Diagnosis of Acute Respiratory Viral Infections By Targeted RNA Sequencing Provides Additional Critical Genetic Virulence and Epidemiological Information
Monday, March 7, 2016
South Exhibit Hall H (Convention Center)
Josh L. Kennedy, MD, Walter Dehority, MD, Kimberly Paffett, Gary Schroth, Stephen Gross, Stephen Young, Darrell Dinwiddie
Rationale: Despite the enormous medical burden caused by respiratory viruses in asthma subjects, the specific genetic variations that influence transmission, virulence, and pathogenesis are poorly understood for most viruses.  We aimed to develop a clinical test that would detect infections and identify viral genetic variations that might influence these critical processes.

Methods: We developed the UNM ResVir Panel, a hybridization-based method to target and enrich complete coding sequences from 12 respiratory viral families, representing more than 34 virus subtypes, and more than 100 virus strains.   We have now evaluated 123 viral nasopharyngeal swabs obtained for clinical purposes.The samples are sequenced in a high-throughput, multiplexed, rapid manner on the Illumina MiSeq. This information is used to determine specific viruses, construct nearly complete genome sequences, assess viral gene expression, detect genetic variation, and conduct phylogenetic analysis.   

Results: We have identified more than 150 viral infections from clinical nasopharyngeal swabs representing 8 of 12 viral families targeted, including 27 co-infections and multiple viruses missed by current clinical testing.. Concordance of viruses detected with clinical PCR testing is >90%, and importantly this targeted RNA sequencing approach can be successfully conducted on very low quantities (<5 ng) of poor quality RNA (RIN <1.0) in a rapid (<72 hours) and low cost manner..

Conclusions: Evaluation of viral pathogens by targeted RNA sequencing provides important information about clinical viral isolates currently not detected by clinical testing that may impact clinical severity of illness and inform clinical management.