Reconstructing the molecular epidemiology of rabies in Switzerland from outbreak to elimination (1967–1997)

Abstract Rabies virus (RABV) is a lethal zoonotic pathogen that remains endemic in some parts of the world despite long-standing vaccination efforts. We present a comprehensive genomic and evolutionary analysis of the sylvatic rabies epidemic in Switzerland (1967–1997) and propose a molecular epidemiological framework describing RABV dynamics from emergence to elimination, with relevance for countries pursuing wildlife rabies elimination. We generated almost whole-genome sequences from 88 RABV-positive brain samples collected across 17 Swiss cantons and 13 host species over three decades. Using Illumina sequencing, 76 genomes were recovered at high coverage, enabling robust Single Nucleotide Polymorphism (SNP) and molecular clock analyses. Phylogenetic reconstruction based on Swiss whole genomes and glycoprotein sequences including additional European strains identified three temporally structured RABV lineages—red (1967–1976), blue (1976–1988), and green (1984–1996)—each consistent with independent introductions from neighbouring countries. Evolutionary analyses indicated a slow substitution rate and predominant purifying selection, with limited adaptive amino-acid change. However, four mutations emerged during the epidemiological peak, suggesting possible modest fitness effects. We found no evidence of major genomic changes associated with cross-species spillovers. Four synonymous variants were underrepresented in carnivore hosts; however, larger datasets may provide stronger evidence for host-associated genetic differences. Genetic divergence showed a strong temporal signal and moderate correlation with geographic distance, consistent with natural and vaccination-induced barriers limiting RABV dispersal, in agreement with the known ecology and control history of the epidemic. These findings provide a genomic framework for understanding sylvatic rabies emergence and elimination and may inform strategies to achieve and sustain the World Health Organization (WHO) goal of zero human deaths from dog-mediated rabies.