A host transcriptional signature for presymptomatic detection of infection in humans exposed to influenza H1N1 or H3N2

Abstract

There is great potential for host-based gene expression analysis to impact the early diagnosis of infectious diseases. In particular, the influenza pandemic of 2009 highlighted the challenges and limitations of traditional pathogen-based testing for suspected upper respiratory viral infection. We inoculated human volunteers with either influenza A (A/Brisbane/59/2007 (H1N1) or A/Wisconsin/67/2005 (H3N2)), and assayed the peripheral blood transcriptome every 8 hours for 7 days. Of 41 inoculated volunteers, 18 (44%) developed symptomatic infection. Using unbiased sparse latent factor regression analysis, we generated a gene signature (or factor) for symptomatic influenza capable of detecting 94% of infected cases. This gene signature is detectable as early as 29 hours post-exposure and achieves maximal accuracy on average 43 hours (p = 0.003, H1N1) and 38 hours (p-value = 0.005, H3N2) before peak clinical symptoms. In order to test the relevance of these findings in naturally acquired disease, a composite influenza A signature built from these challenge studies was applied to Emergency Department patients where it discriminates between swine-origin influenza A/H1N1 (2009) infected and non-infected individuals with 92% accuracy. The host genomic response to Influenza infection is robust and may provide the means for detection before typical clinical symptoms are apparent.

Figure 1. Clinical response to viral challenge.

Average symptom scores over time of individuals with both clinical and microbiologically confirmed infection (symptomatic-infected) following experimental viral inoculation with H1N1 (blue) and H3N2 (red).

Figure 2. Gene expression signatures expressed through factor scores.

An influenza gene expression signature, or factor, evolves over time in symptomatic individuals (blue dots) and distinguishes between symptomatic and asymptomatic individuals (red dots) for both H1N1 (A) and H3N2 (B) viruses at later time points. Heat maps of the top 50 genes in the discriminative factor for H1N1 (c) and H3N2 (d) as they develop over time are shown.

Figure 3. Gene expression signature trajectory over time.

The magnitude of the Influenza Factor varies from inoculation through resolution of disease, for both H1N1 (A) and H3N2 (B) patients. The average factor score at each timepoint for both symptomatic (blue) and asymptomatic (red) individuals are shown. The average time of symptom onset (gray dashed line) and maximal symptoms (black dashed line) are depicted.

Figure 4. Validation of the Influenza Factor in a real-world cohort of individuals presenting with confirmed swine-origin 2009 A/H1N1 infection.

The Influenza Factor scores distinguish individuals with RT-PCR proven H1N1 infection (•) from healthy individuals (○) as demonstrated both by factor score and by ROC curve for healthy vs. H1N1 (insert, AUC 0.98).