Skip directly to search Skip directly to A to Z list Skip directly to page options Skip directly to site content

Volume 23, Number 10—October 2017


Diagnosis of Fatal Human Case of St. Louis Encephalitis Virus Infection by Metagenomic Sequencing, California, 2016

Charles Y. ChiuComments to Author , Lark L. Coffey, Jamie Murkey, Kelly Symmes, Hannah A. Sample, Michael R. Wilson, Samia N. Naccache, Shaun Arevalo, Sneha Somasekar, Scot Federman, Doug Stryke, Paul Vespa, Gary Schiller, Sharon Messenger, Romney Humphries, Steve Miller, and Jeffrey D. Klausner
Author affiliations: University of California, San Francisco, California, USA (C.Y. Chiu, H.A. Sample, M.R. Wilson, S. Arevalo, S. Somasekar, S. Miller); University of California, San Francisco–Abbott Viral Diagnostics and Discovery Center, San Francisco (C.Y. Chiu, S. Arevalo, S. Somasekar, S. Miller); University of California, Davis, California, USA (L.L. Coffey, K. Symmes); University of California, Los Angeles, California, USA (J. Murkey, S. Federman, D. Stryke, P. Vespa, G. Schiller, R. Humphries, J.D. Klausner); University of Southern California, Los Angeles (S.N. Naccache); California Department of Public Health, Richmond, California, USA (S. Messenger)

Main Article

Table 1

Microbiologic testing results for a patient with fatal mosquito-borne St. Louis encephalitis virus infection diagnosed by metagenomic sequencing, California, 2016*

Hospitalization day sample collected
Serum studies
Bacterial cultures 0, 2, 4, 7 Negative
Fungal cultures 0, 2, 4, 7 Negative
Mycobacterial culture 10 Negative
Aspergillus antigen EIA 5 Negative
Adenovirus PCR 19 Negative
CMV DNA quantitative PCR 4, 12 Negative
EBV DNA quantitative PCR 10 Negative
Enterovirus RNA 19 Negative
HSV-1 and HSV-2 PCR 12 Negative
HHV-6 PCR 19 Negative
HIV RNA quantitative PCR 5 Negative
HBV DNA quantitative PCR 9 Negative
Leptospira DNA 14 Negative
Parvovirus B19 DNA 19 Negative
VZV DNA, qualitative PCR 19 Negative
Cryptococcal antigen
CSF studies
HSV 1 and 2 PCR 3 Negative
Fungal culture 3 Negative
Bacterial culture 3
Coccidioides Ab CF, ID 8 Negative
EBV PCR 3, 9 Negative
HHV-6 PCR 3 Negative
JC polyomavirus DNA, PCR 9 Negative
Mycobacterial culture 9 Negative
Mycobacterium tuberculosis DNA PCR 10 Negative
Meningoencephalitis antibody panel† 10 Negative
VDRL 9 Negative
VZV Ab IgG 9 Negative
West Nile virus RNA 9 Negative
mNGS for pathogen detection
Respiratory secretion testing‡
Bacterial culture 4, 5, 8 Candida albicans
Fungal culture 5, 8 C. albicans
Respiratory virus panel§ 4 (NP swab), 5 Negative
Mycoplasma pneumoniae PCR 5
HSV-1 and HSV-2 PCR 5 Negative
CMV PCR 5 Negative
Pneumocystis DFA 5 Negative
Mycobacterial culture 5 Negative
Legionella culture and urinary Ag 5 Negative
Nocardia culture
Serologic testing
Coccidioides IgG/IgM 4, 9 Negative
Coccidioides complement fixation 8 Negative
HCV Ab 9 Negative
HBV, core Ab and hepatitis B e Ab 9 Negative
Mycobacterium tuberculosis quantiferon gold 8 Negative
Q fever antibody 8 Negative
Rapid plasma reagin 10 Negative

*Ab, antibody; Ag, antigen; BAL, bronchoalveolar lavage; CF, complement fixation; CMV, cytomegalovirus; DFA, direct fluorescent antigen; DNA, deoxyribonucleic acid; EBV, Epstein-Barr virus; EIA, enzyme immunoassay; HBV, hepatitis B virus; HCV, hepatitis C virus; HHV-6, human herpesvirus 6; HIV, human immunodeficiency virus; HSV, herpes simplex virus; ID, immunodiffusion; IFA, indirect fluroescent antibody; mNGS, metagenomic next-generation sequencing; NP, nasopharyngeal; RNA, ribonucleic acid; SLEV, St. Louis encephalitis virus; VRDL, Venereal Disease Research Laboratory; VZV, varicella zoster virus.
†Includes IgM and IgG testing for West Nile virus; California encephalitis virus; Eastern equine encephalitis virus; St. Louis encephalitis virus; Western equine encephalitis virus; lymphocytic choriomeningitis virus; herpes simplex virus types 1 and 2 (HSV-1 and 2); adenovirus; influenza A; influenza B; measles (IFA); mumps (IFA); varicella-zoster Ab CF; coxsackie A types 2, 4, 7, 9, 10, and 16; coxsackie B types 1, 2, 3, 4, 5, and 6; echovirus types 4, 7, 9, 11, and 30; and CMV.
‡Testing performed on bronchoalveolar lavage unless noted otherwise.
§Detects the following viruses: influenza A; influenza A H1 seasonal; influenza A H3 seasonal; influenza A 2009 H1N1; influenza B; respiratory syncytial virus A and B; parainfluenza viruses 1–4; human metapneumovirus; human rhinovirus; adenovirus serogroups C and B/E; coronaviruses NL63, HKU1, 229E, and OC43.

Main Article