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

• Published in: Open forum infectious diseases Vol. 6; no. 11; p. ofz466
• Main Authors: Tsalik, Ephraim L, Khine, Ayeaye, Talebpour, Abdossamad, Samiei, Alaleh, Parmar, Vilcy, Burke, Thomas W, Mcclain, Micah T, Ginsburg, Geoffrey S, Woods, Christopher W, Henao, Ricardo, Alavie, Tino
• Format: Journal Article
• Language: English
• Published: United States Oxford University Press 01.11.2019
• Subjects: Editor's Choice; Major; molecular diagnostic techniques; virus diseases; infection; gene expression profiling; real-time polymerase chain reaction
• ISSN: 2328-8957; 2328-8957
• DOI: 10.1093/ofid/ofz466

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 test has been developed yet to accomplish this. Here, Qvella's FAST HR (Richmond Hill, Ontario, Canada) process was developed to quantify previously identified host gene expression signatures in whole blood in <45 minutes. Whole blood was collected from 128 human subjects (mean age 47, range 18-88) with clinically adjudicated, microbiologically confirmed viral infection, bacterial infection, noninfectious illness, or healthy controls. Stabilized mRNA was released from cleaned and stabilized RNA-surfactant complexes using e-lysis, an electrical process providing a quantitative real-time reverse transcription polymerase chain reaction-ready sample. Threshold cycle values (C ) for 10 host response targets were normalized to hypoxanthine phosphoribosyltransferase 1 expression, a control mRNA. The transcripts in the signature were specifically chosen to discriminate viral from nonviral infection (bacterial, noninfectious illness, or healthy). Classification accuracy was determined using cross-validated sparse logistic regression. Reproducibility of mRNA quantification was within 1 cycle as compared to the difference seen between subjects with viral versus nonviral infection (up to 5.0 normalized C difference). Classification of 128 subjects into viral or nonviral etiologies demonstrated 90.6% overall accuracy compared to 82.0% for procalcitonin ( = .06). FAST HR achieved rapid and accurate measurement of the host response to viral infection in less than 45 minutes. These results demonstrate the ability to translate host gene expression signatures to clinical platforms for use in patients with suspected infection. NCT00258869.