Volume 23, Number 10—October 2017
Dispatch
Diagnosis of Fatal Human Case of St. Louis Encephalitis Virus Infection by Metagenomic Sequencing, California, 2016
, 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
Table 1
Microbiologic testing results for a patient with fatal mosquito-borne St. Louis encephalitis virus infection diagnosed by metagenomic sequencing, California, 2016*
| Test |
Hospitalization day sample collected |
Result |
|---|---|---|
| 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 |
5 |
Negative |
| CSF studies | ||
| HSV 1 and 2 PCR | 3 | Negative |
| Fungal culture | 3 | Negative |
| Bacterial culture | 3 | |
| Coccidioides Ab CF, ID | 8 | Negative |
| CMV PCR | 9 | |
| 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 |
9 |
SLEV |
| 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 |
8 |
Negative |
| 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.