Recombination in Australian rabbit caliciviruses
Congratulations to our team who have just submitted a paper studying recombination in rabbit caliciviruses in Australia! We’ve prepared a summary of the paper below. The full paper, which is currently undergoing peer review, is available at: https://www.biorxiv.org/content/10.1101/2021.02.17.431744v1
Previously, five rabbit calicivirus variants were known to circulate in Australian rabbits: the two biocontrol agents RHDV1 and K5, two pandemic viruses RHDV2 and an RHDV1a variant, and the benign RCV-A1 (rabbit calicivirus Australia-1), which circulates in rabbit populations but doesn’t cause any disease. You can read more on the different variants at https://www.vetvoice.com.au/ec/diseases/rabbit-calicivirus. We have been tracking these variants through our diagnostic testing service.
Back in 2017 we started to notice some unusual testing results. Following these up, we discovered two recombinant viruses, which contained the shell of RHDV2 (also designated GI.2) but the internal replication machinery of either RCV-A1 (GI.4c) or the RHDV1a (GI.1a) variant. Caliciviruses have a special naming system where we give a specific “genotype” designation to both the internal replication machinery type as well as the shell type. So we end up with something like GI.1bP-GI.2, where the first part of the name (the bit before the hyphen, ending in P) refers to the replication machinery, and the second part (after the hyphen) refers to the shell. Specifically, the two recombinant viruses were a GI.4cP-GI.2 (which we call the 4c-recombinant) and a GI.4eP-GI.2 (which we call the 4e-recombinant). Importantly, these are both still RHDV2 viruses with the RHDV2 shell. When we talk about immune responses and vaccination, immunity is based on the shell type; so we expect that specific RHDV2 vaccines will work against these recombinant variants as well.
Modified from ViralZone 2008 Swiss Institute of Bioinformatics (https://viralzone.expasy.org/32?outline=all_by_species)
The 4e-recombinant was first detected in NSW in mid-2016 and became the dominant variant detected in this region by early 2017, meaning that we were no longer detecting the ‘old’ RHDV2 virus in this area. Similarly, the 4c-recombinant rapidly became dominant in Victoria, after it was first detected there in early 2017. The 4c-recombinant then spread into Tasmania and, more recently, appears to be spreading into SA and NSW/ACT. In fact, the 4c-recombinant now appears to be replacing the 4e-recombinant in NSW! The ‘old’ RHDV2 is still the dominant variant in WA. But we know that the first detection does not mean the first emergence, since we are not testing every single rabbit. Using some advanced phylogenetic methods, where we build a kind of viral family tree that is linked to time, we estimated the timing of these recombination events. The 4e-recombinant likely emerged in early 2015, while surprisingly, we found that the 4c-recombinant has emerged independently at least 5 times, between late 2015 and early 2017. Several of these 4c-recombinant ‘subvariants’ are continuing to circulate in Australia. Although we knew that recombination was important in rabbit caliciviruses (and also in caliciviruses that infect other species, like human norovirus), the frequency of recombination was unexpected. This is probably normal for caliciviruses, and highlights the need for ongoing surveillance. We were only able to observe this high frequency of recombination because of the intensive testing that we are doing and through the support of all our submitters.
We then looked at changes in the shell of the recombinant viruses and found only a single specific change in the 4e-recombinants and one of the five 4c-recombinant variants, while no specific changes were seen for the other four 4c-recombinant variants. This is further evidence that vaccines against RHDV2 are likely to be effective against these recombinant variants. This also means that the decline in the ‘old’ RHDV2 is not due to immune escape by the recombinants. So why then did the recombinants, especially the 4c-recombinant, spread so well? If the shells are pretty much the same for the ‘old’ RHDV2 and both recombinants, then it must be differences in the internal replication machinery. This was surprising, because the internal parts of the 4c-recombinant come from the benign RCV-A1, which as far as we know doesn’t cause any disease. We have shown previously that the internal replication machinery of RCV-A1 replicates faster than RHDV1. So perhaps having that faster replication machinery is enough of an advantage for the 4c-recombinant to out-race the ‘old’ RHDV2. What this also tells us is that when it comes to who/what can be infected, whether the virus will cause disease, and again immunity, it is the shell that is important. Although the internal machinery of this recombinant is from a benign virus, it is the RHDV2 shell that makes these recombinants lethal, to rabbits of all ages as well as to hares. So ultimately, the new recombinants are still RHDV2 viruses and behave like RHDV2.
So what are the take home messages?
- Rabbit caliciviruses recombine frequently to generate new variants, much more frequently than we previously anticipated.
- This was only detectable through intensive surveillance efforts and the help of hundreds of people across Australia who submitted samples for diagnostic testing.
- And finally, the behaviour of the virus and the rabbit’s immunity depends on the shell, and so far we haven’t seen significant changes in the shell.