Rapid, Sample-to-Answer Host Gene Expression Test to Diagnose Viral Infection

Tsalik, Ephraim LKhine, AyeayeTalebpour, AbdossamadSamiei, AlalehParmar, VilcyBurke, Thomas WMcclain, Micah TGinsburg, Geoffrey SWoods, Christopher WHenao, RicardoAlavie, Tino2020-11-012020-11-012019-11-012328-89572328-8957https://hdl.handle.net/10161/21654Abstract Background Distinguishing bacterial, viral, or other etiologies of acute illness is diagnostically challenging with significant implications for appropriate antimicrobial use. Host gene-expression offers a promising approach although no clinically useful tests have yet been developed to accomplish this. Here, Qvella’s FAST™ HR process was developed to quantify previously identified host gene-expression signatures in whole blood in <45 minutes. Methods Whole blood was collected from 128 human subjects (mean age 47, range 18-88) with clinically adjudicated, microbiologically confirmed viral infection, bacterial infection, non-infectious illness, or healthy controls. Stabilized mRNA was released from cleaned and stabilized RNA-surfactant complexes using e-lysisTM, an electrical process providing a qRT-PCR-ready sample. Threshold cycle values (CT) for 10 host response targets were normalized to HPRT1 expression, a control mRNA. The transcripts in the signature were specifically chosen to discriminate viral from non-viral infection (bacterial, non-infectious illness, or healthy). Classification accuracy was determined using cross-validated sparse logistic regression. Results Reproducibility of mRNA quantification was within 1 cycle as compared to the difference seen between subjects with viral vs. non-viral infection (up to 5.0 normalized CT difference). Classification of 128 subjects into viral or non-viral etiologies demonstrated 90.6% overall accuracy compared to 82.0% for procalcitonin (p=0.06). FASTTM HR achieved rapid and accurate measurement of the host response to viral infection in less than 45 minutes. Conclusions These results demonstrate the ability to translate host gene expression signatures to clinical platforms for use in patients with suspected infection. Science & TechnologyLife Sciences & BiomedicineImmunologyInfectious DiseasesMicrobiologygene expression profilinginfectionmolecular diagnostic techniquesreal-time polymerase chain reactionvirus diseasesCOMMUNITY-ACQUIRED PNEUMONIARNA SIGNATUREBACTERIALCARERapid, Sample-to-Answer Host Gene Expression Test to Diagnose Viral InfectionJournal article2020-11-01