Genomic and serologic characterization of enterovirus A71 brainstem encephalitis. Issue 3 (May 2020)

• Record Type: Journal Article
• Authors: Leon, Kristoffer E.; Schubert, Ryan D.; Casas-Alba, Didac; Hawes, Isobel A.; Ramachandran, Prashanth S.; Ramesh, Akshaya; Pak, John E.; Wu, Wesley; Cheung, Carly K.; Crawford, Emily D.; Khan, Lillian M.; Launes, Cristian; Sample, Hannah A.; Zorn, Kelsey C.; Cabrerizo, Maria; Valero-Rello, Ana; Langelier, Charles; Muñoz-Almagro, Carmen; DeRisi, Joseph L.; Wilson, Michael R.
• Is Part Of: Neurology. Volume 7:Issue 3(2020)
• Publication Date: 2020-05
• Subjects: Neuroimmunology -- Periodicals; Neurology -- Periodicals; 616.8
• DOI: 10.1212/NXI.0000000000000703
• Languages: English
• ISSNs: 2332-7812

Abstract

Abstract : Objective: In 2016, Catalonia experienced a pediatric brainstem encephalitis outbreak caused by enterovirus A71 (EV-A71). Conventional testing identified EV in the periphery but rarely in CSF. Metagenomic next-generation sequencing (mNGS) and CSF pan-viral serology (VirScan) were deployed to enhance viral detection and characterization. Methods: RNA was extracted from the CSF (n = 20), plasma (n = 9), stool (n = 15), and nasopharyngeal samples (n = 16) from 10 children with brainstem encephalitis and 10 children with meningitis or encephalitis. Pathogens were identified using mNGS. Available CSF from cases (n = 12) and pediatric other neurologic disease controls (n = 54) were analyzed with VirScan with a subset (n = 9 and n = 50) validated by ELISA. Results: mNGS detected EV in all samples positive by quantitative reverse transcription polymerase chain reaction (qRT-PCR) (n = 25). In qRT-PCR-negative samples (n = 35), mNGS found virus in 23% (n = 8, 3 CSF samples). Overall, mNGS enhanced EV detection from 42% (25/60) to 57% (33/60) ( p -value = 0.013). VirScan and ELISA increased detection to 92% (11/12) compared with 46% (4/12) for CSF mNGS and qRT-PCR ( p -value = 0.023). Phylogenetic analysis confirmed the EV-A71 strain clustered with a neurovirulent German EV-A71. A single amino acid substitution (S241P) in the EVA71 VP1 protein was exclusive to the CNS in one subject. Conclusion: mNGS with VirScan significantly increased the CNS detection of EVs relative to qRT-PCR, and the latter generated an antigenic profile of the acute EV-A71 immune response. Genomic analysis confirmed the close relation of the outbreak EV-A71 and neuroinvasive German EV-A71. A S241P substitution in VP1 was found exclusively in the CSF.