Insights into the evolution of the new variant rabbit haemorrhagic disease virus (GI.2) and the identification of novel recombinant strains

Abstract

Rabbit haemorrhagic disease (RHD) is a viral disease that affects the European rabbit. RHD was detected in 1984 in China and rapidly disseminated worldwide causing a severe decline in wild rabbit populations. The aetiological agent, rabbit haemorrhagic disease virus (RHDV), is an RNA virus of the family Caliciviridae, genus Lagovirus. Pathogenic (G1-G6 or variants GI.1a-GI.1d) and non-pathogenic strains (GI.4) have been characterized. In 2010, a new variant of RHDV, RHDV2/RHDVb/GI.2, was detected in France. GI.2 arrived to the Iberian Peninsula in 2011, and several recombination events were reported. Here, we sequenced full genomes of 19 samples collected in Portugal between 2014 and 2016. New GI.2 recombinant strains were detected, including triple recombinants. These recombinants possess a non-structural protein p16 related to a non-pathogenic strain. Evolutionary analyses were conducted on GI.2 VP60 sequences. Estimated time to the most recent common ancestor (tMRCA) suggests an emergence of GI.2 in July 2008, not distant from its first detection in 2010. This is the first study on GI.2 evolution and highlights the need of continued monitoring and characterization of complete genome sequences when studying lagoviruses' evolution.

Genetic variability and phylogenetic analysis of Lagovirus europaeus strains GI.1 (RHDV) and GI.2 (RHDV2) based on the RNA-dependent RNA polymerase (RdRp) coding gene

“…A very interesting situation was found for some strains (PSM2, CBMad17-3, CBMad17-2, CBPico17-2, CBPico17-1, CBAlgarve14-3/2014) identified in 2014, 2016 and 2017 in GI.1b (G1), which showed variability at 11.1-12.9%, similar to GI.1a (G6/RHDVa) (11.8-13.6%), but phylogenetically were not found in this group. This suggests that these are G1/RHDV2 recombinants, which is in line with the results of previous studies (Mahar et al, 2016;Lopes et al, 2018;Silverio et al, 2018). Genetic variations of 7.0-10.5% of the remaining strains (CB194Pt, CB147 Pt, Eisenhuettenstadt, SD, AST89) in this group, supported by the results of studies by other authors (Abrantes et al, 2012;Lopes et al, 2017), indicate that these are the G1-non-recombinant strains, both within the studied polymerase gene and in the VP60 and VP10 genes .…”

“…Phylogenetic relations deduced from the RdRp gene had revealed a new phylogenetic group, gathering original non-recombined RHDV2 strains from the period of 2011-2016 circulating in Spain, continental Portugal and the Canary Islands (Lopes et al, 2018;Silverio et al, 2018). The last group in the phylogenetic tree was formed by four strains from Australia, one from Portugal, and by MRCV.…”

RHDV2 epidemic in UK pet rabbits. Part 1: clinical features, gross post mortem and histopathological findings

“…In the UK, RHD was first reported in 1992 in a group of exhibition rabbits (Fuller et al 1993) before spreading through the wild and domestic rabbit population. In 2010, a new serotype of the RHD virus (RHDV2) was identified from an outbreak of RHD in vaccinated meat rabbits in a rabbitry in France (Le Gall-Reculé et al 2011) before spreading rapidly throughout Europe (Neimanis et al 2018, Silvério et al 2018 and reaching other continents including Canada and New Zealand (OIE 2019a). RHDV2 is phylogenetically, antigenically and serotypically distinct from previously identified strains of RHDV (RHDV1) (Le Gall-Reculé et al 2013).…”

Myeloperoxidase and Lysozymes as a Pivotal Hallmark of Immunity Status in Rabbits

“…There was a great interest in this problem due to the rabbit's key contribution to the Mediterranean ecosystems, as it provides food for several endangered endemic species, such as the Iberian lynx (Lynx pardinus) and the Iberian imperial eagle (Aquila heliaca) [3]. The reduction of the wild rabbit population therefore has a negative impact on the persistence of these predators [3,22,23].…”