Rabbit Hemorrhagic Disease Virus 2 (RHDV2; GI.2) Is Replacing Endemic Strains of RHDV in the Australian Landscape within 18 Months of Its Arrival

Abstract

Rabbit hemorrhagic disease virus 2 (RHDV2; Lagovirus GI.2) is a pathogenic calicivirus that affects European rabbits (Oryctolagus cuniculus) and various hare (Lepus) species. GI.2 was first detected in France in 2010 and subsequently caused epidemics in wild and domestic lagomorph populations throughout Europe. In May 2015, GI.2 was detected in Australia. Within 18 months of its initial detection, GI.2 had spread to all Australian states and territories and rapidly became the dominant circulating strain, replacing Rabbit hemorrhagic disease virus (RHDV/GI.1) in mainland Australia. Reconstruction of the evolutionary history of 127 Australian GI.2 isolates revealed that the virus arrived in Australia at least several months before its initial description and likely circulated unnoticed in wild rabbit populations in the east of the continent prior to its detection. GI.2 sequences isolated from five hares clustered with sequences from sympatric rabbit populations sampled contemporaneously, indicating multiple spillover events into hares rather than an adaptation of the Australian GI.2 to a new host. Since the presence of GI.2 in Australia may have wide-ranging consequences for rabbit biocontrol, particularly with the release of the novel biocontrol agent GI.1a/RHDVa-K5 in March 2017, ongoing surveillance is critical to understanding the interactions of the various lagoviruses in Australia and their impact on host populations.IMPORTANCE This study describes the spread and distribution of Rabbit hemorrhagic disease virus 2 (GI.2) in Australia since its first detection in May 2015. Within the first 18 months following its detection, RHDV2 spread from east to west across the continent and became the dominant strain in all mainland states of Australia. This has important implications for pest animal management and for owners of pet and farmed rabbits, as there currently is no effective vaccine available in Australia for GI.2. The closely related RHDV (GI.1) is used to control overabundant wild rabbits, a serious environmental and agricultural pest in this country, and it is currently unclear how the widespread circulation of GI.2 will impact ongoing targeted wild rabbit management operations.

Keywords: RHDV2; biocontrol; calicivirus; distribution; establishment; evolution; rabbit hemorrhagic disease virus.

FIG 1

Pathogenic lagovirus detections in Australia between May 2015 and October 2016. Sites where GI.1 (red triangles), GI.2 (blue circles), and GI.1a-Aus (green squares) were detected are indicated on the map separated into 3-month periods. Filled points indicate detections that were within the respective 3-month period, while hollow points indicate previous detections.

FIG 2

Proportional detections of GI.1, GI.2, GI.1a-Aus, and mixed infections. Detections of each virus are presented as a proportion (y axis) of total cases per month (x axis) between May 2015 and October 2016.

FIG 3

Phylogenies of the nonstructural and structural genes of Australian and global lagoviruses. Maximum likelihood phylogenies of the nonstructural genes (n = 184) (A) and structural genes (VP60 and VP10; n = 184) (B) were inferred using the newly sequenced Australian lagovirus strains (shown in boldface) and representative published sequences. The Australian GI.2 clades are collapsed due to their large size. The accession numbers of published sequences are indicated in the taxon names. The species from which the virus was collected is indicated in the taxon names of newly sequenced samples (O. cun., Oryctolagus cuniculus), and collections from wild animals are indicated by an asterisk next to the species name. The genotype of each cluster is indicated by colored boxes: GI.1, blue; GI.2, red; GI.4, green. To illustrate recombinant strains, the taxon labels are colored according to their structural gene genotype. Taxon label coloring that does not match the colored boxes indicates recombination. Phylogenies were rooted using an early European EBHSV isolate (not shown), and the scale bar is proportional to the number of nucleotide substitutions per site. Bootstrap support values are shown for the major nodes.

FIG 4

Inference of the evolutionary history of Australian GI.1bP-GI.2 samples. A Bayesian MCMC time-scaled phylogenetic tree was constructed from 133 GI.1bP-GI.2 nonstructural gene sequences using a relaxed molecular clock (UCLD) and the GMRF Bayesian skyride model of population growth. Circles at tips are color coded to indicate the Australian state from which the virus was collected. ACT, Australian Capital Territory; NSW, New South Wales; NT, Northern Territory; SA, South Australia; TAS, Tasmania; VIC, Victoria; WA, Western Australia. A selection of representative European GI.1bP-GI.2 sequences (EUR) were also included. Circles at the nodes are colored according to their most likely location, as estimated by ancestral state reconstruction. The size of the circles at the node represents the posterior probability that the ancestor occurred in that state, where larger circles represent a higher probability. The taxon name of BlMt-1, the first GI.2 detected in Australia, is highlighted in pale red. The taxon name of viruses isolated from hares are boldfaced. The time to most recent common ancestor is indicated at major nodes (year/month). The accession numbers of sequences obtained from GenBank are included in the taxon names. The species from which the virus was collected is indicated in the taxon name of newly sequenced samples (O. cun, Oryctolagus cuniculus; L. eur, Lepus europaeus). Samples from wild animals are indicated by an asterisk next to the species name. The scale bar is proportional to time in years. Clades and subclades have been defined arbitrarily for reference to Table 3.

FIG 5

Linear regressions of GI.1bP-GI.2 nonstructural and structural genes. Linear regressions of root-to-tip genetic distances (y axis) against sampling time (x axis) were inferred for GI.1bP-GI.2 Australian (n = 128) and European (n = 5) nonstructural and structural genes.