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Abrantes J, Bertagnoli S, Cavadini P, Esteves PJ, Gavier-Widén D, Hall RN, Lavazza A, Le Gall-Reculé G, Mahar JE, Marchandeau S, Lopes AM. Comment on Shah et al. Genetic Characteristics and Phylogeographic Dynamics of Lagoviruses, 1988-2021. Viruses 2023, 15, 815. Viruses 2024; 16:927. [PMID: 38932219 PMCID: PMC11209181 DOI: 10.3390/v16060927] [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: 02/16/2024] [Revised: 05/22/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
Shah and colleagues [...].
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Affiliation(s)
- Joana Abrantes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; (J.A.); (P.J.E.)
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
| | - Stéphane Bertagnoli
- Laboratoire Interactions Hôtes-Agents Pathogènes, Université de Toulouse, INRAE, ENVT, CEDEX 3, 31076 Toulouse, France;
| | - Patrizia Cavadini
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, 25124 Brescia, Italy; (P.C.); (A.L.)
- WOAH Reference Laboratory for Rabbit Haemorrhagic Disease, Via Bianchi 7/9, 25124 Brescia, Italy
| | - Pedro J. Esteves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; (J.A.); (P.J.E.)
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- CITS—Center of Investigation in Health Technologies, CESPU, 4585-116 Gandra, Portugal
| | - Dolores Gavier-Widén
- Swedish Veterinary Agency (SVA), 75189 Uppsala, Sweden;
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), Box 7028, 75007 Uppsala, Sweden
| | - Robyn N. Hall
- Commonwealth Scientific and Industrial Research Organisation, Health and Biosecurity, Canberra, ACT 2601, Australia;
- Centre for Invasive Species Solutions, Bruce, ACT 2617, Australia
- Ausvet Pty Ltd., Canberra, ACT 2617, Australia
| | - Antonio Lavazza
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, 25124 Brescia, Italy; (P.C.); (A.L.)
- WOAH Reference Laboratory for Rabbit Haemorrhagic Disease, Via Bianchi 7/9, 25124 Brescia, Italy
| | - Ghislaine Le Gall-Reculé
- Ploufragan-Plouzané-Niort Laboratory, Avian & Rabbit Virology, Immunology & Parasitology Unit, French Agency for Food, Environmental and Occupational Health and Safety (Anses), 22440 Ploufragan, France;
| | - Jackie E. Mahar
- Commonwealth Scientific and Industrial Research Organisation, Australian Animal Health Laboratory and Health and Biosecurity, Geelong, VIC 3220, Australia;
| | | | - Ana M. Lopes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; (J.A.); (P.J.E.)
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- UMIB—Unit for Multidisciplinary Research in Biomedicine, ICBAS—School of Medicine and Biomedical Sciences, University of Porto, 4050-313 Porto, Portugal
- ITR—Laboratory for Integrative and Translational Research in Population Health, 4050-600 Porto, Portugal
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Tokarz-Deptuła B, Kulus J, Baraniecki Ł, Stosik M, Deptuła W. Characterisation of Lagovirus europaeus GI-RHDVs (Rabbit Haemorrhagic Disease Viruses) in Terms of Their Pathogenicity and Immunogenicity. Int J Mol Sci 2024; 25:5342. [PMID: 38791380 PMCID: PMC11120834 DOI: 10.3390/ijms25105342] [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: 04/03/2024] [Revised: 05/09/2024] [Accepted: 05/12/2024] [Indexed: 05/26/2024] Open
Abstract
Rabbit haemorrhagic disease viruses (RHDV) belong to the family Caliciviridae, genus Lagovirus europaeus, genogroup GI, comprising four genotypes GI.1-GI.4, of which the genotypes GI.1 and GI.2 are pathogenic RHD viruses, while the genotypes GI.3 and GI.4 are non-pathogenic RCV (Rabbit calicivirus) viruses. Among the pathogenic genotypes GI.1 and GI.2 of RHD viruses, an antigenic variant of RHDV, named RHDVa-now GI.1a-RHDVa, was distinguished in 1996; and in 2010, a variant of RHDV-named RHDVb, later RHDV2 and now GI.2-RHDV2/b-was described; and recombinants of these viruses were registered. Pathogenic viruses of the genotype GI.1 were the cause of a disease described in 1984 in China in domestic (Oryctolagus (O.) cuniculus domesticus) and wild (O. cuniculus) rabbits, characterised by a very rapid course and a mortality rate of 90-100%, which spread in countries all over the world and which has been defined since 1989 as rabbit haemorrhagic disease. It is now accepted that GI.1-RHDV, including GI.1a-RHDVa, cause the predetermined primary haemorrhagic disease in domestic and wild rabbits, while GI.2-RHDV2/b cause it not only in rabbits, including domestic rabbits' young up to 4 weeks and rabbits immunised with rabbit haemorrhagic disease vaccine, but also in five various species of wild rabbits and seven different species of hares, as well as wild ruminants: mountain muskoxen and European badger. Among these viruses, haemagglutination-positive, doubtful and harmful viruses have been recorded and described and have been shown to form phylogenogroups, immunotypes, haematotypes and pathotypes, which, together with traits that alter and expand their infectious spectrum (rabbit, hare, wild ruminant, badger and various rabbit and hare species), are the determinants of their pathogenicity (infectivity) and immunogenicity and thus shape their virulence. These relationships are the aim of our consideration in this article.
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Affiliation(s)
| | - Jakub Kulus
- Institute of Veterinary Medicine, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (J.K.); (W.D.)
| | - Łukasz Baraniecki
- Institute of Biology, University of Szczecin, 71-412 Szczecin, Poland;
| | - Michał Stosik
- Institute of Biological Sciences, Faculty of Biological Sciences, University of Zielona Gora, 65-516 Zielona Gora, Poland;
| | - Wiesław Deptuła
- Institute of Veterinary Medicine, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (J.K.); (W.D.)
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3
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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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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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Almeida T, Lopes AM, Estruch J, Rouco C, Cavadini P, Neimanis A, Gavier-Widén D, Le Gall-Reculé G, Velarde R, Abrantes J. A new HaCV-EBHSV recombinant lagovirus circulating in European brown hares (Lepus europaeus) from Catalonia, Spain. Sci Rep 2024; 14:2872. [PMID: 38311618 PMCID: PMC10838927 DOI: 10.1038/s41598-024-53201-1] [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: 05/31/2023] [Accepted: 01/29/2024] [Indexed: 02/06/2024] Open
Abstract
In 2020/2021, several European brown hare syndrome virus (EBHSV) outbreaks were recorded in European hares (Lepus europaeus) from Catalonia, Spain. Recombination analysis combined with phylogenetic reconstruction and estimation of genetic distances of the complete coding sequences revealed that 5 strains were recombinants. The recombination breakpoint is located within the non-structural protein 2C-like RNA helicase (nucleotide position ~ 1889). For the genomic fragment upstream of the breakpoint, a non-pathogenic EBHSV-related strain (hare calicivirus, HaCV; GII.2) was the most closely related sequence; for the rest of the genome, the most similar strains were the European brown hare syndrome virus (EBHSV) strains recovered from the same 2020/2021 outbreaks, suggesting a recent origin. While the functional impact of the atypical recombination breakpoint remains undetermined, the novel recombinant strain was detected in different European brown hare populations from Catalonia, located 20-100 km apart, and seems to have caused a fatal disease both in juvenile and adult animals, confirming its viability and ability to spread and establish infection. This is the first report of a recombination event involving HaCV and EBHSV and, despite the recombination with a non-pathogenic strain, it appears to be associated with mortality in European brown hares, which warrants close monitoring.
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Affiliation(s)
- Tereza Almeida
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Ana M Lopes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- UMIB-Unit for Multidisciplinary Research in Biomedicine, ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- ITR, Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
| | - Josep Estruch
- Wildlife Ecology & Health Group (WE&H) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Carlos Rouco
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - Patrizia Cavadini
- WOAH Reference Laboratory for Rabbit Haemorrhagic Disease, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia, Italy
| | - Aleksija Neimanis
- Department of Pathology and Wildlife Diseases, National Veterinary Institute, 75189, Uppsala, Sweden
| | - Dolores Gavier-Widén
- Swedish Veterinary Agency (SVA), 75189, Uppsala, Sweden
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), Box 7028, 75007, Uppsala, Sweden
| | - Ghislaine Le Gall-Reculé
- Avian and Rabbit Virology, Immunology and Parasitology Unit, Ploufragan-Plouzané-Niort Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (Anses), 22440, Ploufragan, France
| | - Roser Velarde
- Wildlife Ecology & Health Group (WE&H) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Joana Abrantes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002, Porto, Portugal.
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Cavadini P, Trogu T, Velarde R, Lavazza A, Capucci L. Recombination between non-structural and structural genes as a mechanism of selection in lagoviruses: The evolutionary dead-end of an RHDV2 isolated from European hare. Virus Res 2024; 339:199257. [PMID: 38347757 PMCID: PMC10654597 DOI: 10.1016/j.virusres.2023.199257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 02/15/2024]
Abstract
The genus Lagovirus, belonging to the family Caliciviridae, emerged around the 1980s. It includes highly pathogenic species, rabbit hemorrhagic disease virus (RHDV/GI.1) and European brown hare syndrome virus (EBHSV/GII.1), which cause fatal hepatitis, and nonpathogenic viruses with enteric tropism, rabbit calicivirus (RCV/GI.3,4) and hare calicivirus (HaCV/GII.2). Lagoviruses have evolved along two independent genetic lineages: GI (RHDV and RCV) in rabbits and GII (EBHSV and HaCV) in hares. To be emphasized is that genomes of lagoviruses, like other caliciviruses, are highly conserved at RdRp-VP60 junctions, favoring intergenotypic recombination events at this point. The recombination between an RCV (genotype GI.3), donor of non-structural (NS) genes, and an unknown virus, donor of structural (S) genes, likely led to the emergence of a new lagovirus in the European rabbit, called RHDV type 2 (GI.2), identified in Europe in 2010. New RHDV2 intergenotypic recombinants isolated in rabbits in Europe and Australia originated from similar events between RHDV2 (GI.2) and RHDV (GI.1) or RCV (GI.3,4). RHDV2 (GI.2) rapidly spread worldwide, replacing RHDV and showing several lagomorph species as secondary hosts. The recombination events in RHDV2 viruses have led to a number of viruses with very different combinations of NS and S genes. Recombinant RHDV2 with NS genes from hare lineage (GII) was recently identified in the European hare. This study investigated the first RHDV2 (GI.2) identified in Italy in European hare (RHDV2_Bg12), demonstrating that it was a new virus that originated from the recombination between RHDV2, as an S-gene donor and a hare lagovirus, not yet identified but presumably nonpathogenic, as an NS gene donor. When rabbits were inoculated with RHDV2_Bg12, neither deaths nor seroconversions were recorded, demonstrating that RHDV2_Bg12 cannot infect the rabbit. Furthermore, despite intensive and continuous field surveillance, RHDV2_Bg12 has never again been identified in either hares or rabbits in Italy or elsewhere. This result showed that the host specificity of lagoviruses can depend not only on S genes, as expected until today, but potentially also on some species-specific NS gene sequences. Therefore, because RHDV2 (GI.2) infects several lagomorphs, which in turn probably harbor several specific nonpathogenic lagoviruses, the possibility of new speciation, especially in those other than rabbits, is real. RHDV2 Bg_12 demonstrated this, although the attempt apparently failed.
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Affiliation(s)
- Patrizia Cavadini
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna Via Bianchi 9, 25124 Brescia, Italy
| | - Tiziana Trogu
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna Via Bianchi 9, 25124 Brescia, Italy
| | - Roser Velarde
- Wildlife Ecology & Health group (WEH) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Antonio Lavazza
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna Via Bianchi 9, 25124 Brescia, Italy.
| | - Lorenzo Capucci
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna Via Bianchi 9, 25124 Brescia, Italy
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7
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Lopes AM, Abrantes J. On the virome's hidden diversity: lessons from RHDV. mBio 2023; 14:e0197123. [PMID: 37855614 PMCID: PMC10746256 DOI: 10.1128/mbio.01971-23] [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] [Indexed: 10/20/2023] Open
Abstract
Emerging infectious diseases are a major challenge to human and animal health. While predicting the emergence of pathogens is complex, the advent of high-throughput sequencing technologies has allowed the rapid identification of unknown microbiology diversity within organisms. Here, we discuss an example of a metatranscriptomics output to decipher viral evolution.
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Affiliation(s)
- Ana M. Lopes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- UMIB-Unit for Multidisciplinary Research in Biomedicine, ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- ITR-Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
| | - Joana Abrantes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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8
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Peng NYG, Hall RN, Huang N, West P, Cox TE, Mahar JE, Mason H, Campbell S, O’Connor T, Read AJ, Patel KK, Taggart PL, Smith IL, Strive T, Jenckel M. Utilizing Molecular Epidemiology and Citizen Science for the Surveillance of Lagoviruses in Australia. Viruses 2023; 15:2348. [PMID: 38140589 PMCID: PMC10747141 DOI: 10.3390/v15122348] [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: 10/24/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Australia has multiple lagoviruses with differing pathogenicity. The circulation of these viruses was traditionally determined through opportunistic sampling events. In the lead up to the nationwide release of RHDVa-K5 (GI.1aP-GI.1a) in 2017, an existing citizen science program, RabbitScan, was augmented to allow members of the public to submit samples collected from dead leporids for lagovirus testing. This study describes the information obtained from the increased number of leporid samples received between 2015 and 2022 and focuses on the recent epidemiological interactions and evolutionary trajectory of circulating lagoviruses in Australia between October 2020 and December 2022. A total of 2771 samples were tested from January 2015 to December 2022, of which 1643 were lagovirus-positive. Notable changes in the distribution of lagovirus variants were observed, predominantly in Western Australia, where RHDV2-4c (GI.4cP-GI.2) was detected again in 2021 after initially being reported to be present in 2018. Interestingly, we found evidence that the deliberately released RHDVa-K5 was able to establish and circulate in wild rabbit populations in WA. Overall, the incorporation of citizen science approaches proved to be a cost-efficient method to increase the sampling area and enable an in-depth analysis of lagovirus distribution, genetic diversity, and interactions. The maintenance of such programs is essential to enable continued investigations of the critical parameters affecting the biocontrol of feral rabbit populations in Australia, as well as to enable the detection of any potential future incursions.
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Affiliation(s)
- Nias Y. G. Peng
- Commonwealth Scientific and Industrial Research Organisation, Health and Biosecurity, Canberra, ACT 2601, Australia; (N.Y.G.P.); (R.N.H.); (N.H.); (H.M.); (I.L.S.); (T.S.)
| | - Robyn N. Hall
- Commonwealth Scientific and Industrial Research Organisation, Health and Biosecurity, Canberra, ACT 2601, Australia; (N.Y.G.P.); (R.N.H.); (N.H.); (H.M.); (I.L.S.); (T.S.)
- Centre for Invasive Species Solutions, Bruce, ACT 2617, Australia; (P.W.); (A.J.R.); (K.K.P.); (P.L.T.)
- Ausvet Pty Ltd., Canberra, ACT 2617, Australia
| | - Nina Huang
- Commonwealth Scientific and Industrial Research Organisation, Health and Biosecurity, Canberra, ACT 2601, Australia; (N.Y.G.P.); (R.N.H.); (N.H.); (H.M.); (I.L.S.); (T.S.)
| | - Peter West
- Centre for Invasive Species Solutions, Bruce, ACT 2617, Australia; (P.W.); (A.J.R.); (K.K.P.); (P.L.T.)
- Vertebrate Pest Research Unit, NSW Department of Primary Industries, Orange, NSW 2880, Australia;
| | - Tarnya E. Cox
- Vertebrate Pest Research Unit, NSW Department of Primary Industries, Orange, NSW 2880, Australia;
| | - Jackie E. Mahar
- School of Medical Sciences, The University of Sydney, Sydney, NSW 2050, Australia;
- Commonwealth Scientific and Industrial Research Organisation, Australian Animal Health Laboratory and Health and Biosecurity, Geelong, VIC 3220, Australia
| | - Hugh Mason
- Commonwealth Scientific and Industrial Research Organisation, Health and Biosecurity, Canberra, ACT 2601, Australia; (N.Y.G.P.); (R.N.H.); (N.H.); (H.M.); (I.L.S.); (T.S.)
| | - Susan Campbell
- Department of Primary Industries and Regional Development WA, Albany, WA 6630, Australia;
| | - Tiffany O’Connor
- Centre for Invasive Species Solutions, Bruce, ACT 2617, Australia; (P.W.); (A.J.R.); (K.K.P.); (P.L.T.)
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW 2568, Australia
| | - Andrew J. Read
- Centre for Invasive Species Solutions, Bruce, ACT 2617, Australia; (P.W.); (A.J.R.); (K.K.P.); (P.L.T.)
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW 2568, Australia
| | - Kandarp K. Patel
- Centre for Invasive Species Solutions, Bruce, ACT 2617, Australia; (P.W.); (A.J.R.); (K.K.P.); (P.L.T.)
- Invasive Species Unit, Department of Primary Industries and Regions SA, Urrbrae, SA 5064, Australia
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA 5371, Australia
| | - Patrick L. Taggart
- Centre for Invasive Species Solutions, Bruce, ACT 2617, Australia; (P.W.); (A.J.R.); (K.K.P.); (P.L.T.)
- Vertebrate Pest Research Unit, NSW Department of Primary Industries, Queanbeyan, NSW 2620, Australia
| | - Ina L. Smith
- Commonwealth Scientific and Industrial Research Organisation, Health and Biosecurity, Canberra, ACT 2601, Australia; (N.Y.G.P.); (R.N.H.); (N.H.); (H.M.); (I.L.S.); (T.S.)
| | - Tanja Strive
- Commonwealth Scientific and Industrial Research Organisation, Health and Biosecurity, Canberra, ACT 2601, Australia; (N.Y.G.P.); (R.N.H.); (N.H.); (H.M.); (I.L.S.); (T.S.)
- Centre for Invasive Species Solutions, Bruce, ACT 2617, Australia; (P.W.); (A.J.R.); (K.K.P.); (P.L.T.)
| | - Maria Jenckel
- Commonwealth Scientific and Industrial Research Organisation, Health and Biosecurity, Canberra, ACT 2601, Australia; (N.Y.G.P.); (R.N.H.); (N.H.); (H.M.); (I.L.S.); (T.S.)
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9
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Sahraoui L, Lahouassa H, Maziz-Bettahar S, Lopes AM, Almeida T, Ainbaziz H, Abrantes J. First detection and molecular characterization of rabbit hemorrhagic disease virus (RHDV) in Algeria. Front Vet Sci 2023; 10:1235123. [PMID: 37745217 PMCID: PMC10513046 DOI: 10.3389/fvets.2023.1235123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/11/2023] [Indexed: 09/26/2023] Open
Abstract
Since the first detection of rabbit hemorrhagic disease (RHD), the rabbit hemorrhagic disease virus (RHDV) has been responsible for high morbidity and mortality worldwide, both in domestic and in wild rabbits. Despite the apparent control of RHD in rabbitries through vaccination, several studies highlighted the rapid evolution of RHDV by recombination, which may facilitate the emergence of new pathogenic strains. The aim of this study was to confirm the presence and characterize RHDV in Algeria. For this, rabbit samples were collected in the north of Algeria, between 2018 and 2021, from small farms where the virus was suspected after the sudden death of a high number of rabbits, and from healthy hunted wild rabbits. The domestic rabbits revealed clinical signs and lesions that were suggestive of RHD. RT-PCR showed that 79.31% of the domestic rabbit samples were positive for RHDV, while in 20.69%, including the hunted rabbits, the virus was not detected. Phylogenetic analysis of the Algerian strains allowed the confirmation and identification as GI.2 (RHDV2), and showed a close relation to GI.3P-GI.2 recombinant strains, suggesting a potential introduction from other countries, with an older strain potentially originated from neighboring Tunisia, while more recent isolates grouped with strains from North America. Our study reports for the first time the presence of GI.2 (RHDV2) in Algeria with multiple routes of introduction. Consequently, we propose that RHDV control in Algeria should be based on epidemiological surveys in association with an adequate prophylactic program.
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Affiliation(s)
- Lynda Sahraoui
- Laboratory of Animal Health and Production, Higher National Veterinary School of Algiers, Algiers, Algeria
| | - Hichem Lahouassa
- Laboratory of Animal Health and Production, Higher National Veterinary School of Algiers, Algiers, Algeria
| | - Samia Maziz-Bettahar
- Laboratory of Animal Health and Production, Higher National Veterinary School of Algiers, Algiers, Algeria
- Institute of Veterinary Sciences, Saad Dahlab University of Blida1, Blida, Algeria
| | - Ana M. Lopes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- UMIB - Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
| | - Tereza Almeida
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Hacina Ainbaziz
- Laboratory of Animal Health and Production, Higher National Veterinary School of Algiers, Algiers, Algeria
| | - Joana Abrantes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
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10
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Li Y, Du D, Zhou L, Su L, You C, Zhang H, Yu J, Xiao L, Huang J. First report of GI.1aP-GI.2 recombinants of rabbit hemorrhagic disease virus in domestic rabbits in China. Front Microbiol 2023; 14:1188380. [PMID: 37520350 PMCID: PMC10382137 DOI: 10.3389/fmicb.2023.1188380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
The rabbit hemorrhagic disease virus 2 (RHDV2 or GI.2) is a highly contagious agent leading to lethal disease in rabbits. It frequently recombines with other Lagovirus genus, generating epidemical variants with high pathogenicity. In this study, twenty-two liver samples tested positive for GI.2 VP60 gene, were collected in rabbit farms from several geographical regions in China. All GI.2 positive specimens were submitted for RT-PCR detection, nucleotide sequencing and phylogenetic analysis. In addition, suspected GI.2 recombinants were evaluated for virus virulence. The results showed that nine presumptive recombinants were identified by testing for RdRp-VP60 recombination. In these recombinants, four were selected to fully characterize the genome of novel GI.2 recombinant variants, which were described as GI.1aP-GI.2. The nucleotide sequence of these novel variants showed unique recombination pattern and phylogenetic features compared to currently prevalent GI.2 variants. Furthermore, this distinctive recombination of new variant SCNJ-2021 moderately enhanced the virulence of GI.2, even for rabbits vaccinated against parental GI.2. In conclusion, the novel GI.1aP-GI.2 recombinants were identified in rabbit industry in China for the first time, which expanded the knowledge on the phylodynamics and genomic diversity of GI.2 genotype. The rapid molecular evolution and varied pathogenicity of these virus recombinants highlight the urgent need for epidemiological surveillance and for future prevention of these neglected GI.2 variants.
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Affiliation(s)
- Yan Li
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
| | - Deyan Du
- Huapai Biological Group, Chengdu, China
| | - Long Zhou
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
| | - Liyin Su
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
| | - Chengcheng You
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
| | - Huai Zhang
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
| | - Jifeng Yu
- Sichuan Animal Science Academy, Sichuan Provincial Key Laboratory of Animal Breeding and Genetics, Chengdu, China
| | - Lu Xiao
- Sichuan Animal Science Academy, Sichuan Provincial Key Laboratory of Animal Breeding and Genetics, Chengdu, China
| | - Jian Huang
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
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11
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Lopes AM, Almeida T, Diz S, Côrte-Real JV, Osório HC, Ramilo DW, Rebelo MT, da Fonseca IP, Esteves PJ, Alves PC, Santos N, Abrantes J. The potential role of scavenging flies as mechanical vectors of Lagovirus europaeus/GI.2. Virol J 2023; 20:103. [PMID: 37237382 DOI: 10.1186/s12985-023-02065-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
The European rabbit (Oryctolagus cuniculus) populations of the Iberian Peninsula have been severely affected by the emergence of the rabbit haemorrhagic disease virus (RHDV) Lagovirus europaeus/GI.2 (RHDV2/b). Bushflies and blowflies (Muscidae and Calliphoridae families, respectively) are important RHDV vectors in Oceania, but their epidemiological role is unknown in the native range of the European rabbit. In this study, scavenging flies were collected between June 2018 and February 2019 in baited traps at one site in southern Portugal, alongside a longitudinal capture-mark-recapture study of a wild European rabbit population, aiming to provide evidence of mechanical transmission of GI.2 by flies. Fly abundance, particularly from Calliphoridae and Muscidae families, peaked in October 2018 and in February 2019. By employing molecular tools, we were able to detect the presence of GI.2 in flies belonging to the families Calliphoridae, Muscidae, Fanniidae and Drosophilidae. The positive samples were detected during an RHD outbreak and absent in samples collected when no evidence of viral circulation in the local rabbit population was found. We were able to sequence a short viral genomic fragment, confirming its identity as RHDV GI.2. The results suggest that scavenging flies may act as mechanical vectors of GI.2 in the native range of the southwestern Iberian subspecies O. cuniculus algirus. Future studies should better assess their potential in the epidemiology of RHD and as a tool for monitoring viral circulation in the field.
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Affiliation(s)
- Ana M Lopes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Unidade Multidisciplinar de Investigação Biomédica (UMIB), Universidade do Porto, Porto, 4050-313, Portugal
| | - Tereza Almeida
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Sílvia Diz
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - João V Côrte-Real
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002, Porto, Portugal
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig Maximilian University of Munich (LMU) München, Munich, Germany
| | - Hugo C Osório
- Centro de Estudos de Vectores e Doenças Infecciosas, Instituto Nacional de Saúde Doutor Ricardo Jorge, Marateca, Portugal
- Instituto de Saúde Ambiental, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - David W Ramilo
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Trás-s-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
- Faculdade de Medicina Veterinária, Universidade Lusófona, Lisbon, Portugal
| | - Maria Teresa Rebelo
- CESAM - Centre for Environmental and Marine Studies, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Isabel Pereira da Fonseca
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Trás-s-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
| | - Pedro J Esteves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002, Porto, Portugal
- CITS - Center of Investigation in Health Technologies, CESPU, 4585-116, Gandra, Portugal
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002, Porto, Portugal
| | - Nuno Santos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.
| | - Joana Abrantes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002, Porto, Portugal.
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12
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Tanikawa T, Watanabe S, Mikami O, Miyazaki A. Genetics of the rabbit haemorrhagic disease virus strains responsible for rabbit haemorrhagic disease outbreaks in Japan between 2000 and 2020. J Gen Virol 2023; 104. [PMID: 37159399 DOI: 10.1099/jgv.0.001846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Rabbit haemorrhagic disease (RHD) is a highly contagious and fatal disease in rabbits caused by the rabbit haemorrhagic disease virus (RHDV), which includes two genotypes, RHDV-GI.1 and RHDV2-GI.2. RHDVs tend to recombine among different strains, resulting in significant genetic evolution. This study evaluated the genetics of Japanese RHDV strains associated with six outbreaks between 2000 and 2020 using whole-genome sequencing, genomic recombination and phylogenetic analyses. Genomic recombination analysis using near-complete genomic sequences revealed that two Japanese strains detected in 2000 and 2002 were non-recombinant GI.1 (variant RHDVa-GI.1a) strains of different origins, most closely related to strains identified in PR China in 1997 and the USA in 2001, respectively. In contrast, four recent Japanese GI.2 strains detected between 2019 and 2020 were recombinant viruses harbouring structural protein (SP) genes from GI.2 strains and non-SP (NSP) genes from a benign rabbit calicivirus (RCV) strain of genotype RCV-E1-GI.3 (GI.3P-GI.2) or an RHDV G1-GI.1b variant (GI.1bP-GI.2). Phylogenetic analysis based on SP and NSP regions revealed that the GI.1bP-GI.2 recombinant virus detected in Ehime prefecture and the GI.3P-GI.2 recombinant viruses detected in Ibaraki, Tochigi and Chiba prefectures were most closely related to recombinant viruses identified in Australia in 2017 and Germany in 2017, respectively. These results suggested that past RHD outbreaks in Japan did not result from the evolution of domestic RHDVs but rather represented incursions of foreign RHDV strains, implying that Japan is constantly at risk of RHDV incursion from other countries.
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Affiliation(s)
- Taichiro Tanikawa
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Satoko Watanabe
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Osamu Mikami
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Ayako Miyazaki
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
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13
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Shah PT, Bahoussi AN, Yang C, Yao G, Dong L, Wu C, Xing L. Genetic Characteristics and Phylogeographic Dynamics of Lagoviruses, 1988-2021. Viruses 2023; 15:v15040815. [PMID: 37112796 PMCID: PMC10143477 DOI: 10.3390/v15040815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/19/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Rabbit haemorrhagic disease virus (RHDV), European brown hare syndrome virus (EBHSV), rabbit calicivirus (RCV), and hare calicivirus (HaCV) belong to the genus Lagovirus of the Caliciviridae family that causes severe diseases in rabbits and several hare (Lepus) species. Previously, Lagoviruses were classified into two genogroups, e.g., GI (RHDVs and RCVs) and GII (EBHSV and HaCV) based on partial genomes, e.g., VP60 coding sequences. Herein, we provide a robust phylogenetic classification of all the Lagovirus strains based on full-length genomes, grouping all the available 240 strains identified between 1988 and 2021 into four distinct clades, e.g., GI.1 (classical RHDV), GI.2 (RHDV2), HaCV/EBHSV, and RCV, where the GI.1 clade is further classified into four (GI.1a-d) and GI.2 into six sub-clades (GI.2a-f). Moreover, the phylogeographic analysis revealed that the EBHSV and HaCV strains share their ancestor with the GI.1, while the RCV shares with the GI.2. In addition, all 2020-2021 RHDV2 outbreak strains in the USA are connected to the strains from Canada and Germany, while RHDV strains isolated in Australia are connected with the USA-Germany haplotype RHDV strain. Furthermore, we identified six recombination events in the VP60, VP10, and RNA-dependent RNA polymerase (RdRp) coding regions using the full-length genomes. The amino acid variability analysis showed that the variability index exceeded the threshold of 1.00 in the ORF1-encoded polyprotein and ORF2-encoded VP10 protein, respectively, indicating significant amino acid drift with the emergence of new strains. The current study is an update of the phylogenetic and phylogeographic information of Lagoviruses that may be used to map the evolutionary history and provide hints for the genetic basis of their emergence and re-emergence.
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Affiliation(s)
- Pir Tariq Shah
- Institutes of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China
| | - Amina Nawal Bahoussi
- Institutes of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China
| | - Caiting Yang
- Institutes of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China
| | - Guanhan Yao
- Department of Molecular Genetics and Development, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Li Dong
- Institutes of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China
- Shanxi Provincial Key Laboratory for Prevention and Treatment of Major Infectious Diseases, 92 Wucheng Road, Taiyuan 030006, China
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Changxin Wu
- Institutes of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China
- Shanxi Provincial Key Laboratory for Prevention and Treatment of Major Infectious Diseases, 92 Wucheng Road, Taiyuan 030006, China
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Li Xing
- Institutes of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China
- Shanxi Provincial Key Laboratory for Prevention and Treatment of Major Infectious Diseases, 92 Wucheng Road, Taiyuan 030006, China
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
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14
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Bębnowska D, Hrynkiewicz R, Korona-Głowniak I, Niedźwiedzka-Rystwej P. Immune response in the recombinant strain of Lagovirus europaeus GI.1a. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 110:105427. [PMID: 36958414 DOI: 10.1016/j.meegid.2023.105427] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/09/2023] [Accepted: 03/20/2023] [Indexed: 03/25/2023]
Abstract
Lagovirus europaeus/GI.1 is the virus that causes severe and dangerous rabbit haemorrhagic disease (RHD) in rabbits. Recombination formation in RHD viruses is common. Recombination is thought to play a key role in the evolution of lagoviruses and therefore most likely influences the pathogenicity of L. europaeus/GI strains. Immunological events also play a key role in the control of RHD, and an in-depth knowledge of these phenomena provides insights into the characteristics of the infection, which can help implement appropriate infection control measures. To obtain a more complete picture of RHD caused by different GI.1 strains, it is necessary to correlate the genetic diversity within L. europaeus/GI.1 strains and the immune picture in response to infection. We performed a phylogenetic analysis of the L. europaeus/GI strains and compared the recombinant L. europaeus/GI.1 strain with the GI.1a strain on the basis of a thorough statistical analysis of immunological traits performed previously. Our phylogenetic analysis based on the sequence of the gene encoding the VP60 capsid protein of 34 strains of Lagovirus europaeus showed that the Hartmannsdorf strain forms a separate clade from the other GI.1a strains and is separate from the GI.1b-d strains. Next, we showed significant differences in the levels of individual parameters for non-specific cellular and humoral immunity in infection with the GI.1a strain and the Hartmannsdorf recombinant strain. Against the background of this study, our results indicate that the characteristics of each recombinant should be considered individually.
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Affiliation(s)
| | - Rafał Hrynkiewicz
- Institute of Biology, University of Szczecin, 71-412 Szczecin, Poland
| | - Izabela Korona-Głowniak
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Lublin,1 Chodźki Str., 20-093 Lublin, Poland
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15
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Jammes M, Urbino C, Diouf MB, Peterschmitt M. Refining the emergence scenario of the invasive recombinant Tomato yellow leaf curl virus -IS76. Virology 2023; 578:71-80. [PMID: 36473279 DOI: 10.1016/j.virol.2022.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/02/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022]
Abstract
TYLCV-IS76, a unique recombinant between tomato yellow leaf curl virus (TYLCV) and tomato yellow leaf curl Sardinia virus (TYLCSV), has replaced its parental viruses in southern Morocco. To refine its emergence scenario, its fitness was monitored experimentally in conditions aiming at reproducing natural situations, i.e. superinfection of plants already infected with parental viruses and competition with other TYLCV/TYLCSV recombinants (LSRec) automatically generated in plants coinfected with TYLCV and TYLCSV. TYLCV-IS76 accumulated significantly more than parental viruses regardless of plant age and superinfection delay. Although TYLCV-IS76 and LSRec both accumulated more than parental viruses in laboratory conditions, LSRec were displaced by TYLCV-IS76 in nature like parental viruses were. TYLCV-IS76 did not exhibit any vector transmission advantage over LSRec and TYLCV the most competitive parental virus. Thus, it is apparently only in the plant compartment that the recombination event that generated TYLCV-IS76, induced the competitiveness advantage by which the last became first.
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Affiliation(s)
- Margaux Jammes
- CIRAD, UMR PHIM, F-34398, Montpellier, France; PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Cica Urbino
- CIRAD, UMR PHIM, F-34398, Montpellier, France; PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Mame Boucar Diouf
- CIRAD, UMR PHIM, F-34398, Montpellier, France; PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Michel Peterschmitt
- CIRAD, UMR PHIM, F-34398, Montpellier, France; PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France.
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16
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Confirmation of the Rabbit Hemorrhagic Disease Virus Type 2 (GI.2) Circulation in North Africa. ACTA VET-BEOGRAD 2022. [DOI: 10.2478/acve-2022-0035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Abstract
Rabbit hemorrhagic disease (RHD) is a highly contagious viral disease that causes fatal acute hepatitis in domestic and wild lagomorphs. It has taken on major economic importance in countries like Morocco. In addition to the classical virus (RHDV), a novel emerged genotype (RHDV2) is circulating, especially in the north shore of the Mediterranean basin since 2010. Many small animal farmers reported clinical cases from several rabbitries in Agadir (Morocco) despite systematic vaccination against the RHDV. The main objective was to characterize the current RHDV strains circulating in the studied area to help to choose an adequate vaccine. For that, we extracted viral RNA from rabbit livers, carried out the PCR analyses, and we sequenced the viral structural capsid protein (VP60) of the RHDV. The phylogenetic analysis results allowed us to state that the novel genotype (RHDV2) is circulating in the studied geographical area, and to characterize the isolated sequences. As a conclusion, we recommend updating RHD epidemiological relating data and reviewing the vaccine protocols by both targeting RHDV (GI.1) and RHDV2 (GI.2) in any future preventive program.
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17
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The pathogenicity comparison of Lagovirus europaeus GI.1 and GI.2 strains in China by using relative quantitative assay. Sci Rep 2022; 12:20518. [PMID: 36443356 PMCID: PMC9705280 DOI: 10.1038/s41598-022-25118-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Lagovirus europaeus GI.1 belongs to Lagovirus in the Caliciviridae family. GI.1 causes an acute, septic, and highly lethal disease in rabbits. Lagovirus europaeus GI.2, a new variant of GI.1, has caused explosive mortality in rabbits of all ages in Sichuan Province, China. To explore the differences in pathogenicity of rabbits infected with GI.1/GI.2, we investigated the virulence and disease progression of a naturally occurring GI.1/GI.2 in 4-week-old, 13-week-old, and 25-week-old New Zealand White laboratory rabbits after GI.1/GI.2 infection. Objective measures of disease progression were recorded using continuous body-temperature monitoring. We observed the kittens were infected with GI.2 during the most urgent course of the disease, and GI.1 was not lethal to kittens. We found that the target organ of both GI.1 and GI.2 was the liver, but the disease course of the two viruses was differed. Our study enriches the research on the pathogenicity of GI.1 and GI.2 under the same conditions.
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18
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Perera KD, Johnson D, Lovell S, Groutas WC, Chang KO, Kim Y. Potent Protease Inhibitors of Highly Pathogenic Lagoviruses: Rabbit Hemorrhagic Disease Virus and European Brown Hare Syndrome Virus. Microbiol Spectr 2022; 10:e0014222. [PMID: 35766511 PMCID: PMC9430360 DOI: 10.1128/spectrum.00142-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/03/2022] [Indexed: 11/20/2022] Open
Abstract
Rabbit hemorrhagic disease (RHD) and European brown hare syndrome (EBHS) are highly contagious diseases caused by lagoviruses in the Caliciviridae family. These infectious diseases are associated with high mortality and a serious threat to domesticated and wild rabbits and hares, including endangered species such as riparian brush rabbits (Sylvilagus bachmani riparius). In the United States (U.S.), only isolated cases of RHD had been reported until Spring 2020. However, RHD caused by GI.2/rabbit hemorrhagic disease virus (RHDV)2/b was unexpectedly reported in April 2020 in New Mexico and has subsequently spread to several U.S. states, infecting wild rabbits and hares and making it highly likely that RHD will become endemic in the U.S. Vaccines are available for RHD; however, there is no specific treatment for this disease. Lagoviruses encode a 3C-like protease (3CLpro), which is essential for virus replication and a promising target for antiviral drug development. We have previously generated focused small-molecule libraries of 3CLpro inhibitors and demonstrated the in vitro potency and in vivo efficacy of some protease inhibitors against viruses encoding 3CLpro, including caliciviruses and coronaviruses. Here, we report the development of the enzyme and cell-based assays for the 3CLpro of GI.1c/RHDV, recombinant GI.3P-GI.2 (RHDV2/b), and GII.1/European brown hare syndrome virus (EBHSV) as well as the identification of potent lagovirus 3CLpro inhibitors, including GC376, a protease inhibitor being developed for feline infectious peritonitis. In addition, structure-activity relationship study and homology modeling of the 3CLpro and inhibitors revealed that lagovirus 3CLpro share similar structural requirements for inhibition with other calicivirus 3CLpro. IMPORTANCE Rabbit hemorrhagic disease (RHD) and European brown hare syndrome (EBHS) are viral diseases that affect lagomorphs with significant economic and ecological impacts. RHD vaccines are available, but specific antiviral treatment for these viral infections would be a valuable addition to the current control measures. Lagoviruses encode 3C-like protease (3CLpro), which is essential for virus replication and an attractive target for antiviral drug discovery. We have screened and identified potent small-molecule inhibitors that block lagovirus 3CLpro in the enzyme- and cell-based assays. Our results suggest that these compounds have the potential for further development as antiviral drugs for lagoviruses.
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Affiliation(s)
- Krishani Dinali Perera
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - David Johnson
- Computational Chemical Biology Core, The University of Kansas, Lawrence, Kansas, USA
| | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas, USA
| | - William C. Groutas
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
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19
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Chen M, Fan Z, Hu B, Song Y, Wei H, Qiu R, Zhu W, Xu W, Wang F. Pathogenicity of the newly emerged Lagovirus europaeus GI.2 strain in China in experimentally infected rabbits. Vet Microbiol 2021; 265:109311. [PMID: 34965497 DOI: 10.1016/j.vetmic.2021.109311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/18/2021] [Accepted: 12/19/2021] [Indexed: 11/19/2022]
Abstract
In April 2020, rabbit hemorrhagic virus type 2 (Lagovirus europaeus GI.2), which causes highly infectious fatal rabbit hemorrhagic disease, was emerged in China. The phylogenetic analyses of the complete genome sequence of GI.2 showed that it belonged to the non-recombinant GI.3/GI.2 genotype. However, the pathogenicity of this GI.2 strain differed from that of early typical GI.2 strains in Europe. To prevent the spread of the new strain in China, its pathogenicity urgently needs to be studied. Thus, viral shedding and distribution as well as clinical symptoms, histopathological changes, and serum cytokines were studied in experimentally GI.2/SC2020-infected rabbit adults and kits. The kit group showed a shorter survival time after the challenge than the adult group did. The mortality rate was higher in the kits (80 %) than in the adults (30 %). Viral RNA could be detected in both nasal and fecal swabs, and the main dissemination route appeared to be the fecal route. Viral RNA rapidly increased in the blood of the adults and kits at 6 h post-infection, indicating that blood viral load testing can be used for early diagnosis. The most affected organs were the liver and spleen, and the lesions were more severe in the kits than in the adults. The liver contained the highest viral RNA levels. Moreover, serum interleukin (IL)-6, IL-8, IL-10, and tumor necrosis factor-alpha levels were increased in the infected rabbits. In conclusion, our findings will help to understand the evolutionary trends and pathogenic characteristics of GI.2 strains in China.
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Affiliation(s)
- Mengmeng Chen
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biologicals Engineering and Technology, Ministry of Agriculture, National Center for Engineering Research of Veterinary Bio-products, Nanjing, China
| | - Zhiyu Fan
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biologicals Engineering and Technology, Ministry of Agriculture, National Center for Engineering Research of Veterinary Bio-products, Nanjing, China
| | - Bo Hu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biologicals Engineering and Technology, Ministry of Agriculture, National Center for Engineering Research of Veterinary Bio-products, Nanjing, China
| | - Yanhua Song
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biologicals Engineering and Technology, Ministry of Agriculture, National Center for Engineering Research of Veterinary Bio-products, Nanjing, China
| | - Houjun Wei
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biologicals Engineering and Technology, Ministry of Agriculture, National Center for Engineering Research of Veterinary Bio-products, Nanjing, China
| | - Rulong Qiu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biologicals Engineering and Technology, Ministry of Agriculture, National Center for Engineering Research of Veterinary Bio-products, Nanjing, China
| | - Weifeng Zhu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biologicals Engineering and Technology, Ministry of Agriculture, National Center for Engineering Research of Veterinary Bio-products, Nanjing, China
| | - Weizhong Xu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biologicals Engineering and Technology, Ministry of Agriculture, National Center for Engineering Research of Veterinary Bio-products, Nanjing, China
| | - Fang Wang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biologicals Engineering and Technology, Ministry of Agriculture, National Center for Engineering Research of Veterinary Bio-products, Nanjing, China.
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20
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Arhab Y, Miścicka A, Pestova TV, Hellen CUT. Horizontal gene transfer as a mechanism for the promiscuous acquisition of distinct classes of IRES by avian caliciviruses. Nucleic Acids Res 2021; 50:1052-1068. [PMID: 34928389 PMCID: PMC8789048 DOI: 10.1093/nar/gkab1243] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 11/17/2021] [Accepted: 12/15/2021] [Indexed: 02/05/2023] Open
Abstract
In contrast to members of Picornaviridae which have long 5'-untranslated regions (5'UTRs) containing internal ribosomal entry sites (IRESs) that form five distinct classes, members of Caliciviridae typically have short 5'UTRs and initiation of translation on them is mediated by interaction of the viral 5'-terminal genome-linked protein (VPg) with subunits of eIF4F rather than by an IRES. The recent description of calicivirus genomes with 500-900nt long 5'UTRs was therefore unexpected and prompted us to examine them in detail. Sequence analysis and structural modelling of the atypically long 5'UTRs of Caliciviridae sp. isolate yc-13 and six other caliciviruses suggested that they contain picornavirus-like type 2 IRESs, whereas ruddy turnstone calicivirus (RTCV) and Caliciviridae sp. isolate hwf182cal1 calicivirus contain type 4 and type 5 IRESs, respectively. The suggestion that initiation on RTCV mRNA occurs by the type 4 IRES mechanism was confirmed experimentally using in vitro reconstitution. The high sequence identity between identified calicivirus IRESs and specific picornavirus IRESs suggests a common evolutionary origin. These calicivirus IRESs occur in a single phylogenetic branch of Caliciviridae and were likely acquired by horizontal gene transfer.
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Affiliation(s)
- Yani Arhab
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn NY 11203, USA
| | - Anna Miścicka
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn NY 11203, USA
| | - Tatyana V Pestova
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn NY 11203, USA
| | - Christopher U T Hellen
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn NY 11203, USA
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21
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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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22
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Mohamed F, Gidlewski T, Berninger ML, Petrowski HM, Bracht AJ, de Rueda CB, Barrette RW, Grady M, O'Hearn ES, Lewis CE, Moran KE, Sturgill TL, Capucci L, Root JJ. Comparative susceptibility of eastern cottontails and New Zealand white rabbits to classical rabbit haemorrhagic disease virus (RHDV) and RHDV2. Transbound Emerg Dis 2021; 69:e968-e978. [PMID: 34738741 DOI: 10.1111/tbed.14381] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/22/2021] [Accepted: 10/27/2021] [Indexed: 12/20/2022]
Abstract
Rabbit haemorrhagic disease virus (RHDV) is associated with high morbidity and mortality in the European rabbit (Oryctolagus cuniculus). In 2010, a genetically distinct RHDV named RHDV2 emerged in Europe and spread to many other regions, including North America in 2016. Prior to this study it was unknown if eastern cottontails (ECT(s); Sylvilagus floridanus), one of the most common wild lagomorphs in the United States, were susceptible to RHDV2. In this study, 10 wild-caught ECTs and 10 New Zealand white rabbits (NZWR(s); O. cuniculus) were each inoculated orally with either RHDV (RHDVa/GI.1a; n = 5 per species) or RHDV2 (a recombinant GI.1bP-GI.2; n = 5 per species) and monitored for the development of disease. Three of the five ECTs that were infected with RHDV2 developed disease consistent with RHD and died at 4 and 6 days post-inoculation (DPI). The RHDV major capsid protein/antigen (VP60) was detected in the livers of three ECTs infected with RHDV2, but none was detected in the ECTs infected with RHDV. Additionally, RHD viral RNA was detected in the liver, spleen, intestine and blood of ECTs infected with RHDV2, but not in the ECTs infected with RHDV. RHD viral RNA was detected in urine, oral swabs and rectal swabs in at least two of five ECTs infected with RHDV2. One ECT inoculated with RHDV2 seroconverted and developed a high antibody titre by the end of the experimental period (21 DPI). ECTs inoculated with the classic RHDV did not seroconvert. In comparison, NZWRs inoculated with RHDV2 exhibited high mortality (five of five) at 2 DPI and four of five NZWRs inoculated with RHDV either died or were euthanized at 2 DPI indicating both of these viruses were highly pathogenic to this species. This experiment indicates that ECTs are susceptible to RHDV2 and can shed viral RNA, thereby suggesting this species could be involved in the epidemiology of this virus.
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Affiliation(s)
- Fawzi Mohamed
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Foreign Animal Disease Diagnostic Laboratory, Plum Island Animal Disease Center, Greenport, New York, USA
| | - Thomas Gidlewski
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Disease Program, Fort Collins, Colorado, USA
| | - Mary L Berninger
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Foreign Animal Disease Diagnostic Laboratory, Plum Island Animal Disease Center, Greenport, New York, USA
| | - Heather M Petrowski
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Foreign Animal Disease Diagnostic Laboratory, Plum Island Animal Disease Center, Greenport, New York, USA
| | - Alexa J Bracht
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Foreign Animal Disease Diagnostic Laboratory, Plum Island Animal Disease Center, Greenport, New York, USA
| | - Carla Bravo de Rueda
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Foreign Animal Disease Diagnostic Laboratory, Plum Island Animal Disease Center, Greenport, New York, USA
| | - Roger W Barrette
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Foreign Animal Disease Diagnostic Laboratory, Plum Island Animal Disease Center, Greenport, New York, USA
| | - Meredith Grady
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Disease Program, Fort Collins, Colorado, USA
| | - Emily S O'Hearn
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Foreign Animal Disease Diagnostic Laboratory, Plum Island Animal Disease Center, Greenport, New York, USA
| | - Charles E Lewis
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Foreign Animal Disease Diagnostic Laboratory, Plum Island Animal Disease Center, Greenport, New York, USA
| | - Karen E Moran
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Foreign Animal Disease Diagnostic Laboratory, Plum Island Animal Disease Center, Greenport, New York, USA
| | - Tracy L Sturgill
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, Regionalization Evaluation Services, Raleigh, North Carolina, USA
| | - Lorenzo Capucci
- Istituto Zooprofilattico Sperimenatale della Lombardia e dell'Emilia Romagna and OIE Reference Laboratory for Rabbit Hemorrhagic Disease, Brescia, Italy
| | - J Jeffrey Root
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, Colorado, USA
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23
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Ben Chehida F, Lopes AM, Côrte-Real JV, Sghaier S, Aouini R, Messadi L, Abrantes J. Multiple Introductions of Rabbit Hemorrhagic Disease Virus Lagovirus europaeus/GI.2 in Africa. BIOLOGY 2021; 10:883. [PMID: 34571760 PMCID: PMC8471427 DOI: 10.3390/biology10090883] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022]
Abstract
Rabbit hemorrhagic disease (RHD) causes high mortality and morbidity in European rabbits (Oryctolagus cuniculus). In Africa, the presence of the causative agent, the rabbit hemorrhagic disease virus (RHDV), was first confirmed in 1992 (genotype Lagovirus europaeus/GI.1). In 2015, the new genotype Lagovirus europaeus/GI.2 (RHDV2/b) was detected in Tunisia. Currently, GI.2 strains are present in several North and Sub-Saharan African countries. Considerable economic losses have been observed in industrial and traditional African rabbitries due to RHDV. Like other RNA viruses, this virus presents high recombination rates, with the emergence of GI.2 being associated with a recombinant strain. Recombination events have been detected with both pathogenic (GI.1b and GII.1) and benign (GI.3 and GI.4) strains. We obtained complete genome sequences of Tunisian GI.2 strains collected between 2018 and 2020 and carried out phylogenetic analyses. The results revealed that Tunisian strains are GI.3P-GI.2 strains that were most likely introduced from Europe. In addition, the results support the occurrence of multiple introductions of GI.2 into Africa, stressing the need for characterizing complete genome sequences of the circulating lagoviruses to uncover their origin. Continued monitoring and control of rabbit trade will grant a better containment of the disease and reduce the disease-associated economic losses.
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Affiliation(s)
- Faten Ben Chehida
- Laboratory of Microbiology, Immunology and General Pathology, Institution of Agricultural Research and Higher Education, National School of Veterinary Medicine of Sidi Thabet, University of Manouba, Sidi Thabet 2020, Tunisia; (F.B.C.); (R.A.); (L.M.)
| | - Ana M. Lopes
- CIBIO/InBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal; (A.M.L.); (J.V.C.-R.)
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Unidade Multidisciplinar de Investigação Biomédica (UMIB), Universidade do Porto, 4050-313 Porto, Portugal
| | - João V. Côrte-Real
- CIBIO/InBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal; (A.M.L.); (J.V.C.-R.)
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
| | - Soufien Sghaier
- Department of Virology, Institution of Agricultural Research and Higher Education, Tunisian Institute of Veterinary Research (IRVT), University of Tunis El Manar, Tunis 1006, Tunisia;
| | - Rim Aouini
- Laboratory of Microbiology, Immunology and General Pathology, Institution of Agricultural Research and Higher Education, National School of Veterinary Medicine of Sidi Thabet, University of Manouba, Sidi Thabet 2020, Tunisia; (F.B.C.); (R.A.); (L.M.)
| | - Lilia Messadi
- Laboratory of Microbiology, Immunology and General Pathology, Institution of Agricultural Research and Higher Education, National School of Veterinary Medicine of Sidi Thabet, University of Manouba, Sidi Thabet 2020, Tunisia; (F.B.C.); (R.A.); (L.M.)
| | - Joana Abrantes
- CIBIO/InBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal; (A.M.L.); (J.V.C.-R.)
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
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24
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Asin J, Rejmanek D, Clifford DL, Mikolon AB, Henderson EE, Nyaoke AC, Macías-Rioseco M, Streitenberger N, Beingesser J, Woods LW, Lavazza A, Capucci L, Crossley B, Uzal FA. Early circulation of rabbit haemorrhagic disease virus type 2 in domestic and wild lagomorphs in southern California, USA (2020-2021). Transbound Emerg Dis 2021; 69:e394-e405. [PMID: 34487612 DOI: 10.1111/tbed.14315] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/29/2021] [Accepted: 09/05/2021] [Indexed: 11/28/2022]
Abstract
Rabbit haemorrhagic disease virus type 2 (RHDV2) causes a severe systemic disease with hepatic necrosis. Differently from classic RHDV, which affects only European rabbits (Oryctolagus cuniculus), RHDV2 can affect many leporid species, including hares (Lepus spp.) and cottontail rabbits (Sylvilagus spp.). RHDV2 emerged in Europe in 2010 and spread worldwide. During the last 5 years, there have been multiple outbreaks in North America since the first known event in 2016 in Quebec, Canada, including several detections in British Columbia, Canada, between 2018 and 2019, Washington State and Ohio, USA, in 2018 and 2019, and New York, USA, in 2020. However, the most widespread outbreak commenced in March 2020 in the southwestern USA and Mexico. In California, RHDV2 spread widely across several southern counties between 2020 and 2021, and the aim of this study was to report and characterize these early events of viral incursion and circulation within the state. Domestic and wild lagomorphs (n = 81) collected between August 2020 and February 2021 in California with a suspicion of RHDV2 infection were tested by reverse transcription quantitative real-time PCR on the liver, and histology and immunohistochemistry for pan-lagovirus were performed on liver sections. In addition, whole genome sequencing from 12 cases was performed. During this period, 33/81 lagomorphs including 24/59 domestic rabbits (O. cuniculus), 3/16 desert cottontail rabbits (Sylvilagus audubonii), and 6/6 black-tailed jackrabbits (Lepus californicus) tested positive. All RHDV2-positive animals had hepatic necrosis typical of pathogenic lagovirus infection, and the antigen was detected in sections from individuals of the three species. The 12 California sequences were closely related (98.9%-99.95%) to each other, and also very similar (99.0%-99.4%) to sequences obtained in other southwestern states during the 2020-2021 outbreak; however, they were less similar to strains obtained in New York in 2020 (96.7%-96.9%) and Quebec in 2016 (92.4%-92.6%), suggesting that those events could be related to different viral incursions. The California sequences were more similar (98.6%-98.7%) to a strain collected in British Columbia in 2018, which suggests that that event could have been related to the 2020 outbreak in the southwestern USA.
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Affiliation(s)
- Javier Asin
- California Animal Health and Food Safety Laboratory System, San Bernardino branch, University of California-Davis, San Bernardino, California, USA
| | - Daniel Rejmanek
- California Animal Health and Food Safety Laboratory System, Davis branch, University of California-Davis, Davis, California, USA
| | - Deana L Clifford
- Wildlife Health Laboratory, California Department of Fish and Wildlife, Rancho Cordova, California, USA
| | - Andrea B Mikolon
- California Department of Food and Agriculture, Sacramento, California, USA
| | - Eileen E Henderson
- California Animal Health and Food Safety Laboratory System, San Bernardino branch, University of California-Davis, San Bernardino, California, USA
| | - Akinyi C Nyaoke
- California Animal Health and Food Safety Laboratory System, San Bernardino branch, University of California-Davis, San Bernardino, California, USA
| | - Melissa Macías-Rioseco
- California Animal Health and Food Safety Laboratory System, Tulare branch, University of California-Davis, Tulare, California, USA
| | - Nicolas Streitenberger
- California Animal Health and Food Safety Laboratory System, San Bernardino branch, University of California-Davis, San Bernardino, California, USA
| | - Juliann Beingesser
- California Animal Health and Food Safety Laboratory System, San Bernardino branch, University of California-Davis, San Bernardino, California, USA
| | - Leslie W Woods
- California Animal Health and Food Safety Laboratory System, Davis branch, University of California-Davis, Davis, California, USA
| | - Antonio Lavazza
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna and OIE Reference Laboratory for Rabbit Hemorrhagic Disease, Brescia, Italy
| | - Lorenzo Capucci
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna and OIE Reference Laboratory for Rabbit Hemorrhagic Disease, Brescia, Italy
| | - Beate Crossley
- California Animal Health and Food Safety Laboratory System, Davis branch, University of California-Davis, Davis, California, USA
| | - Francisco A Uzal
- California Animal Health and Food Safety Laboratory System, San Bernardino branch, University of California-Davis, San Bernardino, California, USA
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25
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Velarde R, Abrantes J, Lopes AM, Estruch J, Côrte-Real JV, Esteves PJ, García-Bocanegra I, Ruiz-Olmo J, Rouco C. Spillover event of recombinant Lagovirus europaeus/GI.2 into the Iberian hare (Lepus granatensis) in Spain. Transbound Emerg Dis 2021; 68:3187-3193. [PMID: 34324796 DOI: 10.1111/tbed.14264] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 12/13/2022]
Abstract
Viruses that affect lagomorphs have decades of reported history of spillover events. One of these viruses is the causative agent of the so-called rabbit or 'lagomorph' haemorrhagic disease (e.g. Lagovirus europaeus/GI.1 and L. europaeus/GI.2). In particular, L. europaeus/GI.2 has shown a great capacity to recombine with existing lagoviruses. In fact, it has replaced the former GI.1 genotype in the wild, and recently, an increase on spillover events has been detected among several lagomorph species including European and North American species of hares. In this study, we report for the first time the infection of a wild Iberian hare with GI.2 (RHDV2/b), potential shedding and associated histopathological alterations. We identify the recombinant GI.4P-GI.2 as causative of the infection and discuss plausible causes regarding the origin of the spillover event and its potential consequences for the Iberian hare wild populations, which is an endemic species of the Iberian Peninsula as well as an important game and prey species for many predators, including endangered species.
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Affiliation(s)
- Roser Velarde
- Wildlife Ecology & Health group (WEH) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Joana Abrantes
- Research Centre in Biodiversity and Genetic Resources (CIBIO), Research Network in Biodiversity and Evolutionary Biology (InBIO), University of Porto, Vairao, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Ana M Lopes
- Research Centre in Biodiversity and Genetic Resources (CIBIO), Research Network in Biodiversity and Evolutionary Biology (InBIO), University of Porto, Vairao, Portugal.,Instituto de Ciências Biomédicas Abel Salazar (ICBAS)/Unidade Multidisciplinar de Investigação Biomédica (UMIB), Universidade do Porto, Porto, Portugal
| | - Josep Estruch
- Wildlife Ecology & Health group (WEH) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - João V Côrte-Real
- Research Centre in Biodiversity and Genetic Resources (CIBIO), Research Network in Biodiversity and Evolutionary Biology (InBIO), University of Porto, Vairao, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Pedro J Esteves
- Research Centre in Biodiversity and Genetic Resources (CIBIO), Research Network in Biodiversity and Evolutionary Biology (InBIO), University of Porto, Vairao, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Ignacio García-Bocanegra
- Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), Departamento de Sanidad Animal, Universidad de Córdoba, Córdoba, Spain
| | - Jordi Ruiz-Olmo
- Departament d'Agricultura, Ramaderia, Pesca i Alimentació de la Generalitat de Catalunya, Barcelona, Spain
| | - Carlos Rouco
- Departmento de Botánica, Ecología y Fisiología Vegetal, Universdad de Córdoba, Cordoba, Spain.,Sociedad, Ecología y Gestión del Medio Ambiente, UCO-IESA, Unidad Asociada al CSIC, Córdoba, Spain
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26
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Droillard C, Lemaitre E, Amelot M, Blanchard Y, Keita A, Eterradossi N, Le Gall-Reculé G. Rabbit haemorrhagic disease virus Lagovirus europaeus/GI.1d strain: genome sequencing, in vivo virus replication kinetics, and viral dose effect. BMC Vet Res 2021; 17:257. [PMID: 34321003 PMCID: PMC8320185 DOI: 10.1186/s12917-021-02962-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rabbit haemorrhagic disease virus Lagovirus europaeus/GI.1d variant (GI.1d/RHDV) was identified in 1990 in France, and until the emergence of the new genotype GI.2, it was the main variant circulating in the country. The early stages of RHDV infection have been described in a few studies of rabbits experimentally infected with earlier strains, but no information was given on the minimum infective dose. We report the genomic and phenotypic characterisation of a GI.1d/RHDV strain collected in 2000 in France (GI.1d/00-21). RESULTS We performed in vivo assays in rabbits to study virus replication kinetics in several tissues at the early stage of infection, and to estimate the minimum infective dose. Four tested doses, negligible (10- 1 viral genome copies), low (104), high (107) and very high (1011) were quantified using a method combining density gradient centrifugation of the viral particles and an RT-qPCR technique developed to quantify genomic RNA (gRNA). The GI.1d/00-21 genome showed the same genomic organisation as other lagoviruses; however, a substitution in the 5' untranslated region and a change in the potential p23/2C-like helicase cleavage site were observed. We showed that the liver of one of the two rabbits inoculated via the oral route was infected at 16 h post-infection and all tissues at 39 h post-infection. GI.1d/00-21 induced classical RHD signs (depression) and lesions (haemorrhage and splenomegaly). Although infective dose estimation should be interpreted with caution, the minimum infective dose that infected an inoculated rabbit was lower or equal to 104 gRNA copies, whereas between 104 and 107 gRNA copies were required to also induce mortality. CONCLUSIONS These results provide a better understanding of GI.1d/RHDV infection in rabbits. The genome analysis showed a newly observed mutation in the 5' untranslated region of a lagovirus, whose role remains unknown. The phenotypic analysis showed that the pathogenicity of GI.1d/00-21 and the replication kinetics in infected organs were close to those reported for the original GI.1 strains, and could not alone explain the observed selective advantage of the GI.1d strains. Determining the minimum dose of viral particles required to cause mortality in rabbits is an important input for in vivo studies.
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Affiliation(s)
- Clément Droillard
- Ploufragan-Plouzané-Niort Laboratory, Avian and Rabbit Virology Immunology and Parasitology Unit, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), BP 53, F-22440, Ploufragan, France
| | - Evelyne Lemaitre
- Ploufragan-Plouzané-Niort Laboratory, Avian and Rabbit Virology Immunology and Parasitology Unit, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), BP 53, F-22440, Ploufragan, France
| | - Michel Amelot
- Ploufragan-Plouzané-Niort Laboratory, Department for Breeding and Experimentation in Poultry and Rabbits, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), BP 53, F-22440, Ploufragan, France
| | - Yannick Blanchard
- Ploufragan-Plouzané-Niort Laboratory, Viral Genetics and Biosafety Unit, French Agency for Food Environmental and Occupational Health and Safety (ANSES), BP 53, F-22440, Ploufragan, France
| | - Alassane Keita
- Ploufragan-Plouzané-Niort Laboratory, Department for Breeding and Experimentation in Poultry and Rabbits, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), BP 53, F-22440, Ploufragan, France
| | - Nicolas Eterradossi
- Ploufragan-Plouzané-Niort Laboratory, Avian and Rabbit Virology Immunology and Parasitology Unit, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), BP 53, F-22440, Ploufragan, France
| | - Ghislaine Le Gall-Reculé
- Ploufragan-Plouzané-Niort Laboratory, Avian and Rabbit Virology Immunology and Parasitology Unit, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), BP 53, F-22440, Ploufragan, France.
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27
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Hall RN, King T, O’Connor T, Read AJ, Arrow J, Trought K, Duckworth J, Piper M, Strive T. Age and Infectious Dose Significantly Affect Disease Progression after RHDV2 Infection in Naïve Domestic Rabbits. Viruses 2021; 13:1184. [PMID: 34205750 PMCID: PMC8234499 DOI: 10.3390/v13061184] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 01/02/2023] Open
Abstract
Rabbit haemorrhagic disease virus 2 (RHDV2 or GI.2, referring to any virus with lagovirus GI.2 structural genes) is a recently emerged calicivirus that causes generalised hepatic necrosis and disseminated intravascular coagulation leading to death in susceptible lagomorphs (rabbits and hares). Previous studies investigating the virulence of RHDV2 have reported conflicting results, with case fatality rates ranging from 0% to 100% even within a single study. Lagoviruses are of particular importance in Australia and New Zealand where they are used as biocontrol agents to manage wild rabbit populations, which threaten over 300 native species and result in economic impacts in excess of $200 million AUD annually to Australian agricultural industries. It is critically important that any pest control method is both highly effective (i.e., virulent, in the context of viral biocontrols) and has minimal animal welfare impacts. To determine whether RHDV2 might be a suitable candidate biocontrol agent, we investigated the virulence and disease progression of a naturally occurring Australian recombinant RHDV2 in both 5-week-old and 11-week-old New Zealand White laboratory rabbits after either high or low dose oral infection. Objective measures of disease progression were recorded through continuous body temperature monitoring collars, continuous activity monitors, and twice daily observations. We observed a 100% case fatality rate in both infected kittens and adult rabbits after either high dose or low dose infection. Clinical signs of disease, such as pyrexia, weight loss, and reduced activity, were evident in the late stages of infection. Clinical disease, i.e., welfare impacts, were limited to the period after the onset of pyrexia, lasting on average 12 h and increasing in severity as disease progressed. These findings confirm the high virulence of this RHDV2 variant in naïve rabbits. While age and infectious dose significantly affected disease progression, the case fatality rate was consistently 100% under all conditions tested.
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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
| | - Tegan King
- Health & Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT 2601, Australia; (T.K.); (T.S.)
| | - Tiffany O’Connor
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW 2568, Australia; tiffany.o' (T.O.); (A.J.R.)
| | - Andrew J. Read
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW 2568, Australia; tiffany.o' (T.O.); (A.J.R.)
| | - Jane Arrow
- Wildlife Ecology and Management, Manaaki Whenua-Landcare Research, Lincoln 7608, New Zealand; (J.A.); (K.T.); (J.D.)
| | - Katherine Trought
- Wildlife Ecology and Management, Manaaki Whenua-Landcare Research, Lincoln 7608, New Zealand; (J.A.); (K.T.); (J.D.)
| | - Janine Duckworth
- Wildlife Ecology and Management, Manaaki Whenua-Landcare Research, Lincoln 7608, New Zealand; (J.A.); (K.T.); (J.D.)
| | - 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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28
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Abrantes J, Lopes AM. A Review on the Methods Used for the Detection and Diagnosis of Rabbit Hemorrhagic Disease Virus (RHDV). Microorganisms 2021; 9:972. [PMID: 33946292 PMCID: PMC8146303 DOI: 10.3390/microorganisms9050972] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 01/10/2023] Open
Abstract
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.
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Affiliation(s)
- Joana Abrantes
- CIBIO/InBio-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal;
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
| | - Ana M. Lopes
- CIBIO/InBio-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal;
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS)/Unidade Multidisciplinar de Investigação Biomédica (UMIB), Universidade do Porto, 4050-313 Porto, Portugal
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29
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Müller C, Hrynkiewicz R, Bębnowska D, Maldonado J, Baratelli M, Köllner B, Niedźwiedzka-Rystwej P. Immunity against Lagovirus europaeus and the Impact of the Immunological Studies on Vaccination. Vaccines (Basel) 2021; 9:vaccines9030255. [PMID: 33805607 PMCID: PMC8002203 DOI: 10.3390/vaccines9030255] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 12/14/2022] Open
Abstract
In the early 1980s, a highly contagious viral hemorrhagic fever in rabbits (Oryctolagus cuniculus) emerged, causing a very high rate of mortality in these animals. Since the initial occurrence of the rabbit hemorrhagic disease virus (RHDV), several hundred million rabbits have died after infection. The emergence of genetically-different virus variants (RHDV GI.1 and GI.2) indicated the very high variability of RHDV. Moreover, with these variants, the host range broadened to hare species (Lepus). The circulation of RHDV genotypes displays different virulences and a limited induction of cross-protective immunity. Interestingly, juvenile rabbits (<9 weeks of age) with an immature immune system display a general resistance to RHDV GI.1, and a limited resistance to RHDV GI.2 strains, whereas less than 3% of adult rabbits survive an infection by either RHDV GI.1. or GI.2. Several not-yet fully understood phenomena characterize the RHD. A very low infection dose followed by an extremely rapid viral replication could be simplified to the induction of a disseminated intravascular coagulopathy (DIC), a severe loss of lymphocytes—especially T-cells—and death within 36 to 72 h post infection. On the other hand, in animals surviving the infection or after vaccination, very high titers of RHDV-neutralizing antibodies were induced. Several studies have been conducted in order to deepen the knowledge about the virus’ genetics, epidemiology, RHDV-induced pathology, and the anti-RHDV immune responses of rabbits in order to understand the phenomenon of the juvenile resistance to this virus. Moreover, several approaches have been used to produce efficient vaccines in order to prevent an infection with RHDV. In this review, we discuss the current knowledge about anti-RHDV resistance and immunity, RHDV vaccination, and the further need to establish rationally-based RHDV vaccines.
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Affiliation(s)
- Claudia Müller
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institute, 17493 Greifswald-Insel Riems, Germany;
| | - Rafał Hrynkiewicz
- Institute of Biology, University of Szczecin, Felczaka 3c, 71-412 Szczecin, Poland; (R.H.); (D.B.)
| | - Dominika Bębnowska
- Institute of Biology, University of Szczecin, Felczaka 3c, 71-412 Szczecin, Poland; (R.H.); (D.B.)
| | | | | | - Bernd Köllner
- Institute of Immunology, Friedrich-Loeffler-Institute, 17493 Greifswald-Insel Riems, Germany
- Correspondence: (B.K.); (P.N.-R.)
| | - Paulina Niedźwiedzka-Rystwej
- Institute of Biology, University of Szczecin, Felczaka 3c, 71-412 Szczecin, Poland; (R.H.); (D.B.)
- Correspondence: (B.K.); (P.N.-R.)
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30
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Abade Dos Santos FA, Pinto A, Burgoyne T, Dalton KP, Carvalho CL, Ramilo DW, Carneiro C, Carvalho T, Peleteiro MC, Parra F, Duarte MD. Spillover events of rabbit haemorrhagic disease virus 2 (recombinant GI.4P-GI.2) from Lagomorpha to Eurasian badger. Transbound Emerg Dis 2021; 69:1030-1045. [PMID: 33683820 DOI: 10.1111/tbed.14059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 11/30/2022]
Abstract
Rabbit haemorrhagic disease (RHD) is a major threat to domestic and wild European rabbits. Presently, in Europe, the disease is caused mainly by Rabbit haemorrhagic disease virus 2 (RHDV2/b or Lagovirus europaeus GI.2), the origin of which is still unclear, as no RHDV2 reservoir hosts were identified. After the RHDV2 emergence in 2010, viral RNA was detected in a few rodent species. Furthermore, RHDV2 was found to cause disease in some hare species resembling the disease in rabbits, evidencing the ability of the virus to cross the species barrier. In this study, through molecular, histopathologic, antigenic and morphological evidences, we demonstrate the presence and replication of RHDV2 in Eurasian badgers (Meles meles) found dead in the district of Santarém, Portugal, between March 2017 and January 2020. In these animals, we further classify the RHDV2 as a Lagovirus europaeus recombinant GI.4P-GI.2. Our results indicate that Meles meles is susceptible to RHDV2, developing systemic infection, and excreting the virus in the faeces. Given the high viral loads seen in several organs and matrices, we believe that transmission to the wild rabbit is likely. Furthermore, transmission electron microscopy data show the presence of calicivirus compatible virions in the nucleus of hepatocytes, which constitutes a paradigm shift for caliciviruses' replication cycle.
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Affiliation(s)
- Fábio A Abade Dos Santos
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of. Av. da Universidade Técnica, Lisbon, Portugal.,National Institute for Agrarian and Veterinary Research (INIAV, I.P.), Av. da República, Quinta do Marquês, Oeiras, Portugal.,Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Oviedo, Spain
| | - Andreia Pinto
- Paediatric Respiratory Medicine, Primary Ciliary Dyskinesia Centre, Harefield NHS Trust, London, UK
| | - Thomas Burgoyne
- Paediatric Respiratory Medicine, Primary Ciliary Dyskinesia Centre, Harefield NHS Trust, London, UK.,UCL Institute of Ophthalmology, University College London, London, UK
| | - Kevin P Dalton
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Oviedo, Spain
| | - Carina L Carvalho
- National Institute for Agrarian and Veterinary Research (INIAV, I.P.), Av. da República, Quinta do Marquês, Oeiras, Portugal
| | - David W Ramilo
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of. Av. da Universidade Técnica, Lisbon, Portugal
| | - Carla Carneiro
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of. Av. da Universidade Técnica, Lisbon, Portugal
| | - Tânia Carvalho
- Champalimaud Center for the Unknown, Champalimaud Foundation, Lisboa, Portugal
| | - M Conceição Peleteiro
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of. Av. da Universidade Técnica, Lisbon, Portugal
| | - Francisco Parra
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Oviedo, Spain
| | - Margarida D Duarte
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of. Av. da Universidade Técnica, Lisbon, Portugal.,National Institute for Agrarian and Veterinary Research (INIAV, I.P.), Av. da República, Quinta do Marquês, Oeiras, Portugal
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31
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Abade dos Santos FA, Magro C, Carvalho CL, Ruivo P, Duarte MD, Peleteiro MC. A Potential Atypical Case of Rabbit Haemorrhagic Disease in a Dwarf Rabbit. Animals (Basel) 2020; 11:ani11010040. [PMID: 33379183 PMCID: PMC7823764 DOI: 10.3390/ani11010040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/08/2020] [Accepted: 12/21/2020] [Indexed: 01/08/2023] Open
Abstract
Simple Summary We report an unusual clinical case in a pet rabbit vaccinated against rabbit haemorrhagic disease virus (RHDV, GI.1), that developed a prolonged hepatic disease, and was diagnosed RHDV2 (GI.2) positive post-mortem. This finding is a warning to all veterinarians that rabbit haemorrhagic disease should also be considered for differential diagnosis despite the history of RHDV vaccination and the need to update vaccination programs against the current RHDV2 circulating strains. Abstract Rabbit haemorrhagic disease (RHD) is a highly contagious infectious disease of European wild and domestic rabbits. Rabbit haemorrhagic disease virus (RHDV, GI.1) emerged in 1986 in Europe, rapidly spreading all over the world. Several genotypes of RHDV have been recognised over time, but in 2010, a new virus (RHDV2/RHDVb, GI.2) emerged and progressively replaced the previous RHDV strains, due to the lack of cross-immunity conferred between RHDV and RHDV2. RHDV2 has a high mutation rate, similarly to the other calivirus and recombines with strains of RHDV and non-pathogenic calicivirus (GI.4), ensuring the continuous emergence of new field strains. Although this poses a threat to the already endangered European rabbit species, the available vaccines against RHDV2 and the compliance of biosafety measures seem to be controlling the infection in the rabbit industry Pet rabbits, especially when kept indoor, are considered at lower risk of infections, although RHDV2 and myxoma virus (MYXV) constitute a permanent threat due to transmission via insects. Vaccination against these viruses is therefore recommended every 6 months (myxomatosis) or annually (rabbit haemorrhagic disease). The combined immunization for myxomatosis and RHDV through a commercially available bivalent vaccine with RHDV antigen has been extensively used (Nobivac® Myxo-RHD, MSD, Kenilworth, NJ, USA). This vaccine however does not confer proper protection against the RHDV2, thus the need for a rabbit clinical vaccination protocol update. Here we report a clinical case of hepatitis and alteration of coagulation in a pet rabbit that had been vaccinated with the commercially available bivalent vaccine against RHDV and tested positive to RHDV2 after death. The animal developed a prolonged and atypical disease, compatible with RHD. The virus was identified to be an RHDV2 recombinant strain, with the structural backbone of RHDV2 (GI.2) and the non-structural genes of non-pathogenic-A1 strains (RCV-A1, GI.4). Although confirmation of the etiological agent was only made after death, the clinical signs and analytic data were very suggestive of RHD.
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Affiliation(s)
- Fábio A. Abade dos Santos
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal; (M.D.D.); (M.C.P.)
- Instituto Nacional de Investigação Agrária e Veterinária (INIAV, I.P.), Av. da República, Quinta do Marquês, 2780-157 Oeiras, Portugal;
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
- Correspondence:
| | - Carolina Magro
- VetOeiras, Hospital Médico-Veterinário, Estrada de Oeiras n18-20, 2780-114 Oeiras, Portugal;
| | - Carina L. Carvalho
- Instituto Nacional de Investigação Agrária e Veterinária (INIAV, I.P.), Av. da República, Quinta do Marquês, 2780-157 Oeiras, Portugal;
| | - Pedro Ruivo
- Instituto de Medicina Molecular João Lobo Antunes (IMM), Faculdade de Medicina, Universidade de Lisboa, 1070-312 Lisbon, Portugal;
| | - Margarida D. Duarte
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal; (M.D.D.); (M.C.P.)
- Instituto Nacional de Investigação Agrária e Veterinária (INIAV, I.P.), Av. da República, Quinta do Marquês, 2780-157 Oeiras, Portugal;
| | - Maria C. Peleteiro
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal; (M.D.D.); (M.C.P.)
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32
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Szillat KP, Höper D, Beer M, König P. Full-genome sequencing of German rabbit haemorrhagic disease virus uncovers recombination between RHDV (GI.2) and EBHSV (GII.1). Virus Evol 2020; 6:veaa080. [PMID: 33324492 PMCID: PMC7724246 DOI: 10.1093/ve/veaa080] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Rabbit haemorrhagic disease virus (RHDV; genotypes GI.1 and GI.2) and European brown hare syndrome virus (EBHSV; genotype GII.1) are caliciviruses belonging to the genus Lagovirus. These viruses pose a serious threat to wild and domestic rabbit and hare populations around the world. In recent years, an expanding genetic diversity has been described within the genus, with recombination events occurring between the different genotypes. Here, we generated and analysed 56 full-genome sequences of RHDV and EBHSV from rabbit and hare livers, collected in Germany between the years 2013 and 2020. We could show that genotype Gl.2 (RHDV-2) almost entirely replaced Gl.1 (classical RHDV) in the German rabbit population. However, GI.1 is still present in Germany and has to be included into disease control and vaccination strategies. Three recombinant strains were identified from rabbit samples that contain the structural genes of genotype Gl.2 and the non-structural genes of genotype Gl.1b. Of special interest is the finding that sequences from two hare samples showed recombination events between structural genes of RHDV Gl.2 and non-structural genes of EBHSV GII.1, a recombination between different genogroups that has not been described before. These findings lead to the assumption that also a recombination of the non-structural genes of RHDV Gl.2 with the structural genes of EBHSV Gll.1 might be possible and therefore increase the potential genetic variability of lagoviruses immensely. Our findings underline the importance of whole genome analysis with next-generation sequencing technology as one of new tools now available for in-depth studies that allow in depth molecular epidemiology with continuous monitoring of the genetic variability of viruses that would otherwise likely stay undetected if only routine diagnostic assays are used.
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Affiliation(s)
- Kevin P Szillat
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Patricia König
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
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Abrantes J, Lopes AM, Lemaitre E, Ahola H, Banihashem F, Droillard C, Marchandeau S, Esteves PJ, Neimanis A, Le Gall-Reculé G. Retrospective Analysis Shows That Most RHDV GI.1 Strains Circulating Since the Late 1990s in France and Sweden Were Recombinant GI.3P-GI.1d Strains. Genes (Basel) 2020; 11:E910. [PMID: 32784857 PMCID: PMC7464634 DOI: 10.3390/genes11080910] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/27/2020] [Accepted: 08/06/2020] [Indexed: 12/27/2022] Open
Abstract
Recombination is one of the major sources of genetic variation in viruses. RNA viruses, such as rabbit hemorrhagic disease virus (RHDV), are among the viruses with the highest recombination rates. Several recombination events have been described for RHDV, mostly as a consequence of their genomic architecture. Here, we undertook phylogenetic and recombination analyses of French and Swedish RHDV strains from 1994 to 2016 and uncovered a new intergenotypic recombination event. This event occurred in the late 1990s/early 2000s and involved nonpathogenic GI.3 strains as donors for the nonstructural part of the genome of these recombinants, while pathogenic GI.1d strains contributed to the structural part. These GI.3P-GI.1d recombinant strains did not entirely replace GI.1d (nonrecombinant) strains, but became the dominant strains in France and Sweden, likely due to a fitness advantage associated with this genomic architecture. GI.3P-GI.1d (P stands for polymerase) strains persisted until 2013 and 2016 in Sweden and France, respectively, and cocirculated with the new genotype GI.2 in France. Since strains from the first GI.2 outbreaks were GI.3P-GI.2, we hypothesize that GI.3P-GI.1d could be the parental strain. Our results confirm the outstanding recombination ability of RHDV and its importance in the evolution of lagoviruses, which was only revealed by studying complete genomic sequences.
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Affiliation(s)
- Joana Abrantes
- CIBIO/InBio-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal; (J.A.); (A.M.L.); (P.J.E.)
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
| | - Ana M. Lopes
- CIBIO/InBio-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal; (J.A.); (A.M.L.); (P.J.E.)
- Instituto de Ciências Biomédicas Abel Salazar/Unidade Multidisciplinar de Investigação Biomédica, Universidade do Porto, 4050-313 Porto, Portugal
| | - Evelyne Lemaitre
- Unité de Virologie, Immunologie, Parasitologie, Aviaires et Cunicoles, Laboratoire de Ploufragan-Plouzané-Niort, Agence nationale de sécurité sanitaire, de l’alimentation, de l’environnement et du travail (Anses), 22440 Ploufragan, France; (E.L.); (C.D.)
| | - Harri Ahola
- Department of Microbiology, National Veterinary Institute (SVA), Ulls väg 2B, SE75189 Uppsala, Sweden; (H.A.); (F.B.)
| | - Fereshteh Banihashem
- Department of Microbiology, National Veterinary Institute (SVA), Ulls väg 2B, SE75189 Uppsala, Sweden; (H.A.); (F.B.)
| | - Clément Droillard
- Unité de Virologie, Immunologie, Parasitologie, Aviaires et Cunicoles, Laboratoire de Ploufragan-Plouzané-Niort, Agence nationale de sécurité sanitaire, de l’alimentation, de l’environnement et du travail (Anses), 22440 Ploufragan, France; (E.L.); (C.D.)
| | - Stéphane Marchandeau
- Unité Petite Faune Sédentaire et Espèces Outre-Mer, Direction de la Recherche et de l’Appui Scientifique, Office Français de la Biodiversité (OFB), 44300 Nantes, France;
| | - Pedro J. Esteves
- CIBIO/InBio-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal; (J.A.); (A.M.L.); (P.J.E.)
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
| | - Aleksija Neimanis
- Department of Pathology and Wildlife Diseases, National Veterinary Institute (SVA), Ulls väg 2B, SE75189 Uppsala, Sweden
| | - Ghislaine Le Gall-Reculé
- Unité de Virologie, Immunologie, Parasitologie, Aviaires et Cunicoles, Laboratoire de Ploufragan-Plouzané-Niort, Agence nationale de sécurité sanitaire, de l’alimentation, de l’environnement et du travail (Anses), 22440 Ploufragan, France; (E.L.); (C.D.)
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