Gh the lens of the genomic response, it is possible to correctly distinguish individuals as infected or uninfected with influenza well before they have clinically relevant symptoms or would be ill enough to present for clinical evaluation. The potential power of this approach is manifested by full discriminative ability of the genomic signature as early as 53 hours post-viral exposure, at a time when the average clinical score of symptomatic individuals is only 2.4. Symptoms of this nature and severity are clinically vague and would be typical of very mild allergies [22] or even symptoms due to sequelae of chronic smoking [23]. Therefore, genomic analyses demonstrate the potential to identify viral infection either before symptoms emerge or among what otherwise are common, nonspecific upper respiratory symptoms, when early intervention with antiviral medications could have profound impact on both individualsymptoms and disease transmission [24,25,26]. Furthermore, we show that the overall trajectory of the Influenza Factor tracks closely with symptom scores over time, but also that the observed genomic response tends to significantly precede changes in clinical scores in symptomatic individuals. None of our affected individuals developed severe infection, but the characteristics of the timing and development of these signatures suggest that, similar to recent work with Dengue infections [9], genomic signatures may potentially prove invaluable for predicting clinical outcomes. However, further longitudinal studies with patients who eventually exhibit more severe disease will be required to fully assess this potential. The nature of the individual components of the genomic response to influenza infection and the biological pathways they represent lend plausibility to this discovery. In particular, interferon stimulated pathways such as those including RSAD2, IRF7, MX1, OAS3, MDA-5, RIG-I and others are incorporated and thought to drive both innate and, to a lesser degree, adaptive immune responses to viral infection [18,27,28,29]. Many of these pathways are consistent with those identified in acutely ill pediatric influenza subjects [30] and recent studies of the genomic response following vaccination with live, attenuated influenza MedChemExpress EW-7197 vaccine reported a profile of `immune activation’ which shares a number of genes with the Influenza Factor described here [31,32]. Interestingly, a few genes which consistently feature prominently in the Influenza Factor are not clearly tied to inflammatory or immunologic pathways, and their significance remains unclear. Previously published work with bacterial respiratory infections has yielded quite different genomic results [4,5] suggesting that some aspects of the host response are specific at least for major classes of pathogens (e.g., viral vs. bacterial). The genomic pathways identified suggest we are largely measuring FGF-401 web indicators of the development/amplification of the immune response to the virus similar to previous work [13,16,32], and that these indicators parallel (and usually precede) clinical symptom development in time. The immunologic pathways observed in these studies that are known to be commonly activated early on at the primary site of infection (i.e., respiratory epithelium) [29,33], exhibit relatively delayed appearance in the periphery. This delay seems logical, as early innate responses at the site of infection would be expected to have an initially minor impact on global peripheral gene.Gh the lens of the genomic response, it is possible to correctly distinguish individuals as infected or uninfected with influenza well before they have clinically relevant symptoms or would be ill enough to present for clinical evaluation. The potential power of this approach is manifested by full discriminative ability of the genomic signature as early as 53 hours post-viral exposure, at a time when the average clinical score of symptomatic individuals is only 2.4. Symptoms of this nature and severity are clinically vague and would be typical of very mild allergies [22] or even symptoms due to sequelae of chronic smoking [23]. Therefore, genomic analyses demonstrate the potential to identify viral infection either before symptoms emerge or among what otherwise are common, nonspecific upper respiratory symptoms, when early intervention with antiviral medications could have profound impact on both individualsymptoms and disease transmission [24,25,26]. Furthermore, we show that the overall trajectory of the Influenza Factor tracks closely with symptom scores over time, but also that the observed genomic response tends to significantly precede changes in clinical scores in symptomatic individuals. None of our affected individuals developed severe infection, but the characteristics of the timing and development of these signatures suggest that, similar to recent work with Dengue infections [9], genomic signatures may potentially prove invaluable for predicting clinical outcomes. However, further longitudinal studies with patients who eventually exhibit more severe disease will be required to fully assess this potential. The nature of the individual components of the genomic response to influenza infection and the biological pathways they represent lend plausibility to this discovery. In particular, interferon stimulated pathways such as those including RSAD2, IRF7, MX1, OAS3, MDA-5, RIG-I and others are incorporated and thought to drive both innate and, to a lesser degree, adaptive immune responses to viral infection [18,27,28,29]. Many of these pathways are consistent with those identified in acutely ill pediatric influenza subjects [30] and recent studies of the genomic response following vaccination with live, attenuated influenza vaccine reported a profile of `immune activation’ which shares a number of genes with the Influenza Factor described here [31,32]. Interestingly, a few genes which consistently feature prominently in the Influenza Factor are not clearly tied to inflammatory or immunologic pathways, and their significance remains unclear. Previously published work with bacterial respiratory infections has yielded quite different genomic results [4,5] suggesting that some aspects of the host response are specific at least for major classes of pathogens (e.g., viral vs. bacterial). The genomic pathways identified suggest we are largely measuring indicators of the development/amplification of the immune response to the virus similar to previous work [13,16,32], and that these indicators parallel (and usually precede) clinical symptom development in time. The immunologic pathways observed in these studies that are known to be commonly activated early on at the primary site of infection (i.e., respiratory epithelium) [29,33], exhibit relatively delayed appearance in the periphery. This delay seems logical, as early innate responses at the site of infection would be expected to have an initially minor impact on global peripheral gene.
