Host Genetic Variation Does Not Determine Spatio-Temporal Patterns of European Bat 1 Lyssavirus

Abstract

The majority of bat rabies cases in Europe are attributed to European bat 1 lyssavirus (EBLV-1), circulating mainly in serotine bats (Eptesicus serotinus). Two subtypes have been defined (EBLV-1a and EBLV-1b), each associated with a different geographical distribution. In this study, we undertake a comprehensive sequence analysis based on 80 newly obtained EBLV-1 nearly complete genome sequences from nine European countries over a 45-year period to infer selection pressures, rates of nucleotide substitution, and evolutionary time scale of these two subtypes in Europe. Our results suggest that the current lineage of EBLV-1 arose in Europe ∼600 years ago and the virus has evolved at an estimated average substitution rate of ∼4.19×10−5 subs/site/year, which is among the lowest recorded for RNA viruses. In parallel, we investigate the genetic structure of French serotine bats at both the nuclear and mitochondrial level and find that they constitute a single genetic cluster. Furthermore, Mantel tests based on interindividual distances reveal the absence of correlation between genetic distances estimated between viruses and between host individuals. Taken together, this indicates that the genetic diversity observed in our E. serotinus samples does not account for EBLV-1a and -1b segregation and dispersal in Europe.

Landscape genetic analyses of Cervus elaphus and Sus scrofa: comparative study and analytical developments

“…Working with inter-individual rather than interpopulation distances makes it possible to avoid having to arbitrarily define "populations" or "groups" among sampled sequences (see, for instance, Manel et al 2003;Prunier et al 2013;Lecocq et al 2016). Having to define such groups is associated with several limitations: the partition is often completely arbitrary, hides intra-group differentiation and decreases the number of available pairwise distance estimates (Troupin et al 2017). As preliminary analyses, isolation-by-distance was tested by regressing pairwise genetic distances against pairwise log-transformed geographic distances (i.e., great-circle distances estimated with the R package "fields"; Nychka et al 2017).…”

Mechanisms for European BatLyssavirussubtype 1 persistence in non-synanthropic bats: insights from a modeling study

“…Moreover, our findings indicate that the migratory species may contribute to pathogen persistence in species encountered along the migratory path. Given the potential for long-range seasonal movements of M. schreibersii [29,32], this species may represent a central vector for spatial dispersion of EBLV-1 in southern Europe, where this bat species is abundant, possibly contributing to reconcile the discrepancy observed between the phylogeographical clusters of EBLV-1 variants and the geographic distribution of its common host species E. serotinus [30].…”

“…These bat species may be particularly important for the spatial diffusion and maintenance of EBLV-1 in European bats. Sequence analyses of EBLV-1 genomes from nine European countries indeed uncovered the geographic separation between phylogeographical clusters of EBLV-1 variants that cannot be fully explained by the geographic distribution of E. serotinus [30], a sedentary bat species [31]. Other bat species are thought therefore to be implicated in EBLV-1 circulation, with migratory species potentially assuming a prominent role in carrying the pathogen across different host populations at distant areas [32].…”

Circumstances of Human–Bat interactions and risk of lyssavirus transmission in metropolitan France

“…The first was a probe-based (TaqMan) RT-qPCR for detecting the different phyloclades of RABV previously defined (Troupin et al, 2017); in the second RT-qPCR, an intercalating dye (SYBR Green) was used for the detection of other lyssavirus species (pan-lyssa RT-qPCR).…”