Higher abundance of enterovirus A species in the gut of children with islet autoimmunity

Abstract

Enteroviruses (EVs) are prime candidate environmental triggers of islet autoimmunity (IA), with potential as vaccine targets for type 1 diabetes prevention. However, the use of targeted virus detection methods and the selective focus on EVs by most studies increases the risk for substantial investigation bias and an overestimated association between EV and type 1 diabetes. Here we performed comprehensive virome-capture sequencing to examine all known vertebrate-infecting viruses without bias in 182 specimens (faeces and plasma) collected before or at seroconversion from 45 case children with IA and 48 matched controls. From >2.6 billion reads, 28 genera of viruses were detected and 62% of children (58/93) were positive for ≥1 vertebrate-infecting virus. We identified 129 viruses as differentially abundant between the gut of cases and controls, including 5 EV-A types significantly more abundant in the cases. Our findings further support EV's hypothesised contribution to IA and corroborate the proposal that viral load may be an important parameter in disease pathogenesis. Furthermore, our data indicate a previously unrecognised association of IA with higher EV-A abundance in the gut of children and provide a catalog of viruses to be interrogated further to determine a causal link between virus infection and type 1 diabetes.

Figure 1

Viruses detected by VirCapSeq-VERT. (A) Heatmap of viral reads (log2 scale) detected in 32 case and control faeces (n = 64). Only viruses with ≥100 reads matched by BLAST at the species level were included and represented at the genus level. Number of viruses detected per specimen, frequency of each virus within the case/control group, and the mean log read counts (Abundance) are summarised by bar charts. (B) Heatmap of viral reads detected in 59 case and control plasma specimens (n = 118). (C) Frequency of EV-A and EV-B types sequenced from faeces of case and control children.

Figure 2

Viruses detected by VirCapSeq-VERT in faecal specimens based on the 50 reads per 100,000 raw counts (50P100K) threshold. Heatmap of virus reads (log2 scale) detected by VirCapSeq-VERT in 32 case and 32 control faeces (n = 64). Viruses represented at the genus level. Number of viruses detected per specimen, frequency of each virus within the case or control group, and the mean log read counts (Abundance) are summarised by bar charts.

Figure 3

Higher abundance of enterovirus A in the gut of children with islet autoimmunity. Volcano plot of viruses differentially abundant between case and control in the gut. Only viruses with ≥2-fold difference (marked by dotted vertical line) and false discovery rate <5% (q < 0.05) as determined by edgeR are represented. Enterovirus A types represented in red: Coxsackievirus A2 (CVA2), CVA5, CVA6, CVA8 and CVA14. Enterovirus B types represented in blue: ECHOvirus E6 (E6), E18, E25, E30, CVB3, CVB4 and CVB5. All other viruses represented in grey.