Characterization of old RHDV strains by complete genome sequencing identifies a novel genetic group

Ana M. Lopes,Maria J. Magalhães,Diogo Silvério,Joana Abrantes,Pedro J. Esteves,Helena Areal,Paulo C. Alves

doi:10.1038/s41598-017-13902-2

Abstract

Rabbit hemorrhagic disease (RHD) is a veterinary disease that affects the European rabbit and has a significant economic and ecological negative impact. In Portugal, rabbit hemorrhagic disease virus (RHDV) was reported in 1989 and still causes enzootic outbreaks. Several recombination events have been detected in RHDV strains, including in the first reported outbreak. Here we describe the occurrence of recombination in RHDV strains recovered from rabbit and Iberian hare samples collected in the mid-1990s in Portugal. Characterization of full genomic sequences revealed the existence of a single recombination breakpoint at the boundary of the non-structural and the structural encoding regions, further supporting the importance of this region as a recombination hotspot in lagoviruses. Phylogenetic analysis showed that in the structural region, the recombinant strains were similar to pathogenic G1 strains, but in the non-structural region they formed a new group that diverged ~13% from known strains. No further reports of such group exist, but this recombination event was also detected in an Iberian hare that was associated with the earliest species jump in RHDV. Our results highlight the importance of the characterization of full genomes to disclose RHDV evolution and show that lagoviruses’ diversity has been significantly undersampled.

Highlights

In the last decades, the European rabbit (Oryctolagus cuniculus) populations have contracted dramatically, in the Iberian Peninsula, the species’ original range, due to the rabbit hemorrhagic disease (RHD)[1]
We report the occurrence of recombination in rabbit hemorrhagic disease virus (RHDV) strains recovered from European rabbit and Iberian hare (Lepus granatensis) samples collected in the 1990s in Portugal where these two species live in sympatry
The distinct positioning of the four strains in the maximum likelihood (ML) phylogenetic trees suggests that they are recombinants and that recombination occurred between G1 and a phylogenetically distinct genetic group that had never been reported for the non-structural part

Summary

Introduction

The European rabbit (Oryctolagus cuniculus) populations have contracted dramatically, in the Iberian Peninsula, the species’ original range, due to the rabbit hemorrhagic disease (RHD)[1]. An additional subgenomic RNA (sgRNA) is present in the RHDV virions and encodes both the major and the minor structural proteins[7]. GENECONV with the characterization of a weakly pathogenic and several non-pathogenic strains[14,15,16,17,18,19,20] support the emergence from circulating non-pathogenic lagoviruses. While both hypotheses are not mutually exclusive, they have yet to be confirmed. With the arrival of RHDV2, a rapid and complete replacement of Iberian G1 strains was observed that probably resulted from some adaptive advantage of RHDV2 over G133,34

Methods

Results

Conclusion