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Hall RN, Trought K, Strive T, Duckworth JA, Jenckel M. First Detection and Circulation of RHDV2 in New Zealand. Viruses 2024; 16:519. [PMID: 38675862 PMCID: PMC11053765 DOI: 10.3390/v16040519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/19/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Rabbit haemorrhage disease virus 2 (RHDV2) is a highly pathogenic lagovirus that causes lethal disease in rabbits and hares (lagomorphs). Since its first detection in Europe in 2010, RHDV2 has spread worldwide and has been detected in over 35 countries so far. Here, we provide the first detailed report of the detection and subsequent circulation of RHDV2 in New Zealand. RHDV2 was first detected in New Zealand in 2018, with positive samples retrospectively identified in December 2017. Subsequent time-resolved phylogenetic analysis suggested a single introduction into the North Island between March and November 2016. Genetic analysis identified a GI.3P-GI.2 variant supporting a non-Australian origin for the incursion; however, more accurate identification of the source of the incursion remains challenging due to the wide global distribution of the GI.3P-GI.2 variant. Furthermore, our analysis suggests the spread of the virus between the North and South Islands of New Zealand at least twice, dated to mid-2017 and around 2018. Further phylogenetic analysis also revealed a strong phylogeographic pattern. So far, no recombination events with endemic benign New Zealand rabbit caliciviruses have been identified. This study highlights the need for further research and surveillance to monitor the distribution and diversity of lagoviruses in New Zealand and to detect incursions of novel variants.
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Affiliation(s)
- Robyn N. Hall
- CSIRO Health & Biosecurity, Acton, ACT 2601, Australia
- Centre for Invasive Species Solutions, Bruce, ACT 2617, Australia
- Ausvet Pty Ltd., Fremantle, WA 6160, Australia;
| | - Katherine Trought
- Manaaki Whenua-Landcare Research, Lincoln 7608, New Zealand; (K.T.); (J.A.D.)
| | - Tanja Strive
- CSIRO Health & Biosecurity, Acton, ACT 2601, Australia
- Centre for Invasive Species Solutions, Bruce, ACT 2617, Australia
| | - Janine A. Duckworth
- Manaaki Whenua-Landcare Research, Lincoln 7608, New Zealand; (K.T.); (J.A.D.)
| | - Maria Jenckel
- CSIRO Health & Biosecurity, Acton, ACT 2601, Australia
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2
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Smertina E, Keller LM, Huang N, Flores-Benner G, Correa-Cuadros JP, Duclos M, Jaksic FM, Briceño C, Ramirez VN, Díaz-Gacitúa M, Carrasco-Fernández S, Smith IL, Strive T, Jenckel M. First Detection of Benign Rabbit Caliciviruses in Chile. Viruses 2024; 16:439. [PMID: 38543804 PMCID: PMC10974056 DOI: 10.3390/v16030439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 02/29/2024] [Accepted: 03/06/2024] [Indexed: 05/23/2024] Open
Abstract
Pathogenic lagoviruses (Rabbit hemorrhagic disease virus, RHDV) are widely spread across the world and are used in Australia and New Zealand to control populations of feral European rabbits. The spread of the non-pathogenic lagoviruses, e.g., rabbit calicivirus (RCV), is less well studied as the infection results in no clinical signs. Nonetheless, RCV has important implications for the spread of RHDV and rabbit biocontrol as it can provide varying levels of cross-protection against fatal infection with pathogenic lagoviruses. In Chile, where European rabbits are also an introduced species, myxoma virus was used for localised biocontrol of rabbits in the 1950s. To date, there have been no studies investigating the presence of lagoviruses in the Chilean feral rabbit population. In this study, liver and duodenum rabbit samples from central Chile were tested for the presence of lagoviruses and positive samples were subject to whole RNA sequencing and subsequent data analysis. Phylogenetic analysis revealed a novel RCV variant in duodenal samples that likely originated from European RCVs. Sequencing analysis also detected the presence of a rabbit astrovirus in one of the lagovirus-positive samples.
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Affiliation(s)
- Elena Smertina
- Commonwealth Scientific and Industrial Research Organisation, Health and Biosecurity, Black Mountain, Canberra, ACT 2601, Australia; (E.S.); (L.M.K.); (N.H.); (I.L.S.); (T.S.)
| | - Luca M. Keller
- Commonwealth Scientific and Industrial Research Organisation, Health and Biosecurity, Black Mountain, Canberra, ACT 2601, Australia; (E.S.); (L.M.K.); (N.H.); (I.L.S.); (T.S.)
| | - Nina Huang
- Commonwealth Scientific and Industrial Research Organisation, Health and Biosecurity, Black Mountain, Canberra, ACT 2601, Australia; (E.S.); (L.M.K.); (N.H.); (I.L.S.); (T.S.)
| | - Gabriela Flores-Benner
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (G.F.-B.); (J.P.C.-C.); (F.M.J.)
- Center of Applied Ecology and Sustainability (CAPES), Santiago 8331150, Chile; (M.D.); (S.C.-F.)
| | - Jennifer Paola Correa-Cuadros
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (G.F.-B.); (J.P.C.-C.); (F.M.J.)
- Center of Applied Ecology and Sustainability (CAPES), Santiago 8331150, Chile; (M.D.); (S.C.-F.)
| | - Melanie Duclos
- Center of Applied Ecology and Sustainability (CAPES), Santiago 8331150, Chile; (M.D.); (S.C.-F.)
- Centro de Investigación para la Sustentabilidad, Universidad Andrés Bello (CIS-UNAB), Santiago 8370251, Chile
| | - Fabian M. Jaksic
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (G.F.-B.); (J.P.C.-C.); (F.M.J.)
- Center of Applied Ecology and Sustainability (CAPES), Santiago 8331150, Chile; (M.D.); (S.C.-F.)
| | - Cristóbal Briceño
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago 8330111, Chile; (C.B.); (V.N.R.)
| | - Victor Neira Ramirez
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago 8330111, Chile; (C.B.); (V.N.R.)
| | | | - Sebastián Carrasco-Fernández
- Center of Applied Ecology and Sustainability (CAPES), Santiago 8331150, Chile; (M.D.); (S.C.-F.)
- Magíster en Recursos Naturales, Facultad de Ciencias de la Vida, Universidad Andrés Bello, República 440, Santiago 8370251, Chile
| | - Ina L. Smith
- Commonwealth Scientific and Industrial Research Organisation, Health and Biosecurity, Black Mountain, Canberra, ACT 2601, Australia; (E.S.); (L.M.K.); (N.H.); (I.L.S.); (T.S.)
| | - Tanja Strive
- Commonwealth Scientific and Industrial Research Organisation, Health and Biosecurity, Black Mountain, Canberra, ACT 2601, Australia; (E.S.); (L.M.K.); (N.H.); (I.L.S.); (T.S.)
| | - Maria Jenckel
- Commonwealth Scientific and Industrial Research Organisation, Health and Biosecurity, Black Mountain, Canberra, ACT 2601, Australia; (E.S.); (L.M.K.); (N.H.); (I.L.S.); (T.S.)
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Koh EY, Ong J, Wang Y, Toh X, Fernandez CJ, Huangfu T, Hall RN, Toh S, Lim K, Sng W, Lim HP, Ho K, Chang SF, Yap HH. Rabbit haemorrhagic disease virus 2 from Singapore 2020 outbreak revealed an Australian recombinant variant. Virus Evol 2023; 9:vead029. [PMID: 37207001 PMCID: PMC10190043 DOI: 10.1093/ve/vead029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 03/25/2023] [Accepted: 04/27/2023] [Indexed: 05/21/2023] Open
Abstract
Rabbit haemorrhagic disease (RHD) is a significant and debilitating viral disease affecting lagomorphs. In September 2020, Singapore reported its first cases of RHD virus (RHDV) infection in domesticated rabbits. The initial findings reported that the outbreak strain belonged to genotype GI.2 (RHDV2/RHDVb), and epidemiological investigations could not identify the definitive source of the virus origin. Further recombination detection and phylogenetic analyses of the Singapore outbreak strain revealed that the RHDV was a GI.2 structural (S)/GI.4 non-structural (NS) recombinant variant. Sequence analyses on the National Centre for Biotechnology Information (NCBI) database showed high homology to recently emerged Australian variants, which were prevalent in local Australian lagomorph populations since 2017. Time-structured and phylogeographic analyses for the S and NS genes revealed a close genetic relationship between the Singapore RHDV strain and the Australian RHDV variants. More thorough epidemiological inquiries are necessary to ascertain how an Australian RHDV was introduced into the Singapore rabbit population, and opportune development of RHDV diagnostics and vaccines will be important to safeguard lagomorphs from future RHDV infection and disease management.
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Affiliation(s)
| | - Jasmine Ong
- Centre for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore Botanic Gardens 259569, Singapore
| | - Yifan Wang
- Centre for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore Botanic Gardens 259569, Singapore
| | - Xinyu Toh
- Centre for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore Botanic Gardens 259569, Singapore
| | - Charlene Judith Fernandez
- Centre for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore Botanic Gardens 259569, Singapore
| | - Taoqi Huangfu
- Centre for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore Botanic Gardens 259569, Singapore
| | | | - Steffie Toh
- Centre for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore Botanic Gardens 259569, Singapore
| | - Kelvin Lim
- Veterinary Health Management, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore Botanic Gardens 259569, Singapore
| | - Wendy Sng
- Veterinary Health Management, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore Botanic Gardens 259569, Singapore
| | - Hwee Ping Lim
- Veterinary Health Management, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore Botanic Gardens 259569, Singapore
| | - Kelvin Ho
- Veterinary Health Management, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore Botanic Gardens 259569, Singapore
| | - Siow Foong Chang
- Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore Botanic Gardens 259569, Singapore
| | - Him Hoo Yap
- Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore Botanic Gardens 259569, Singapore
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Mahar JE, Jenckel M, Huang N, Smertina E, Holmes EC, Strive T, Hall RN. Frequent intergenotypic recombination between the non-structural and structural genes is a major driver of epidemiological fitness in caliciviruses. Virus Evol 2021; 7:veab080. [PMID: 34754513 PMCID: PMC8570162 DOI: 10.1093/ve/veab080] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/14/2021] [Accepted: 09/15/2021] [Indexed: 12/21/2022] Open
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 3 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 2-year period highlights the high frequency of these events, detectable only through intensive surveillance, and demonstrates the importance of recombination in lagovirus evolution.
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Affiliation(s)
- Jackie E Mahar
- Marie Bashir Institute for Infectious Disease and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Maria Jenckel
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Black Mountain, ACT 2601, Australia
| | - Nina Huang
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Black Mountain, ACT 2601, Australia
| | - Elena Smertina
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Black Mountain, ACT 2601, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Disease and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Tanja Strive
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Black Mountain, ACT 2601, Australia
| | - Robyn N Hall
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Black Mountain, ACT 2601, Australia
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Hall RN, King T, O’Connor TW, Read AJ, Vrankovic S, Piper M, Strive T. Passive Immunisation against RHDV2 Induces Protection against Disease but Not Infection. Vaccines (Basel) 2021; 9:vaccines9101197. [PMID: 34696305 PMCID: PMC8537872 DOI: 10.3390/vaccines9101197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/15/2021] [Accepted: 10/15/2021] [Indexed: 11/16/2022] Open
Abstract
Rabbit haemorrhagic disease virus 2 (RHDV2) is a lagovirus in the family Caliciviridae. The closely related Rabbit haemorrhagic disease virus (RHDV, termed RHDV1 throughout this manuscript for clarity) has been used extensively as a biocontrol agent in Australia since the mid-1990s to manage wild rabbit populations, a major economic and environmental pest species. Releasing RHDV1 into populations with a high proportion of rabbits less than 8–10 weeks of age leads to non-lethal infection in many of these young animals, with subsequent seroconversion and long-term immunity against reinfection. In contrast, RHDV2 causes lethal disease even in young rabbits, potentially offering substantial benefits for rabbit management programs over RHDV1. However, it is not clear how acquired resistance from maternal antibodies may influence immunity after RHDV2 infection. In this study, we assessed serological responses after RHDV2 challenge in young rabbits of three different ages (5-, 7-, or 9-weeks-old) that were passively immunised with either high- (titre of 2560 by RHDV IgG ELISA; 2.41 mg/mL total protein) or low- (titre of 160–640 by RHDV IgG ELISA; 1.41 mg/mL total protein) dose RHDV2 IgG to simulate maternal antibodies. All rabbits treated with a high dose and 75% of those treated with a low dose of RHDV2 IgG survived virus challenge. Surviving animals developed robust lagovirus-specific IgA, IgM, and IgG responses within 10 days post infection. These findings demonstrate that the protection against RHDV2 conferred by passive immunisation is not sterilising. Correspondingly, this suggests that the presence of maternal antibodies in wild rabbit populations may impede the effectiveness of RHDV2 as a biocontrol.
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Affiliation(s)
- Robyn N. Hall
- Health & Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT 2601, Australia; (T.K.); (T.S.)
- Centre for Invasive Species Solutions, Bruce, ACT 2617, Australia
- Correspondence: ; Tel.: +61-2-6246-4245
| | - Tegan King
- Health & Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT 2601, Australia; (T.K.); (T.S.)
| | - Tiffany W. O’Connor
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW 2568, Australia (A.J.R.); (S.V.)
| | - Andrew J. Read
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW 2568, Australia (A.J.R.); (S.V.)
| | - Sylvia Vrankovic
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW 2568, Australia (A.J.R.); (S.V.)
| | - Melissa Piper
- Agriculture & Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT 2601, Australia;
| | - Tanja Strive
- Health & Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT 2601, Australia; (T.K.); (T.S.)
- Centre for Invasive Species Solutions, Bruce, ACT 2617, Australia
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Tsoleridis T, Chappell JG, Monchatre-Leroy E, Umhang G, Shi M, Bennett M, Tarlinton RE, McClure CP, Holmes EC, Ball JK. Discovery and Prevalence of Divergent RNA Viruses in European Field Voles and Rabbits. Viruses 2019; 12:E47. [PMID: 31906044 PMCID: PMC7019641 DOI: 10.3390/v12010047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 12/24/2019] [Accepted: 12/27/2019] [Indexed: 12/13/2022] Open
Abstract
The advent of unbiased metagenomic virus discovery has revolutionized studies of virus biodiversity and evolution. Despite this, our knowledge of the virosphere, including in mammalian species, remains limited. We used unbiased metagenomic sequencing to identify RNA viruses in European field voles and rabbits. Accordingly, we identified a number of novel RNA viruses including astrovirus, rotavirus A, picorna-like virus and a morbilli-like paramyxovirus. In addition, we identified a sobemovirus and a novel luteovirus that likely originated from the rabbit diet. These newly discovered viruses were often divergent from those previously described. The novel astrovirus was most closely related to a virus sampled from the rodent-eating European roller bird (Coracias garrulous). PCR screening revealed that the novel morbilli-like paramyxovirus in the UK field vole had a prevalence of approximately 4%, and shared common ancestry with other rodent morbilli-like viruses sampled globally. Two novel rotavirus A sequences were detected in a UK field vole and a French rabbit, the latter with a prevalence of 5%. Finally, a highly divergent picorna-like virus found in the gut of the French rabbit virus was only ~35% similar to an arilivirus at the amino acid level, suggesting the presence of a novel viral genus within the Picornaviridae.
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Affiliation(s)
- Theocharis Tsoleridis
- School of Life Sciences, The University of Nottingham, Nottingham NG7 2UH, UK; (J.G.C.); (C.P.M.)
- Wolfson Centre for Global Virus Infections, The University of Nottingham, Nottingham NG7 2UH, UK
| | - Joseph G. Chappell
- School of Life Sciences, The University of Nottingham, Nottingham NG7 2UH, UK; (J.G.C.); (C.P.M.)
- Wolfson Centre for Global Virus Infections, The University of Nottingham, Nottingham NG7 2UH, UK
| | - Elodie Monchatre-Leroy
- Anses, Laboratoire de la Rage et de la Faune Sauvage, 54220 Malzeville, France; (E.M.-L.); (G.U.)
| | - Gérald Umhang
- Anses, Laboratoire de la Rage et de la Faune Sauvage, 54220 Malzeville, France; (E.M.-L.); (G.U.)
| | - Mang Shi
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (M.S.); (E.C.H.)
| | - Malcolm Bennett
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK; (M.B.); (R.E.T.)
| | - Rachael E. Tarlinton
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK; (M.B.); (R.E.T.)
| | - C. Patrick McClure
- School of Life Sciences, The University of Nottingham, Nottingham NG7 2UH, UK; (J.G.C.); (C.P.M.)
- Wolfson Centre for Global Virus Infections, The University of Nottingham, Nottingham NG7 2UH, UK
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (M.S.); (E.C.H.)
| | - Jonathan K. Ball
- School of Life Sciences, The University of Nottingham, Nottingham NG7 2UH, UK; (J.G.C.); (C.P.M.)
- Wolfson Centre for Global Virus Infections, The University of Nottingham, Nottingham NG7 2UH, UK
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Mahar JE, Hall RN, Shi M, Mourant R, Huang N, Strive T, Holmes EC. The discovery of three new hare lagoviruses reveals unexplored viral diversity in this genus. Virus Evol 2019; 5:vez005. [PMID: 30997155 PMCID: PMC6456799 DOI: 10.1093/ve/vez005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Our knowledge of mammalian viruses has been strongly skewed toward those that cause disease in humans and animals. However, recent metagenomic studies indicate that most apparently healthy organisms carry viruses, and that these seemingly benign viruses may comprise the bulk of virus diversity. The bias toward studying viruses associated with overt disease is apparent in the lagoviruses (family Caliciviridae) that infect rabbits and hares: although most attention has been directed toward the highly pathogenic members of this genus—rabbit haemorrhagic disease virus and European brown hare syndrome virus—a number of benign lagoviruses have also been identified. To determine whether wild European brown hares in Australia might also carry undetected benign viruses, we used a meta-transcriptomics approach to explore the gut and liver RNA viromes of these invasive animals. This led to the discovery of three new lagoviruses. While one was only detected in a single hare, the other two viruses were detected in 20 per cent of all animals tested. All three viruses were most closely related to other hare lagoviruses, but were phylogenetically distinct from both known viruses and from each other, indicating that lagoviruses have circulated for longer than previously assumed. Their evolution was also characterised by complex recombination events. Mapping mutations onto the lagovirus phylogeny revealed no amino acid changes that were consistently associated with virulence phenotype. Overall, our study points to extensive unsampled diversity in this genus, such that additional metagenomic studies are needed to fill gaps in the lagovirus phylogeny and better understand the evolutionary history of this important group of mammalian viruses.
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Affiliation(s)
- Jackie E Mahar
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Robyn N Hall
- CSIRO Health and Biosecurity, Clunies Ross St, Black Mountain, Australian Capital Territory, Australia.,Centre for Invasive Species Solutions, Building 22, University Drive South, University of Canberra, Bruce, Australian Capital Territory, Australia
| | - Mang Shi
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Roslyn Mourant
- CSIRO Health and Biosecurity, Clunies Ross St, Black Mountain, Australian Capital Territory, Australia
| | - Nina Huang
- CSIRO Health and Biosecurity, Clunies Ross St, Black Mountain, Australian Capital Territory, Australia.,Centre for Invasive Species Solutions, Building 22, University Drive South, University of Canberra, Bruce, Australian Capital Territory, Australia
| | - Tanja Strive
- CSIRO Health and Biosecurity, Clunies Ross St, Black Mountain, Australian Capital Territory, Australia.,Centre for Invasive Species Solutions, Building 22, University Drive South, University of Canberra, Bruce, Australian Capital Territory, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
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Desselberger U. Caliciviridae Other Than Noroviruses. Viruses 2019; 11:v11030286. [PMID: 30901945 PMCID: PMC6466229 DOI: 10.3390/v11030286] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 12/24/2022] Open
Abstract
Besides noroviruses, the Caliciviridae family comprises four other accepted genera: Sapovirus, Lagovirus, Vesivirus, and Nebovirus. There are six new genera proposed: Recovirus, Valovirus, Bavovirus, Nacovirus, Minovirus, and Salovirus. All Caliciviridae have closely related genome structures, but are genetically and antigenically highly diverse and infect a wide range of mammalian host species including humans. Recombination in nature is not infrequent for most of the Caliciviridae, contributing to their diversity. Sapovirus infections cause diarrhoea in pigs, humans and other mammalian hosts. Lagovirus infections cause systemic haemorrhagic disease in rabbits and hares, and vesivirus infections lead to lung disease in cats, vesicular disease in swine, and exanthema and diseases of the reproductive system in large sea mammals. Neboviruses are an enteric pathogen of cattle, differing from bovine norovirus. At present, only a few selected caliciviruses can be propagated in cell culture (permanent cell lines or enteroids), and for most of the cultivatable caliciviruses helper virus-free, plasmid only-based reverse genetics systems have been established. The replication cycles of the caliciviruses are similar as far as they have been explored: viruses interact with a multitude of cell surface attachment factors (glycans) and co-receptors (proteins) for adsorption and penetration, use cellular membranes for the formation of replication complexes and have developed mechanisms to circumvent innate immune responses. Vaccines have been developed against lagoviruses and vesiviruses, and are under development against human noroviruses.
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Affiliation(s)
- Ulrich Desselberger
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK.
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9
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Host-Specific Glycans Are Correlated with Susceptibility to Infection by Lagoviruses, but Not with Their Virulence. J Virol 2018; 92:JVI.01759-17. [PMID: 29187537 DOI: 10.1128/jvi.01759-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 11/16/2017] [Indexed: 11/20/2022] Open
Abstract
Rabbit hemorrhagic disease virus (RHDV) and European brown hare syndrome virus (EBHSV) are two lagoviruses from the family Caliciviridae that cause fatal diseases in two leporid genera, Oryctolagus and Lepus, respectively. In the last few years, several examples of host jumps of lagoviruses among leporids were recorded. In addition, a new pathogenic genotype of RHDV emerged, and many nonpathogenic strains of lagoviruses have been described. The molecular mechanisms behind host shifts and the emergence of virulence are unknown. Since RHDV uses glycans of the histo-blood group antigen type as attachment factors to initiate infection, we studied if glycan specificities of the new pathogenic RHDV genotype, nonpathogenic lagoviruses, and EBHSV potentially play a role in determining the host range and virulence of lagoviruses. We observed binding to A, B, or H antigens of the histo-blood group family for all strains known to primarily infect European rabbits (Oryctolagus cuniculus), which have recently been classified as GI strains. However, we could not explain the emergence of virulence, since similar glycan specificities were found in several pathogenic and nonpathogenic strains. In contrast, EBHSV, recently classified as GII.1, bound to terminal β-linked N-acetylglucosamine residues of O-glycans. Expression of these attachment factors in the upper respiratory and digestive tracts in three lagomorph species (Oryctolagus cuniculus, Lepus europaeus, and Sylvilagus floridanus) showed species-specific patterns regarding susceptibility to infection by these viruses, indicating that species-specific glycan expression is likely a major contributor to lagovirus host specificity and range.IMPORTANCE Lagoviruses constitute a genus of the family Caliciviridae comprising highly pathogenic viruses, RHDV and EBHSV, that infect rabbits and hares, respectively. Recently, nonpathogenic strains were discovered and new pathogenic strains have emerged. In addition, host jumps between lagomorphs have been observed. The mechanisms responsible for the emergence of pathogenicity and host species range are unknown. Previous studies showed that RHDV strains attach to glycans expressed in the upper respiratory and digestive tracts of rabbits, the likely portals of virus entry. Here, we studied the glycan-binding properties of novel pathogenic and nonpathogenic strains looking for a link between glycan binding and virulence or between glycan specificity and host range. We found that glycan binding did not correlate with virulence. However, expression of glycan motifs in the upper respiratory and digestive tracts of lagomorphs revealed species-specific patterns associated with the host ranges of the virus strains, suggesting that glycan diversity contributes to lagovirus host ranges.
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