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

Abstract

The diversity of lagoviruses (Caliciviridae) in Australia has increased considerably. By the end of 2017, five variants from three viral genotypes were present in populations of Australian rabbits, while prior to 2014 only two variants were known. To understand the interactions between these lagovirus variants we monitored their geographical distribution and relative incidence over time through a landscape-scale competition study, and from this, revealed potential drivers of epidemiological fitness. Within three years of the arrival of GI.1bP-GI.2 (RHDV2) into Australia, we observed the emergence of two novel recombinant lagovirus variants, GI.4eP-GI.2 (4e-recombinant) in New South Wales and GI.4cP-GI.2 (4c-recombinant) in Victoria. Although both novel recombinants contain the non-structural genes from benign, rabbit-specific, enterotropic viruses, these variants were recovered from the livers of both rabbits and hares that had died acutely. This suggests that determinants of host and tissue tropism for lagoviruses are associated with the structural genes, and that tropism is intricately connected with pathogenicity. Phylogenetic analyses demonstrated that the 4c-recombinant emerged independently on multiple occasions, with five distinct lineages observed. Both new recombinant variants replaced the previous dominant parental RHDV2 in their respective geographical areas, despite sharing an identical or near-identical (i.e., single amino acid change) major capsid protein with the parental virus. This suggests that epidemiological fitness of these recombinants was not driven by antigenic variation in the capsid, implicating the non-structural genes as key drivers of epidemiological fitness. Molecular clock estimates place the GI4.e recombination event in early to mid-2015, while the five GI.4c recombination events occurred from late 2015 through to early 2017. The emergence of at least six viable recombinant variants within a two-year period highlights an unprecedented frequency of these events, detectable only due to intensive surveillance, and demonstrates the importance of recombination in lagovirus evolution.

Age and Infectious Dose Significantly Affect Disease Progression after RHDV2 Infection in Naïve Domestic Rabbits

“…A previous study using this variant also reported a 100% CFR in laboratory rabbits [ 34 ], while studies reporting lower CFR used GI.3P-GI.2 variants or variants where the NS genotype was unknown [ 14 , 28 , 30 , 32 , 33 ]. The importance of recombination in generating genetic diversity in lagoviruses [ 19 , 56 ], and the fitness benefits conferred by the NS proteins [ 57 ], are only beginning to be understood, and functional analyses remain challenging without a robust cell culture system. It is critically important for future RHDV2 pathogenesis and epidemiological studies that the full variant genotype is specified.…”

Multiple Introductions of Rabbit Hemorrhagic Disease Virus Lagovirus europaeus/GI.2 in Africa

“…The key role of recombination in the evolution of GI.2 is well-documented [ 12 , 13 , 14 , 15 , 16 ]. Indeed, several intergenotypic and intergenogroup recombination events between pathogenic and benign strains (GI.1b, GI.3, GI.4c, GI.4e and GII.1) have been described [ 12 , 14 , 16 , 17 ], including in association with the emergence of this new genotype [ 12 ]. This places GI.2 as an orphan capsid-type lagovirus.…”

Age and infectious dose significantly affect disease progression after RHDV2 infection in naïve domestic rabbits

“…The importance of recombination in generating genetic diversity in lagoviruses [19,56], and the fitness benefits conferred by the NS proteins [57], are only beginning to be understood, and functional analyses remain challenging without a robust cell culture system. It is critically important for future RHDV2 pathogenesis and epidemiological studies that the full variant genotype is specified.…”