Direct Diagnosis of Echovirus 12 Meningitis Using Metagenomic Next Generation Sequencing

Madjid Morsli,Aurelie Morand,Christine Zandotti,Michel Drancourt,Philippe Colson

doi:10.3390/pathogens10050610

Abstract

The current point-of-care diagnosis of enterovirus meningitis does not identify the viral genotype, which is prognostic. In this case report, more than 81% of an Echovirus 12 genome were detected and identified by metagenomic next-generation sequencing, directly from the cerebrospinal fluid collected in a 6-month-old child with meningeal syndrome and meningitis: introducing Echovirus 12 as an etiological agent of acute meningitis in the pediatric population.

Highlights

The highly diverse viral genus Enterovirus encompasses more than 300 genotypes [1].Some Enterovirus members are responsible for central nervous system (CNS) infections, which clinical and epidemiological characteristics and prognosis, vary according to the precisely identified enterovirus, and some genotypes have been associated with a particular clinical severity and mortality [2]
In order to challenge Enterovirus genotyping at the POC laboratory, we developed a unique protocol to diagnose and genotype Enterovirus CNS infection directly from the cerebrospinal fluid (CSF) using metagenomic Next-Generation Sequencing
BLAST analysis of the contigs generated by metagenomic Next-Generation Sequencing (mNGS) after assembling reads with Spades, yielded as best match the Echovirus

Summary

Introduction

The highly diverse viral genus Enterovirus encompasses more than 300 genotypes [1].Some Enterovirus members are responsible for central nervous system (CNS) infections, which clinical and epidemiological characteristics and prognosis, vary according to the precisely identified enterovirus, and some genotypes have been associated with a particular clinical severity and mortality [2]. In order to challenge Enterovirus genotyping at the POC laboratory, we developed a unique protocol to diagnose and genotype Enterovirus CNS infection directly from the cerebrospinal fluid (CSF) using metagenomic Next-Generation Sequencing (mNGS). The viral RNA was extracted and purified following an in-house developed protocol, using QIAamp Viral RNA Mini Kit (Qiagen) and RNA was purified by magnetic DynaBeads (Thermo Fisher, Waltham, MA, USA).

Results

Conclusion