Deep sequencing to identify the causes of viral encephalitis.
Deep sequencing allows for a rapid, accurate characterization of microbial DNA and RNA sequences in many types of samples. Deep sequencing (also called next generation sequencing or NGS) is being developed to assist with the diagnosis of a wide variety of infectious diseases. In this study, seven frozen brain samples from deceased subjects with recent encephalitis were investigated. RNA from each sample was extracted, randomly reverse transcribed and sequenced. The sequence analysis was performed in a blinded fashion and confirmed with pathogen-specific PCR. This analysis successfully identified measles virus sequences in two brain samples and herpes simplex virus type-1 sequences in three brain samples. No pathogen was identified in the other two brain specimens. These results were concordant with pathogen-specific PCR and partially concordant with prior neuropathological examinations, demonstrating that deep sequencing can accurately identify viral infections in frozen brain tissue.
Division of Infectious Diseases, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States of America.
Benjamin K
BK
Chan
Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America.
Theodore
T
Wilson
Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America.
Kael F
KF
Fischer
Division of Infectious Diseases, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States of America.
John D
JD
Kriesel
D001921:Brain / Q000821:virology*; D018792:Encephalitis, Viral / Q000175:diagnosis / Q000821:virology*; D006561:Herpes Simplex / Q000175:diagnosis / Q000821:virology; D018259:Herpesvirus 1, Human / Q000235:genetics / Q000302:isolation & purification*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008457:Measles / Q000175:diagnosis / Q000821:virology; D008459:Measles virus / Q000235:genetics / Q000302:isolation & purification*; D012367:RNA, Viral / Q000235:genetics / Q000302:isolation & purification*
D012367:RNA, Viral