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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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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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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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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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Cavadini P, Molinari S, Merzoni F, Vismarra A, Posautz A, Alzaga Gil V, Chiari M, Giannini F, Capucci L, Lavazza A. Widespread occurrence of the non-pathogenic hare calicivirus (HaCV Lagovirus GII.2) in captive-reared and free-living wild hares in Europe. Transbound Emerg Dis 2020; 68:509-518. [PMID: 32603021 PMCID: PMC8247275 DOI: 10.1111/tbed.13706] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 06/01/2020] [Accepted: 06/23/2020] [Indexed: 12/25/2022]
Abstract
The Lagovirus genus comprises both pathogenic viruses as European brown hare syndrome virus (EBHSV- GII.1) and rabbit hemorrhagic disease viruses (RHDV-GI.1 and RHDV2-GI.2), that principally infect European brown hares (Lepus europeaus) and European rabbits (Oryctolagus cuniculus), respectively, causing severe necrotic hepatitis, spleen enlargement and disseminated haemorrhage. This genus includes also non-pathogenic agents, such as rabbit calicivirus (RCV-E1 - GI.3) and the non-pathogenic hare Lagovirus, provisionally named hare calicivirus (HaCV - GII.2). The latter had been identified for the first time in 2012 in the gut contents and faeces of healthy young hares raised in a breeding farm. In this study, we further investigated the presence of HaCV by testing the intestinal tract of 621 wild hares collected between 2010 and 2018 in Northern and Central Italy, and in 2011 in Austria, Germany and Spain. These wild hares were found dead for causes other than EBHS or were healthy hares shot during the hunting season. Forty-three out of 322 hare samples from Italy and 14 out of 299 samples from Austria and Germany were positive for HaCV-GII.2 by RT-PCR using universal primers for lagoviruses and primers specific for HaCV. Sequence analysis of the full capsid protein gene conducted on 12 strains representative of different years and locations indicated that these viruses belong to the same, single cluster as the prototype strain initially identified at the hares' farm (HaCV_Bs12_1). The relatively high level of genetic variation (88% nt identity) within this cluster suggests HaCVs may have been circulating widely in Europe for some time.
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Affiliation(s)
- Patrizia Cavadini
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna and OIE Reference Laboratory for Rabbit Haemorrhagic Disease, Brescia, Italy
| | - Stefano Molinari
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna and OIE Reference Laboratory for Rabbit Haemorrhagic Disease, Brescia, Italy
| | - Francesca Merzoni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna and OIE Reference Laboratory for Rabbit Haemorrhagic Disease, Brescia, Italy
| | - Alice Vismarra
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna and OIE Reference Laboratory for Rabbit Haemorrhagic Disease, Brescia, Italy
| | - Annika Posautz
- Department of Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | | | - Mario Chiari
- D.G. Welfare, Regional Health Authority of Lombardy, Milan, Italy
| | - Francesca Giannini
- Parco Nazionale Arcipelago Toscano, Portoferraio, Località-Enfola, Italy
| | - Lorenzo Capucci
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna and OIE Reference Laboratory for Rabbit Haemorrhagic Disease, Brescia, Italy
| | - Antonio Lavazza
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna and OIE Reference Laboratory for Rabbit Haemorrhagic Disease, Brescia, Italy
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