Abstract
Vampire bat rabies (VBR) poses a major threat to animal and human health and is a chronic economic burden across Central America. Current efforts to reduce the burden, including vaccinating humans and livestock, and bat population control, would benefit from deeper understanding of viral circulation in the bat reservoir. However, long term viral maintenance of VBR arises through complex spatial processes, including co-circulation of viral lineages and transboundary viral invasions. We hypothesise that the highly heterogeneous, narrow, landscape of Central America could favour viral diffusion along ‘transmission corridors’, which may be strategic points to target interventions. To understand epidemiological linkages within and across countries, international scale molecular level monitoring is required, but existing national surveillance systems are largely disjoined and most lack capacity for virus molecular characterisation.
We present viral genomic data from 7 countries derived from a new cooperation involving the 9 member countries (Belize, Costa Rica, Dominican Republic, El Salvador, Guatemala, Honduras, Mexico, Nicaragua and Panama) of the International Regional Organisation for Agricultural Health (OIRSA). Rabies positive brain samples are preserved in duplicate on Whatman or Qiagen FTA cards for robust sample banking in the country of origin, and room temperature shipping to regional reference laboratories. Rabies genomes are enriched by amplification of 400bp overlapping regions, prior to WGS using Oxford Nanopore Technologies MinION. Regionally derived sequences and spatiotemporal metadata are analysed using IQTREE for phylogenetic tree generation and MADDOG for high-resolution lineage assignment with results updated on a map for internal reporting.
Initially, 126 FTA cards were obtained from 7 countries from wild and domestic animals, spanning 8 years. Whole genome sequencing (WGS) coverage of >90% was obtained for 65% of the first 58 samples processed using two initial primer schemes (broadly representing ‘North’ and ‘South’ viral circulation). We found strong amplification bias towards lineages most closely related with the reference sequences, but only 7% of samples were undetectable. Our analysis designated 3 new rabies lineages, for which we observed within-country co-circulation, and revealed high levels of viral sharing between neighbouring countries according to the clustering of the phylogenetic tree.
Our regional rabies sequencing network has built laboratory and data analysis capacity in a region where few full rabies genomes were previously available. Future work will apply evolutionary landscape resistance models to our growing VBR dataset to reveal the spatial-temporal dynamics of VBR dispersal and transmission corridors, ultimately supporting more efficient rabies prevention strategies.