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 in recent years. 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 evolutionary interactions among these lagovirus variants we monitored their geographical distribution and relative incidence over time in a continental-scale competition study. Within three years of the incursion of rabbit haemorrhagic disease virus 2 (RHDV2, denoted genotype GI.1bP-GI.2 [polymerase genotype]P-[capsid genotype]) into Australia, two novel recombinant lagovirus variants emerged: RHDV2-4e (genotype GI.4eP-GI.2) in New South Wales and RHDV2-4c (genotype GI.4cP-GI.2) in Victoria. Although both novel recombinants contain non-structural genes related to those 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 the 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 RHDV2-4c recombinant emerged independently on multiple occasions, with five distinct lineages observed. Both the new RHDV2-4e and 4c recombinant variants replaced the previous dominant parental RHDV2 (genotype GI.1bP-GI.2) in their respective geographical areas, despite sharing an identical or near-identical (i.e. single amino acid change) VP60 major capsid protein with the parental virus. This suggests that the observed replacement by these recombinants was not driven by antigenic variation in VP60, implicating the non-structural genes as key drivers of epidemiological fitness. Molecular clock estimates place the RHDV2-4e recombination event in early to mid-2015, while the five RHDV2-4c 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 the high frequency of these events, detectable only through intensive surveillance, and demonstrates the importance of recombination in lagovirus evolution.

Rabbit Haemorrhagic Disease Virus 2 (RHDV2; GI.2) in Ireland Focusing on Wild Irish Hares (Lepus timidus hibernicus): An Overview of the First Outbreaks and Contextual Review

“…The authors speculate that this demonstrates that the European brown hare is less susceptible to RHDV2 than sympatric rabbits. However, there is evidence to suggest that RHDV2 strains became more pathogenic over time [ 10 , 57 ].…”

“…Lagoviruses exhibit rapid evolution, typical of RNA viruses generally [ 57 ]. This may be for several hypothetical reasons, including an evolutionary arms race versus the host immune system, variation in host genetic susceptibility/infectivity/resistance, etc.…”

“…[ 25 ]. This is some evidence from Sweden and Australia to suggest that, even over short periods of the epidemic detectable RHDV2 strain, variation has emerged with differing phenotypic characteristics [ 10 , 57 ]. In Sweden, it was reported that viral strains sampled early in the epidemic used in inoculations studies were less pathogenic than later strains [ 10 ].…”

“…It has been speculated that the selection pressure on the pathogen is favouring increased virulence, as evidenced by an experimental infection study of rabbits using a newer Australian strain of RHDV2, whereby death or severe disease requiring euthanasia occurred within 96 hours post-infection for all study animals [ 27 ], equivalent to classical RHDV1 pathogenicity. RHDV2 appears to have increased diversity relative to RHDV1, partly due to the recognised recombinant events with pathogenic and non-pathogenic viruses [ 57 , 58 ]. Capucci et al [ 59 ] also suggested that more virulent strains of RHDV2 have emerged over time since emergence, based on the mortality in experimental conditions in rabbits inoculated with circulating strains from Italy in 2014 and 2015.…”

“…This speed of evolution and diversity complicates any assessment of the threat posed by these viruses—the threat is also diversifying and evolving. For example, Mahar et al [ 57 ] reported at least six viable recombination events in a two-year period since the discovery of RHDV2 in mid-2015 in Australia [ 57 , 60 ]. However, recent experimental work from Australia suggests that in rabbits, the presence of maternal antibodies, from surviving exposed does to their kits, could provide protection from disease [ 29 ].…”