IFI27 transcription is an early predictor for COVID-19 outcomes, a multi-cohort observational study

Abstract

Purpose: Robust biomarkers that predict disease outcomes amongst COVID-19 patients are necessary for both patient triage and resource prioritisation. Numerous candidate biomarkers have been proposed for COVID-19. However, at present, there is no consensus on the best diagnostic approach to predict outcomes in infected patients. Moreover, it is not clear whether such tools would apply to other potentially pandemic pathogens and therefore of use as stockpile for future pandemic preparedness.

Methods: We conducted a multi-cohort observational study to investigate the biology and the prognostic role of interferon alpha-inducible protein 27 (IFI27) in COVID-19 patients.

Results: We show that IFI27 is expressed in the respiratory tract of COVID-19 patients and elevated IFI27 expression in the lower respiratory tract is associated with the presence of a high viral load. We further demonstrate that the systemic host response, as measured by blood IFI27 expression, is associated with COVID-19 infection. For clinical outcome prediction (e.g., respiratory failure), IFI27 expression displays a high sensitivity (0.95) and specificity (0.83), outperforming other known predictors of COVID-19 outcomes. Furthermore, IFI27 is upregulated in the blood of infected patients in response to other respiratory viruses. For example, in the pandemic H1N1/09 influenza virus infection, IFI27-like genes were highly upregulated in the blood samples of severely infected patients.

Conclusion: These data suggest that prognostic biomarkers targeting the family of IFI27 genes could potentially supplement conventional diagnostic tools in future virus pandemics, independent of whether such pandemics are caused by a coronavirus, an influenza virus or another as yet-to-be discovered respiratory virus.

Keywords: COVID-19; IFI27; SARS-CoV-2; biomarkers; early predictor.

Figure 1

Lower airway IFI27 gene expression in COVID-19 patients A In Cohort 1, spatial expression heatmap of normalised COVID-19 RNAscope signal was determined using STRISH analysis. The heatmap colour shows average RNAscope signal per cell per rectangle area that contains a similar number of cells (fewer than 100 cells per rectangle). Red boxes indicate areas of overexposure in the original RNAscope microscopy, which were excluded from the analysis. B Quality metrics of four multiplexed Visium samples, indicating the number of genes and reads per spot with summary statistics. C Normalised expression of IFI27 across four samples measured in the same Visium experimental slide (poly-A protocol) (blue as low and yellow- red as high). D Binned values of normalised expression of IFI27 across Visium samples. E Upset plot describing the overlapping gene sets across 5 studies. The size of the gene set varies across the studies with a small number of common genes including IFI27 shared across all studies (18-20).

Figure 2

Upper respiratory tract IFI27 gene expression in COVID-19. (A) IFI27 expression in primary human nasal epithelial cells at 72 hours post-SARS-CoV-2 (QLD/02) or Mock infection. (B) IFI27 gene expression in nasopharyngeal samples in Cohort 2 (n=137). SARS-CoV-2 virus load (as measured by Ct values) is used as a proxy of local disease activity. A statistically non-significant p-value of the linear regression model (represented by R²) indicates that there is no association between IFI27 expression and viral RNA in the upper respiratory tract. (C) IFI27 gene expression in nasopharyngeal samples in Cohort 3 (n=60). ‘Mild’ disease is defined as the presence of COVID-19 disease in a patient who does not require hospitalization. ‘Moderate’ disease is defined as the presence of COVID-19 disease in a patient who requires hospitalization. ‘Severe’ disease is defined as the presence of COVID-19 disease in a patient who requires mechanical ventilation in an intensive care unit. p value is calculated using Mann-Whitney U test. **p < 0.01; ns, not significant. Data shows mean ± SEM. IFI27 gene expression is measured by qPCR normalized to house-keeping genes.

Figure 3

Blood IFI27 gene expression in COVID-19 patients (prospective cohorts). (A) Blood IFI27 expression in Cohort 7 (n=44), between those patients with a positive SARS-CoV-2 PCR (labelled as ‘positive’) (n=29) and those without (labelled as ‘negative’) (n=15). (B) Blood IFI27 gene expression in Cohort 7 grouped by patients who developed complications (labelled as “adverse outcomes”) (n=20) versus those who did not developed complications (labelled as “no adverse outcomes”) (n=24). (C) Blood IFI27 expression levels grouped by how the patients were managed after infection was diagnosed. A total of 37 patients had adequate follow-up data, including those being managed at home (n=13), admitted to hospital ward (n=20) or admitted to intensive care unit (n=4)”. (D) Area-under-the-curve of Receiver-Operator-Characteristics curve (AUROC) analysis of blood IFI27 gene expression levels in predicting composite outcome in Cohort 7 (n=44) IFI27 gene-expression level (‘IFI27’), total number of symptoms (‘Symptoms’), C-reactive protein (‘CRP’) and lymphocyte count (‘Lymphocytes’). (E) IFI27 expression in Cohort 8, in patients without SARS-CoV-2 (Control) and then those with mild, moderate, and severe disease (as defined in Table 1 ). Data shows mean ± SEM and statistical significance was determined as described in the Methods. *p < 0.05; **p < 0.01; ns, not significant.

Figure 4

(A) IFI27 like genes have prognostic value in influenza virus infection a IFI27 expression in the blood of 107 influenza patients.(B, C) the IFI27 gene family; interferon alpha-inducible protein 27-like protein 1 (IFI27L1) were best suited to discriminating disease outcome in compared to interferon alpha-inducible protein 27-like protein 2 (IFI27L2). ‘Moderate’ disease is defined as the presence of influenza in a patient who requires hospitalization. ‘Severe’ disease is defined as the presence of influenza in a patient who requires mechanical ventilation in an intensive care unit. p value is calculated using Mann-Whitney U test. **p <0.01; ****p<0.0001; ns = not significant. Data shows mean ± SEM.