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

Charles Y Chiu, 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, Jeffrey D Klausner, Charles Y Chiu, 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, Jeffrey D Klausner

Abstract

We used unbiased metagenomic next-generation sequencing to diagnose a fatal case of meningoencephalitis caused by St. Louis encephalitis virus in a patient from California in September 2016. This case is associated with the recent 2015-2016 reemergence of this virus in the southwestern United States.

Keywords: California; SLEV; St. Louis encephalitis virus; United States; West Nile virus; Zika virus; arboviruses; flavivirus infections; mNGS; meningitis/encephalitis; metagenomic next-generation sequencing; mosquitoborne infections; outbreak surveillance; vector-borne infections; viruses; whole-genome viral sequencing.

Figures

Figure
Figure
Phylogeny and spread of St. Louis encephalitis virus. A) Multiple sequence alignment of 32 complete SLEV genomes from GenBank and the 2 SLEV genomes corresponding to the case-patient’s strain and a strain from a mosquito collected in June 2016 from Kern County, California (red circles and text). Alignment was performed using MAFFT (10), followed by tree generation using a neighbor-joining algorithm using Geneious (11). The cluster containing the 2014–2016 California and Arizona SLEV genome, including those from the case-patient and 2016 mosquito pool, is rooted by SLEV strains sequenced from mosquitoes collected in Argentina in 1978 and 2005 (black circles). Isolates are named by location, year of collection, strain name, and GenBank accession number. Bootstrap support values are given for each node. Scale bar indicates nucleotide substitutions per site. B) Geographic spread of SLEV in the Americas, from Argentina in 2005 to California and Arizona during 2014–2016. Because genome sequences from US states reporting SLEV activity are not publicly available and surveillance for SLEV in South and Central America is not routinely performed, the pathway or pathways by which the virus came to the southwestern United States remain unclear (question mark). SLEV, St. Louis encephalitis virus.

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