Genetic analysis of Rabbit hemorrhagic disease virus (RHDV) from Germany, 2013-2020. Genetic analysis of Rabbit hemorrhagic disease virus (RHDV) from Germany, 2013-2020

Rabbit hemorrhagic disease virus (RHDV) and European brown hare syndrome virus (EBHSV) are caliciviruses of the genus Lagovirus. These viruses pose a serious threat to wild and domestic rabbit and hare populations around the world. In the recent years, an expanding genetic diversity has been described within the genus, with recombination events occurring between the different Gl genotypes. In this study, we generated 56 full genome sequences of RHDV and EBHSV from rabbit and hare samples, collected in Germany between 2013 and 2020. We show that genotype Gl.2 almost entirely replaced Gl.1 in the German rabbit population. Three recombinant strains were identified from rabbit samples that contain the structural genes of Gl.2 and the non-structural genes of Gl.1b. Furthermore, sequences from two hare samples show recombination events between RHDV and EBHSV, a recombination that has not been described previously. Our findings underline the importance of next-generation sequencing as a tool for in-depth studies that allow monitoring of the genetic variability of viruses that would otherwise likely be undetected.