Meningitis Caused by the Live Varicella Vaccine Virus: Metagenomic Next Generation Sequencing, Immunology Exome Sequencing and Cytokine Multiplex Profiling

Abstract

Varicella vaccine meningitis is an uncommon delayed adverse event of vaccination. Varicella vaccine meningitis has been diagnosed in 12 children, of whom 3 were immunocompromised. We now report two additional cases of vaccine meningitis in twice-immunized immunocompetent children and we perform further testing on a prior third case. We used three methods to diagnose or investigate cases of varicella vaccine meningitis, none of which have been used previously on this disease. These include metagenomic next-generation sequencing and cytokine multiplex profiling of cerebrospinal fluid and immunology exome analysis of white blood cells. In one new case, the diagnosis was confirmed by metagenomic next-generation sequencing of cerebrospinal fluid. Both varicella vaccine virus and human herpesvirus 7 DNA were detected. We performed cytokine multiplex profiling on the cerebrospinal fluid of two cases and found ten elevated biomarkers: interferon gamma, interleukins IL-1RA, IL-6, IL-8, IL-10, IL-17F, chemokines CXCL-9, CXCL-10, CCL-2, and G-CSF. In a second new case, we performed immunology exome sequencing on a panel of 356 genes, but no errors were found. After a review of all 14 cases, we concluded that (i) there is no common explanation for this adverse event, but (ii) ingestion of an oral corticosteroid burst 3-4 weeks before onset of vaccine meningitis may be a risk factor in some cases.

Keywords: IL-10; IL-6; Oka strain; corticosteroids; herpes zoster; human herpesvirus 6; human herpesvirus 7; innate immunity; serious adverse event; varicella-zoster virus.

Figure 1

Identification of varicella vaccine virus DNA in CSF by mNGS. (A) Overview. Samples were processed on liquid handling robots; initially nucleic acid was extracted, and DNA and RNA underwent library preparation before being pooled and sequenced on the Illumina Novaseq at a sequencing depth of 42.2 million reads. Sequencing data were then analyzed using the open source IDseq pipeline. (B) Individual steps. The pipeline matched all data against the human genome, with removal of human reads (blue). Remaining non-host reads (red) underwent quality processing with the removal of redundant, low quality, and low complexity reads. The remaining reads were matched against the NCBI database for potential pathogens, with 16.9 rPM matching to the VZV genome (green). (C) VZV genes. Further analysis found 8 reads aligning with the ORF0 reference gene (panel C1) and 44 reads with the ORF62 reference gene (panel C2). Black lines within the reads (green) represent nucleotide mismatches or single nucleotide polymorphisms against the reference genome (blue). DNA, deoxyribonucleic acid; RNA, ribonucleic acid; VZV, varicella zoster virus; vOka, vaccine strain; ORF, open reading frame; CDS, CoDing Sequence.

Figure 2

Identification of human herpesvirus 7 DNA in CSF by mNGS. The HHV7 nucleotide sequence includes 144,861 bp. The genome encodes ~100 open reading frames (ORFs). U30 includes 2816 bp; it is a capsid assembly protein. U31 includes 6179 bp, including the read from the mNGS of patient 13; it is a tegument protein. U = ORF located in the unique portion of the genome.

Figure 3

Fourteen cases of varicella vaccine meningitis. The cases are arranged first by whether the child had one varicella vaccination (green bar) or two varicella vaccinations (blue bar). Then, the height of each bar graph indicates the age of the patients when they developed meningitis. The year under each bar indicates the year in which the case was first reported in the medical literature. Data about the first 12 cases are taken from Reference 5.

Figure 4

Cytokine levels in CSF from patients with HSV1, HSV2, enterovirus, and VZV infections in the central nervous system. Cytokine data about HSV1, HSV2, and enterovirus were obtained from References 38–46; data about VZV are from the current report. Bars: red = IL-6; blue = IL-8; green = IL-10; black = CXCL10.