Recombination at the emergence of the pathogenic rabbit haemorrhagic disease virus Lagovirus europaeus/GI.2

Abstract

Rabbit haemorrhagic disease is a viral disease that emerged in the 1980s and causes high mortality and morbidity in the European rabbit (Oryctolagus cuniculus). In 2010, a new genotype of the rabbit haemorrhagic disease virus emerged and replaced the former circulating Lagovirus europaeus/GI.1 strains. Several recombination events have been reported for the new genotype Lagovirus europaeus/ GI.2, with pathogenic (variants GI.1a and GI.1b) and benign (genotype GI.4) strains that served as donors for the non-structural part while GI.2 composed the structural part; another recombination event has also been described at the p16/p23 junction involving GI.4 strains. In this study, we analysed new complete coding sequences of four benign GI.3 strains and four GI.2 strains. Phylogenetic and recombination detection analyses revealed that the first GI.2 strains, considered as non-recombinant, resulted from a recombination event between GI.3 and GI.2, with GI.3 as the major donor for the nonstructural part and GI.2 for the structural part. Our results indicate that recombination contributed to the emergence, persistence and dissemination of GI.2 as a pathogenic form and that all described GI.2 strains so far are the product of recombination. This highlights the need to study full-genomic sequences of lagoviruses to understand their emergence and evolution. Since the 1980s, European rabbits worldwide, either domestic or wild, have been affected by rabbit haemorrhagic disease 1. This highly contagious and fatal disease is caused by the rabbit haemorrhagic disease virus (RHDV), a single-stranded positive-sense RNA virus that belongs to the family Caliciviridae, genus Lagovirus. Benign rabbit caliciviruses that confer more or less protection against pathogenic strains, as well as moderately pathogenic strains, including Michigan rabbit calicivirus (MRCV), have also been described 2-7. In 2010, a new pathogenic lagovirus was identified in France 8 , formerly designated as RHDV2 or RHDVb and now as Lagovirus europaeus/GI.2 according to a proposal for a unified nomenclature for lagoviruses 9. GI.2 caused unusual mortalities in rabbits vaccinated against GI.1 (former G1-G6) strains 8, 10. Further analysis revealed genetic differences that were reflected in its positioning in a phylogenetic tree based on capsid protein (VP60) sequences. GI.2 constituted a new phylogenetic group 8, 11 with more than 15% divergence from all know benign and pathogenic lagoviruses. Other unique characteristics include its ability to fatally infect rabbits younger than two months (previously resistant to the disease) 11, 12 and several hare species (Lepus spp.) 13-17. Differences in disease duration, mortality rates, and in the frequency of occurrence of subacute/chronic forms have also been

Immunity against Lagovirus europaeus and the Impact of the Immunological Studies on Vaccination

“…Therefore, early after the introduction of such inactivated ‘liver’ vaccines, several recombinant vaccines containing RHDV and the RHDV-2 capsid protein VP1 expressed in different in-vitro expression systems were developed [ 57 , 58 , 59 , 60 , 61 , 62 , 63 ]. The vaccines against RHDV were demonstrated to have limited cross protection against RHDV-2, and vice versa; for this reason, the current vaccines contain one or both virus-derived antigens in their formulation [ 64 , 65 , 66 , 67 , 68 ]. To date, two different types of genomic recombination have been described: one in the RHDV VP60 sequence region, and a second between the structural and nonstructural genome regions [ 64 ].…”

Frequent intergenotypic recombination between the non-structural and structural genes is a major driver of epidemiological fitness in caliciviruses

“…Instead, we found that the GI.2 capsid was retained and that the emerging recombinant variants acquired alternative NS genes. It is becoming increasingly clear that recombination is a major driver of calicivirus diversity, facilitating the emergence of new variants including those with pandemic and panzootic potential [24, 25, 62, 63]. However, the frequency at which viable recombination occurs and the genetic drivers of epidemiological fitness are still poorly understood.…”

“…Recombination is an important evolutionary mechanism in many RNA viruses [23]. In the Caliciviridae , recombination frequently occurs at the junction between the NS and structural genes, effectively mixing a set of structural genes with an entirely new set of NS genes [24–26]. Recombinant lagoviruses are defined by the nomenclature [RdRp genotype]P-[capsid genotype], and can include combinations of two pathogenic RHDVs (e.g.…”

“…GI.1bP-GI.2) as well as the seemingly more common combination of a benign RCV and a pathogenic RHDV (e.g. GI.4eP-GI.1a, GI.4eP-GI.2, GI.3P-GI.2) [24, 27–32]. Retrospective phylogenetic analyses have demonstrated that all GI.2 viruses so far described are recombinants (GI.3P-GI.2), implying that GI.2 is an orphan capsid-type [24].…”

“…GI.4eP-GI.1a, GI.4eP-GI.2, GI.3P-GI.2) [24, 27–32]. Retrospective phylogenetic analyses have demonstrated that all GI.2 viruses so far described are recombinants (GI.3P-GI.2), implying that GI.2 is an orphan capsid-type [24]. Intergenogroup recombinants between GI (rabbit and hare) and GII (hare) viruses have also been reported, with two GII.1P-GI.2 viruses recovered from hares in Germany in 2014 and 2019 [33].…”