Wallis test with Dunn’s correction.

Fig. 3. Serum biomarkers in relation to disease status and severity, and correlation between those markers and peripheral cell counts.

A–C C-Reactive protein (CRP), D-dimer and ferritin levels showed similar trends being significantly higher in COVID-19 patients than NC. There was no significant trend in relation to severity of COVID-19 disease. HIV-1 infected patients with both COVID-19 and tuberculosis had higher levels of all three markers than those with COVID-19 alone. Comparisons between the NC and COVID-19 groups were performed using a Mann Whitney test and other comparisons were performed using a Kruskal-Wallis test. D Lactate dehydrogenase was significantly higher in COVID-19 patients than NC, with levels tending to increase with increasing COVID-19 disease severity. There was however no relationship with HIV-1 and/or tuberculosis status. Comparisons between the NC and COVID-19 groups were performed using a Mann Whitney test and other comparisons were performed using a Kruskal-Wallis test (two sided). E, F Correlation matrix of serum biomarkers in COVID-19 patients (E) and NC participants (F). Amongst COVID-19 patients there was strong positive correlation between total white cell (WCC) and neutrophil counts, and moderate between ferritin and LDH, and between lymphocyte and monocyte counts. In NC participants, the relationship between total white cell (WCC) and neutrophil counts, and between ferritin and LDH was also observed. Positive correlations are indicated in blue and negative correlation in red. Spearman R-values are indicated in each square. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. Line indicates the median value and shaded area the normal range.

Fig. 4. Serum anti-nucleocapsid IgG levels in n = 104 COVID-19 patients in relation to the presence of HIV-1 and/or tuberculosis co-infection.

A Although no significant quantitative difference in cut-off index was observed by HIV-1 and or tuberculosis status, 8/15 tuberculosis patients in total and 5/8 with HIV-1 and tuberculosis were below threshold for positivity of 1.0. The >1 cut-off value represents the manufacturer’s cut-off. The >0.165 cut-off value represents the optimal cut-off value defined by ROC curve analyses on 197 participants that improved the performance of the test to give a sensitivity of 100% (95%CI: 94.0-100%). B There was a significant trend towards decreased antibody levels in participants with Lower percentage CD4 lymphocytes. Comparisons were performed using a Kruskal-Wallis test. C No significant difference in ability to neutralize SARS-CoV-2 pseudovirus between groups was observed although a minority not prescribed antiretroviral therapy (darker shading) tended to have lower ID₅₀ values. D In subset of n = 24 HIV-1 co-infected patients for whom the absolute CD4 count was available, there was no trend between neutralising antibody level and CD4 (p = 0.34) and patients with tuberculosis (pink) did not form a distinct subgroup. Correlation was tested by a two-tailed non-parametric Spearman rank test.

Fig. 5. SARS-CoV-2 antigen-specific CD8 T cell response in COVID-19 patients.

A Proportion of COVID-19 patients (n = 95) exhibiting a detectable SARS-CoV-2 CD8 T cell response. B Comparison of the magnitude of SARS-CoV-2-specific CD4 and CD8 T cells in COVID-19 patients exhibiting a SARS-COV-2 CD4 T cells response in in absence of CD8 responses (n = 45, light blue) and in patients exhibiting both a CD4 and CD8 SARS-CoV-2 response to SARS-CoV-2 (n = 34, dark blue). C Prevalence and frequencies of SARS-CoV-2-specific CD8 T cells in 95 COVID-19 patients stratified by HIV and/or tuberculosis co-infection. D Polyfunctional profile of SARS-CoV-2-specific CD8 T cells in 34 COVID-19 patients, stratified by WHO score and outcome. Line indicates the median value and shaded area the normal range. A two-sided Wilcoxon rank test was used to compare response patterns between groups. E Comparison of the memory differentiation profile (left) and activation profile (right) between SARS-CoV-2-specific CD4 T cells and SARS-CoV-2-specific CD8 T cells. N = 95 patients, statistical comparisons were calculated using a two-sided Mann-Whitney test.