scholarly journals Comparative Analysis of RNA Virome Composition in Rabbits and Associated Ectoparasites

2020 ◽  
Vol 94 (11) ◽  
Author(s):  
Jackie E. Mahar ◽  
Mang Shi ◽  
Robyn N. Hall ◽  
Tanja Strive ◽  
Edward C. Holmes
Keyword(s):  
Comparative Analysis ◽  
Myxoma Virus ◽  
European Rabbit ◽  
Rabbit Hemorrhagic Disease Virus ◽  
Gut Contents ◽  
Mechanical Transmission ◽  
Hemorrhagic Disease ◽  
Vertebrate Species ◽  
Invertebrate Species ◽  
Virus Diversity

ABSTRACT Ectoparasites play an important role in virus transmission among vertebrates. Little, however, is known about the nature of those viruses that pass between invertebrates and vertebrates. In Australia, flies and fleas support the mechanical transmission of two viral biological controls against wild rabbits—rabbit hemorrhagic disease virus (RHDV) and myxoma virus. We compared virome compositions in rabbits and these ectoparasites, sequencing total RNA from multiple tissues and gut contents of wild rabbits, fleas collected from these rabbits, and flies trapped sympatrically. Meta-transcriptomic analyses identified 50 novel viruses from multiple RNA virus families. Rabbits and their ectoparasites were characterized by markedly different viromes, with virus abundance greatest in flies. Although viral contigs from six virus families/groups were found in both rabbits and ectoparasites, they clustered in distinct host-dependent lineages. A novel calicivirus and a picornavirus detected in rabbit cecal content were vertebrate specific; the newly detected calicivirus was distinct from known rabbit caliciviruses, while the picornavirus clustered with sapeloviruses. Several picobirnaviruses were also identified that fell in diverse phylogenetic positions, compatible with the idea that they are associated with bacteria. Further comparative analysis revealed that the remaining viruses found in rabbits, and all those from ectoparasites, were likely associated with invertebrates, plants, and coinfecting endosymbionts. While no full genomes of vertebrate-associated viruses were detected in ectoparasites, small numbers of reads from rabbit astrovirus, RHDV, and other lagoviruses were present in flies. This supports a role for flies in the mechanical transmission of RHDV, while their involvement in astrovirus transmission merits additional exploration. IMPORTANCE Ectoparasites play an important role in the transmission of many vertebrate-infecting viruses, including Zika and dengue viruses. Although it is becoming increasingly clear that invertebrate species harbor substantial virus diversity, it is unclear how many of the viruses carried by invertebrates have the potential to infect vertebrate species. We used the European rabbit (Oryctolagus cuniculus) as a model species to compare virome compositions in a vertebrate host and known associated ectoparasite mechanical vectors, in this case, fleas and blowflies. In particular, we aimed to infer the extent of viral transfer between these distinct types of host. Our analysis revealed that despite extensive viral diversity in both rabbits and associated ectoparasites, and the close interaction of these vertebrate and invertebrate species, biological viral transmission from ectoparasites to vertebrate species is rare. We did, however, find evidence to support the idea of a role of blowflies in transmitting viruses without active replication in the insect.

scholarly journals Evolution and Phylogeography of the Nonpathogenic Calicivirus RCV-A1 in Wild Rabbits in Australia

2010 ◽  
Vol 84 (23) ◽  
pp. 12397-12404 ◽  
Author(s):  
Marlene Jahnke ◽  
Edward C. Holmes ◽  
Peter J. Kerr ◽  
John D. Wright ◽  
Tanja Strive
Keyword(s):  
Myxoma Virus ◽  
European Rabbit ◽  
Rabbit Hemorrhagic Disease Virus ◽  
Recent Common Ancestor ◽  
Hemorrhagic Disease ◽  
Evolutionary Analysis ◽  
Wild Rabbit ◽  
Most Recent Common Ancestor ◽  
Capsid Sequence ◽  
Australian Continent

ABSTRACT Despite its potential importance for the biological control of European rabbits, relatively little is known about the evolution and molecular epidemiology of rabbit calicivirus Australia 1 (RCV-A1). To address this issue we undertook an extensive evolutionary analysis of 36 RCV-A1 samples collected from wild rabbit populations in southeast Australia between 2007 and 2009. Based on phylogenetic analysis of the entire capsid sequence, six clades of RCV-A1 were defined, each exhibiting strong population subdivision. Strikingly, our estimates of the time to the most recent common ancestor of RCV-A1 coincide with the introduction of rabbits to Australia in the mid-19th century. Subsequent divergence events visible in the RCV-A1 phylogenies likely reflect key moments in the history of the European rabbit in Australia, most notably the bottlenecks in rabbit populations induced by the two viral biocontrol agents used on the Australian continent, myxoma virus and rabbit hemorrhagic disease virus (RHDV). RCV-A1 strains therefore exhibit strong phylogeographic separation and may constitute a useful tool to study recent host population dynamics and migration patterns, which in turn could be used to monitor rabbit control in Australia.

scholarly journals Benign Rabbit Caliciviruses Exhibit Evolutionary Dynamics Similar to Those of Their Virulent Relatives

2016 ◽  
Vol 90 (20) ◽  
pp. 9317-9329 ◽  
Author(s):  
Jackie E. Mahar ◽  
Leila Nicholson ◽  
John-Sebastian Eden ◽  
Sebastián Duchêne ◽  
Peter J. Kerr ◽  
...  
Keyword(s):  
Disease Virus ◽  
Evolutionary Dynamics ◽  
Purifying Selection ◽  
Myxoma Virus ◽  
European Rabbit ◽  
Rabbit Hemorrhagic Disease Virus ◽  
Tissue Tropism ◽  
Hemorrhagic Disease ◽  
Rabbit Hemorrhagic Disease ◽  
Highly Virulent

ABSTRACTTwo closely related caliciviruses cocirculate in Australia: rabbit hemorrhagic disease virus (RHDV) and rabbit calicivirus Australia 1 (RCV-A1). RCV-A1 causes benign enteric infections in the European rabbit (Oryctolagus cuniculus) in Australia and New Zealand, while its close relative RHDV causes a highly pathogenic infection of the liver in the same host. The comparison of these viruses provides important information on the nature and trajectory of virulence evolution, particularly as highly virulent strains of RHDV may have evolved from nonpathogenic ancestors such as RCV-A1. To determine the evolution of RCV-A1 we sequenced the full-length genomes of 44 RCV-A1 samples isolated from healthy rabbits and compared key evolutionary parameters to those of its virulent relative, RHDV. Despite their marked differences in pathogenicity and tissue tropism, RCV-A1 and RHDV have evolved in a very similar manner. Both viruses have evolved at broadly similar rates, suggesting that their dynamics are largely shaped by high background mutation rates, and both exhibit occasional recombination and an evolutionary environment dominated by purifying selection. In addition, our comparative analysis revealed that there have been multiple changes in both virulence and tissue tropism in the evolutionary history of these and related viruses. Finally, these new genomic data suggest that either RCV-A1 was introduced into Australia after the introduction of myxoma virus as a biocontrol agent in 1950 or there was drastic reduction of the rabbit population, and hence of RCV-A1 genetic diversity, perhaps coincident with the emergence of myxoma virus.IMPORTANCEThe comparison of closely related viruses that differ profoundly in propensity to cause disease in their hosts offers a powerful opportunity to reveal the causes of changes in virulence and to study how such changes alter the evolutionary dynamics of these pathogens. Here we describe such a novel comparison involving two closely related RNA viruses that cocirculate in Australia, the highly virulent rabbit hemorrhagic disease virus (RHDV) and the nonpathogenic rabbit calicivirus Australia 1 (RCV-A1). Both viruses infect the European rabbit, but they differ in virulence, tissue tropism, and mechanisms of transmission. Surprisingly, and despite these fundamental differences, RCV-A1 and RHDV have evolved at very similar (high) rates and with strong purifying selection. Furthermore, candidate key mutations were identified that may play a role in virulence and/or tissue tropism and therefore warrant further investigation.

scholarly journals A Review on the Methods Used for the Detection and Diagnosis of Rabbit Hemorrhagic Disease Virus (RHDV)

2021 ◽  
Vol 9 (5) ◽  
pp. 972
Author(s):  
Joana Abrantes ◽  
Ana M. Lopes
Keyword(s):  
Disease Virus ◽  
Diagnostic Tests ◽  
High Throughput Sequencing ◽  
Current Knowledge ◽  
European Rabbit ◽  
Rabbit Hemorrhagic Disease Virus ◽  
Hemorrhagic Disease ◽  
Rabbit Hemorrhagic Disease ◽  
Detection And Diagnosis

Since the early 1980s, the European rabbit (Oryctolagus cuniculus) has been threatened by the rabbit hemorrhagic disease (RHD). The disease is caused by a lagovirus of the family Caliciviridae, the rabbit hemorrhagic disease virus (RHDV). The need for detection, identification and further characterization of RHDV led to the development of several diagnostic tests. Owing to the lack of an appropriate cell culture system for in vitro propagation of the virus, much of the methods involved in these tests contributed to our current knowledge on RHD and RHDV and to the development of vaccines to contain the disease. Here, we provide a comprehensive review of the RHDV diagnostic tests used since the first RHD outbreak and that include molecular, histological and serological techniques, ranging from simpler tests initially used, such as the hemagglutination test, to the more recent and sophisticated high-throughput sequencing, along with an overview of their potential and their limitations.

Comparative analysis of rabbit hemorrhagic disease virus strains originating from outbreaks in the Russian Federation

2016 ◽  
Vol 161 (7) ◽  
pp. 1973-1979 ◽  
Author(s):  
Galina Burmakina ◽  
Nina Malogolovkina ◽  
Andrey Lunitsin ◽  
Ilya Titov ◽  
Sodnom Tsybanov ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Disease Virus ◽  
Russian Federation ◽  
Rabbit Hemorrhagic Disease Virus ◽  
Hemorrhagic Disease ◽  
Rabbit Hemorrhagic Disease ◽  
The Russian Federation ◽  
Virus Strains

Experimental Study of the Mechanical Transmission of Rabbit Hemorrhagic Disease Virus (RHDV2/b) by Aedes albopictus (Diptera: Culicidae) and Phlebotomus papatasi (Diptera: Psychodidae)

2021 ◽  
Author(s):  
C Calvete ◽  
S Delacour ◽  
R V Oropeza-Velasquez ◽  
R Estrada ◽  
M P Sarto ◽  
...  
Keyword(s):  
Disease Virus ◽  
Aedes Albopictus ◽  
Clinical Signs ◽  
Sand Fly ◽  
Rabbit Hemorrhagic Disease Virus ◽  
Mechanical Transmission ◽  
Hemorrhagic Disease ◽  
Phlebotomus Papatasi ◽  
Rabbit Hemorrhagic Disease ◽  
Clinical Changes

Abstract Rabbit hemorrhagic disease (RHD) is caused by a lagovirus mainly affecting European rabbits (Oryctolagus cuniculus), although other European and North American lagomorph species are also susceptible to fatal infection by the new viral variant RHDV2/b. In the present work, direct mechanical transmission of the rabbit hemorrhagic disease virus (RHDV2/b variant) by the hematophagous Diptera Aedes albopictus (Skuse) (Diptera: Culicidae) and the sand fly Phlebotomus papatasi (Scopoli) (Diptera: Psychodidae) was tested. For each species, six and three laboratory rabbits were exposed to bites of dipterous females partially fed on RHDV2/b viral suspension 2 h and 24 h prior to exposure, respectively. The rabbits were then monitored for clinical changes and mortality for 35 d, and seroconversion was assessed by indirect ELISA. No rabbit died or showed clinical signs of disease, and seroconversion was recorded in two rabbits challenged with P. papatasi females fed the viral suspension 2 h prior to exposure. The number of RHDV2/b RNA copies/female was higher in Ae. albopictus than in P. papatasi but the decrease over time of RNA load in Ae. albopictus was greater than that in P. papatasi. The results of this study suggest the inability of Ae. albopictus to serve as a direct mechanical vector of RHDV2/b, but sand flies could play a role in the local transmission of RHD.

scholarly journals Further studies on the mechanism of mosquito transmission of myxomatosis in the European rabbit

1956 ◽  
Vol 54 (2) ◽  
pp. 258-283 ◽  
Author(s):  
M. F. Day ◽  
Frank Fenner ◽  
Gwendolyn M. Woodroofe ◽  
G. A. McIntyre
Keyword(s):  
Infected Animal ◽  
Skin Lesions ◽  
Quantitative Information ◽  
Myxoma Virus ◽  
European Rabbit ◽  
Rabbit Serum ◽  
Mechanical Transmission ◽  
Normal Rabbit Serum ◽  
Biological Mechanism ◽  
Virus Load

Proof of the existence of multiplication of myxoma virus in mosquitoes has been sought by a variety of experiments with Aedes aegypti and Anopheles annulipes. All were completely negative. All features of transmission are compatible with a purely mechanical and none is compatible with a ‘biological’ mechanism.In mechanical transmission important features of the infected animal host are the number and accessibility of viruliferous skin lesions, and the location and concentration of virus in these lesions.By inducing mosquitoes to probe through infectious skin lesions and subsequently permitting them to make many successive probes on marked skin sites on the backs of susceptible rabbits, it has been possible to obtain quantitative information on the median minimum virus load of probing mosquitoes, and the rates of loss due to probing and the passage of time.A preparation of myxoma virus suspended in normal rabbit serum had a half-lifetime of 11 days at 4° C., 5 days at 18–20° C., and 31 hr. at 27–28° C. Apart from losses due to probing (about 12% of the virus load per probe) viable virus on the proboscis of the mosquito probably disappears at about the same rates.

scholarly journals Limited overlap in RNA virome composition among rabbits and their ectoparasites reveals barriers to virus transmission

2019 ◽  
Author(s):  
Jackie E. Mahar ◽  
Mang Shi ◽  
Robyn N. Hall ◽  
Tanja Strive ◽  
Edward C. Holmes
Keyword(s):  
Rna Virus ◽  
Virus Transmission ◽  
Myxoma Virus ◽  
Gut Contents ◽  
Mechanical Transmission ◽  
The Novel ◽  
Caecal Content ◽  
Rabbit Haemorrhagic Disease ◽  
Haemorrhagic Disease

AbstractEctoparasites play an important role in virus transmission among vertebrates. However, little is known about the extent and composition of viruses that pass between invertebrates and vertebrates. In Australia, flies and fleas support the mechanical transmission of viral biological controls against wild rabbits - rabbit haemorrhagic disease virus (RHDV) and myxoma virus. We compared virome structure and composition in rabbits and these associated ectoparasites, sequencing total RNA from multiple tissues and gut contents of wild rabbits, fleas collected from these rabbits, and flies trapped sympatrically. Meta-transcriptomic analyses identified 50 novel viruses from multiple RNA virus families. Rabbits and their ectoparasites were characterised by markedly different viromes: although viral contigs from six virus families/groups were found in both rabbits and ectoparasites, none were vertebrate-associated. A novel calicivirus and picornavirus detected in rabbit caecal content were vertebrate-specific: the newly detected calicivirus was distinct from known rabbit caliciviruses, while the novel picornavirus clustered with the Sapeloviruses. Several Picobirnaviridae were also identified, falling in diverse phylogenetic positions suggestive of an association with co-infecting bacteria. The remaining viruses found in rabbits, and all those from ectoparasites, were likely associated with invertebrates, plants and co-infecting endosymbionts. While no full genomes of vertebrate-associated viruses were detected in ectoparasites, suggestive of major barriers to biological transmission with active replication, small numbers of reads from rabbit astrovirus, RHDV and other lagoviruses were present in flies. This supports the role of flies in the mechanical transmission of RHDV and implies that they may assist the spread of astroviruses.

scholarly journals Punctuated evolution of myxoma virus: rapid and disjunct evolution of a recent viral lineage in Australia

2018 ◽  
Author(s):  
Peter J. Kerr ◽  
John-Sebastian Eden ◽  
Francesca Di Giallonardo ◽  
David Peacock ◽  
June Liu ◽  
...  
Keyword(s):  
Myxoma Virus ◽  
Rabbit Hemorrhagic Disease Virus ◽  
Hemorrhagic Disease ◽  
Partial Recovery ◽  
Wild Rabbit ◽  
Genome Sequences ◽  
Selection Pressures ◽  
Rabbit Hemorrhagic Disease ◽  
Evolutionary Event ◽  
European Rabbits

ABSTRACTMyxoma virus (MYXV) has been evolving in a novel host species – European rabbits – in Australia since 1950. Previous studies of viruses sampled from 1950 to 1999 revealed a remarkably clock-like evolutionary process across all Australian lineages of MYXV. Through an analysis of 49 newly generated MYXV genome sequences isolated in Australia between 2008 and 2017 we show that MYXV evolution in Australia can be characterized by three lineages, one of which exhibited a greatly elevated rate of evolutionary change and a dramatic break-down of temporal structure. Phylogenetic analysis revealed that this apparently punctuated evolutionary event occurred between 1996 and 2012. The branch leading to the rapidly evolving lineage contained a relatively high number of non-synonymous substitutions, and viruses in this lineage reversed a mutation found in the progenitor standard laboratory strain (SLS) and all previous sequences that disrupts the reading frame of theM005L/Rgene. Analysis of genes encoding proteins involved in DNA synthesis or RNA transcription did not reveal any mutations likely to cause rapid evolution. Although there was some evidence for recombination across the MYXV phylogeny, this was not associated with the increase in evolutionary rate. The period from 1996 to 2012 saw significant declines in wild rabbit numbers, due to the introduction of rabbit hemorrhagic disease and prolonged drought in south-eastern Australia, followed by the partial recovery of populations. We therefore suggest that a rapidly changing environment for virus transmission changed the selection pressures faced by MYXV and altered the course of virus evolution.IMPORTANCEThe co-evolution of myxoma virus (MYXV) and European rabbits in Australia is one of the most important natural ‘experiments’ in evolutionary biology, providing insights into virus adaptation to new hosts and the evolution of virulence. Previous studies of MYXV evolution have also shown that the virus evolves both relatively rapidly and in a strongly clock-like manner. Using newly acquired MYXV genome sequences from Australia we show that the virus has experienced a dramatic change in evolutionary behavior over the last 20 years, with a break-down in clock-like structure, the appearance of a rapidly evolving virus lineage, and the accumulation of multiple non-synonymous and indel mutations. We suggest that this punctuated evolutionary event likely reflects a change in selection pressures as rabbit numbers declined following the introduction of rabbit hemorrhagic disease virus and drought in the geographic regions inhabited by rabbits.

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