Temporal Dynamics and Turnover of Rabbit Hemorrhagic Disease Virus 2 (RHDV2/GI.2) in Wild Lagomorphs from Northeastern Spain

In Mediterranean ecosystems, emerging lagoviruses, particularly rabbit hemorrhagic disease virus 2 (RHDV2/GI.2), have caused substantial mortality in European rabbits (Oryctolagus cuniculus) and, sporadically, hares (Lepus spp.). Recombination is common among RNA viruses, including lagoviruses, and shapes their evolution, influencing pathogenicity, epidemiology, and host range. However, the viral dynamics of recombinant strains in wild populations remain largely unknown. In this work, we analyse RHDV2/GI.2 coding sequences from European rabbits (n = 44), European brown hares (Lepus europaeus, n = 21) and one Iberian hare (Lepus granatensis) collected in Catalonia (NE Spain) between 2014 and 2024, to characterise temporal patterns and turnover of the different recombinant lineages. All strains shared the GI.2 capsid backbone but with four distinct non-structural genomic profiles: GI.3P–GI.2, GI.1bP–GI.2, GI.4(p16)–GI.1bP–GI.2, and GI.4P–GI.2. The four recombinant strains were detected in European brown hares, whereas rabbits were infected by only three, with the same recombinant present in areas where both species coexist. The Iberian hare was infected by a GI.4P-GI.2 recombinant, where rabbits showed the same lineage. Generalised additive models revealed significant interactions between recombinant type and year of detection, indicating contrasting turnover and temporal dynamics. Over the decade, GI.3P-GI.2 appeared transiently in 2014, GI.1bP-GI.2 strains dominated until 2019, and GI.4-related recombinants progressively replaced them, with GI.4P-GI.2 prevailing from 2020 onwards. Our findings suggest that recombinant strains may have been progressively replaced over time in leporid species from northeastern Iberia, involving variation in the non-structural genomic region that potentially contributes to differences in viral fitness, and supporting the role of recombination as a driver of viral dynamics and evolution.