Divergent Rhabdovirus Discovered in a Patient with New-Onset Nodding Syndrome

Abstract

A divergent rhabdovirus was discovered in the bloodstream of a 15-year-old girl with Nodding syndrome from Mundri West County in South Sudan. Nodding syndrome is a progressive degenerative neuropathy of unknown cause affecting thousands of individuals in Sub-Saharan Africa. The index case was previously healthy until she developed head-nodding seizures four months prior to presentation. Virus discovery by VIDISCA-NGS on the patient's plasma detected multiple sequence reads belonging to a divergent rhabdovirus. The viral load was 3.85 × 10³ copies/mL in the patient's plasma and undetectable in her cerebrospinal fluid. Further genome walking allowed for the characterization of full coding sequences of all the viral proteins (N, P, M, U1, U2, G, U3, and L). We tentatively named the virus "Mundri virus" (MUNV) and classified it as a novel virus species based on the high divergence from other known viruses (all proteins had less than 43% amino acid identity). Phylogenetic analysis revealed that MUNV forms a monophyletic clade with several human-infecting tibroviruses prevalent in Central Africa. A bioinformatic machine-learning algorithm predicted MUNV to be an arbovirus (bagged prediction strength (BPS) of 0.9) transmitted by midges (BPS 0.4) with an artiodactyl host reservoir (BPS 0.9). An association between MUNV infection and Nodding syndrome was evaluated in a case-control study of 72 patients with Nodding syndrome (including the index case) matched to 65 healthy households and 48 community controls. No subject, besides the index case, was positive for MUNV RNA in their plasma. A serological assay detecting MUNV anti-nucleocapsid found, respectively, in 28%, 22%, and 16% of cases, household controls and community controls to be seropositive with no significant differences between cases and either control group. This suggests that MUNV commonly infects children in South Sudan yet may not be causally associated with Nodding syndrome.

Keywords: next-generation sequencing; nodding syndrome; rhabdoviruses; tibroviruses; virus discovery.

Figure 1

Genome sequence coverage and genome composition of Mundri virus.

Figure 2

Phylogenetic reconstruction of Mundri virus G protein with its closest ancestors.

Figure 3

Host prediction of human-infecting tibroviruses using a machine-learning algorithm.

Figure 4

ELISA dilution series specific for Mundri virus anti-nucleocapsid IgG antibodies of index case acute, index case 12-month follow-up, and Dutch control sample.

Figure 5

(Left panel) Mundri virus (MUNV) anti-nucleocapsid IgG concentrations in South Sudanese children and Dutch controls. (Middle panel) MUNV anti-nucleocapsid IgG concentrations amongst NS cases, household controls and community controls. Large red diamond: index case, large blue diamond: healthy sibling of the index case. (Right panel) MUNV anti-nucleocapsid IgG concentrations across different age groups in South Sudanese children: cases (red), household controls (blue), and community controls (green). The dotted line represents the seropositivity cut-off: 0.127 AU/mL, based on 2 standard deviations above the median antibody concentration of the Dutch controls. Differences between groups were calculated using the Mann–Whitney U test.