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Updated: Jun 19, 2026
High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
Published on: March 5, 2022
Identification of Host Gene Transcripts by Machine Learning and Their Application to Predict Outcome in Ebola Virus
Jocelyn G Pérez1,2,3, Natasha Y Rickett3, Stephan Günther4
1School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.
Background:
In humans, Ebola virus disease (EVD) has a high mortality rate. While viral load is a known prognostic factor, it is not effective in predicting outcomes across all patients. Exploring host transcriptomic signatures may provide additional predictive value.
Methods:
Here, the transcript abundance of 4 candidate host genes (VCAM1, TUBG1, MS4A4A, ISG15) was quantified by reverse transcription quantitative polymerase chain reaction (RT-qPCR) in blood samples from hospitalized patients with Ebola virus (EBOV) collected during the 2013-2016 West African outbreak. Samples were taken for diagnostic purposes during the acute phase of infection. Associations between target gene expression, viral load, and outcome (survival/death) were assessed, and machine learning models were trained and tested to predict patient outcome.
Results:
EBOV cycle threshold (Ct) values were significantly higher in hospitalized survivors compared to fatalities. During the acute phase, the transcript abundance of VCAM1 and MS4A4A was higher in fatal cases, while TUBG1 expression was elevated in survivors; ISG15 expression did not differ by outcome. In support vector machine models, EBOV Ct alone classified patient outcomes with 86.9% accuracy, while MS4A4A alone reached 82.6%. Combining EBOV Ct with MS4A4A improved prediction to 91.3%. The best-performing model, integrating EBOV Ct, ISG15, and MS4A4A, achieved 100% accuracy in the test set.
Discussion:
Host gene expression markers, particularly MS4A4A, in combination with viral load, improved outcome prediction in EVD beyond viral load alone in ambiguous cases with mid-range Ct values. These findings highlight the utility of host transcript-based assays to inform clinical management and for benchmarking the effectiveness of medical countermeasures during outbreaks.
