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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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2
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Rajao DS, Anderson TK, Kitikoon P, Stratton J, Lewis NS, Vincent AL. Antigenic and genetic evolution of contemporary swine H1 influenza viruses in the United States. Virology 2018; 518:45-54. [PMID: 29453058 PMCID: PMC8608352 DOI: 10.1016/j.virol.2018.02.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 02/03/2018] [Accepted: 02/05/2018] [Indexed: 01/02/2023]
Abstract
Several lineages of influenza A viruses (IAV) currently circulate in North American pigs. Genetic diversity is further increased by transmission of IAV between swine and humans and subsequent evolution. Here, we characterized the genetic and antigenic evolution of contemporary swine H1N1 and H1N2 viruses representing clusters H1-α (1A.1), H1-β (1A.2), H1pdm (1A.3.3.2), H1-γ (1A.3.3.3), H1-δ1 (1B.2.2), and H1-δ2 (1B.2.1) currently circulating in pigs in the United States. The δ1-viruses diversified into two new genetic clades, H1-δ1a (1B.2.2.1) and H1-δ1b (1B.2.2.2), which were also antigenically distinct from the earlier H1-δ1-viruses. Further characterization revealed that a few key amino acid changes were associated with antigenic divergence in these groups. The continued genetic and antigenic evolution of contemporary H1 viruses might lead to loss of vaccine cross-protection that could lead to significant economic impact to the swine industry, and represents a challenge to public health initiatives that attempt to minimize swine-to-human IAV transmission.
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Affiliation(s)
- Daniela S Rajao
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, 1920 Dayton Avenue, PO Box 70, Ames, IA 50010, USA
| | - Tavis K Anderson
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, 1920 Dayton Avenue, PO Box 70, Ames, IA 50010, USA
| | - Pravina Kitikoon
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, 1920 Dayton Avenue, PO Box 70, Ames, IA 50010, USA
| | - Jered Stratton
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, 1920 Dayton Avenue, PO Box 70, Ames, IA 50010, USA
| | - Nicola S Lewis
- Department of Zoology, University of Cambridge, Downing St, Cambridge CB2 3EJ, UK
| | - Amy L Vincent
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, 1920 Dayton Avenue, PO Box 70, Ames, IA 50010, USA.
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3
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Reddy YV, Susmitha B, Patil S, Krishnajyothi Y, Putty K, Ramakrishna KV, Sunitha G, Devi BV, Kavitha K, Deepthi B, Krovvidi S, Reddy YN, Reddy GH, Singh KP, Maan NS, Hemadri D, Maan S, Mertens PP, Hegde NR, Rao PP. Isolation and evolutionary analysis of Australasian topotype of bluetongue virus serotype 4 from India. Transbound Emerg Dis 2017; 65:547-556. [PMID: 29120083 DOI: 10.1111/tbed.12738] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Indexed: 12/13/2022]
Abstract
Bluetongue (BT) is a Culicoides-borne disease caused by several serotypes of bluetongue virus (BTV). Similar to other insect-borne viral diseases, distribution of BT is limited to distribution of Culicoides species competent to transmit BTV. In the tropics, vector activity is almost year long, and hence, the disease is endemic, with the circulation of several serotypes of BTV, whereas in temperate areas, seasonal incursions of a limited number of serotypes of BTV from neighbouring tropical areas are observed. Although BTV is endemic in all the three major tropical regions (parts of Africa, America and Asia) of the world, the distribution of serotypes is not alike. Apart from serological diversity, geography-based diversity of BTV genome has been observed, and this is the basis for proposal of topotypes. However, evolution of these topotypes is not well understood. In this study, we report the isolation and characterization of several BTV-4 isolates from India. These isolates are distinct from BTV-4 isolates from other geographical regions. Analysis of available BTV seg-2 sequences indicated that the Australasian BTV-4 diverged from African viruses around 3,500 years ago, whereas the American viruses diverged relatively recently (1,684 CE). Unlike Australasia and America, BTV-4 strains of the Mediterranean area evolved through several independent incursions. We speculate that independent evolution of BTV in different geographical areas over long periods of time might have led to the diversity observed in the current virus population.
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Affiliation(s)
- Y V Reddy
- Ella Foundation, Hyderabad, Telangana, India
| | - B Susmitha
- PVNR Telangana Veterinary University, Hyderabad, Telangana, India
| | - S Patil
- PVNR Telangana Veterinary University, Hyderabad, Telangana, India
| | - Y Krishnajyothi
- Veterinary Biological & Research Institute, Hyderabad, Telangana, India
| | - K Putty
- PVNR Telangana Veterinary University, Hyderabad, Telangana, India
| | - K V Ramakrishna
- Animal Disease Diagnostic Laboratory, Eluru, Andhra Pradesh, India
| | - G Sunitha
- Veterinary Biological & Research Institute, Hyderabad, Telangana, India
| | - B V Devi
- Veterinary Biological & Research Institute, Hyderabad, Telangana, India
| | - K Kavitha
- Veterinary Biological & Research Institute, Hyderabad, Telangana, India
| | - B Deepthi
- Veterinary Biological & Research Institute, Hyderabad, Telangana, India
| | - S Krovvidi
- Sreenidhi Institute of Science and Technology, Telangana, India
| | - Y N Reddy
- PVNR Telangana Veterinary University, Hyderabad, Telangana, India
| | - G H Reddy
- Veterinary Biological & Research Institute, Hyderabad, Telangana, India
| | - K P Singh
- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - N S Maan
- LLR University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - D Hemadri
- National Institute of Veterinary Epidemiology & Disease Informatics, Bengaluru, Karnataka, India
| | - S Maan
- LLR University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - P P Mertens
- The Pirbright Institute, Pirbright, Woking, UK
| | - N R Hegde
- Ella Foundation, Hyderabad, Telangana, India
| | - P P Rao
- Ella Foundation, Hyderabad, Telangana, India
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4
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Lopes AM, Silvério D, Magalhães MJ, Areal H, Alves PC, Esteves PJ, Abrantes J. Characterization of old RHDV strains by complete genome sequencing identifies a novel genetic group. Sci Rep 2017; 7:13599. [PMID: 29051566 PMCID: PMC5648873 DOI: 10.1038/s41598-017-13902-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 04/04/2017] [Indexed: 11/11/2022] Open
Abstract
Rabbit hemorrhagic disease (RHD) is a veterinary disease that affects the European rabbit and has a significant economic and ecological negative impact. In Portugal, rabbit hemorrhagic disease virus (RHDV) was reported in 1989 and still causes enzootic outbreaks. Several recombination events have been detected in RHDV strains, including in the first reported outbreak. Here we describe the occurrence of recombination in RHDV strains recovered from rabbit and Iberian hare samples collected in the mid-1990s in Portugal. Characterization of full genomic sequences revealed the existence of a single recombination breakpoint at the boundary of the non-structural and the structural encoding regions, further supporting the importance of this region as a recombination hotspot in lagoviruses. Phylogenetic analysis showed that in the structural region, the recombinant strains were similar to pathogenic G1 strains, but in the non-structural region they formed a new group that diverged ~13% from known strains. No further reports of such group exist, but this recombination event was also detected in an Iberian hare that was associated with the earliest species jump in RHDV. Our results highlight the importance of the characterization of full genomes to disclose RHDV evolution and show that lagoviruses’ diversity has been significantly undersampled.
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Affiliation(s)
- Ana M Lopes
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Diogo Silvério
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal
| | - Maria J Magalhães
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Helena Areal
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Paulo C Alves
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.,Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, 59812, Montana, USA
| | - Pedro J Esteves
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.,Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (CESPU), Gandra, Portugal
| | - Joana Abrantes
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.
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5
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Benign Rabbit Caliciviruses Exhibit Evolutionary Dynamics Similar to Those of Their Virulent Relatives. J Virol 2016; 90:9317-29. [PMID: 27512059 DOI: 10.1128/jvi.01212-16] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 07/26/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Two closely related caliciviruses cocirculate in Australia: rabbit hemorrhagic disease virus (RHDV) and rabbit calicivirus Australia 1 (RCV-A1). RCV-A1 causes benign enteric infections in the European rabbit (Oryctolagus cuniculus) in Australia and New Zealand, while its close relative RHDV causes a highly pathogenic infection of the liver in the same host. The comparison of these viruses provides important information on the nature and trajectory of virulence evolution, particularly as highly virulent strains of RHDV may have evolved from nonpathogenic ancestors such as RCV-A1. To determine the evolution of RCV-A1 we sequenced the full-length genomes of 44 RCV-A1 samples isolated from healthy rabbits and compared key evolutionary parameters to those of its virulent relative, RHDV. Despite their marked differences in pathogenicity and tissue tropism, RCV-A1 and RHDV have evolved in a very similar manner. Both viruses have evolved at broadly similar rates, suggesting that their dynamics are largely shaped by high background mutation rates, and both exhibit occasional recombination and an evolutionary environment dominated by purifying selection. In addition, our comparative analysis revealed that there have been multiple changes in both virulence and tissue tropism in the evolutionary history of these and related viruses. Finally, these new genomic data suggest that either RCV-A1 was introduced into Australia after the introduction of myxoma virus as a biocontrol agent in 1950 or there was drastic reduction of the rabbit population, and hence of RCV-A1 genetic diversity, perhaps coincident with the emergence of myxoma virus. IMPORTANCE The comparison of closely related viruses that differ profoundly in propensity to cause disease in their hosts offers a powerful opportunity to reveal the causes of changes in virulence and to study how such changes alter the evolutionary dynamics of these pathogens. Here we describe such a novel comparison involving two closely related RNA viruses that cocirculate in Australia, the highly virulent rabbit hemorrhagic disease virus (RHDV) and the nonpathogenic rabbit calicivirus Australia 1 (RCV-A1). Both viruses infect the European rabbit, but they differ in virulence, tissue tropism, and mechanisms of transmission. Surprisingly, and despite these fundamental differences, RCV-A1 and RHDV have evolved at very similar (high) rates and with strong purifying selection. Furthermore, candidate key mutations were identified that may play a role in virulence and/or tissue tropism and therefore warrant further investigation.
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6
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Resolving the Origin of Rabbit Hemorrhagic Disease Virus: Insights from an Investigation of the Viral Stocks Released in Australia. J Virol 2015; 89:12217-20. [PMID: 26378178 DOI: 10.1128/jvi.01937-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/10/2015] [Indexed: 11/20/2022] Open
Abstract
To resolve the evolutionary history of rabbit hemorrhagic disease virus (RHDV), we performed a genomic analysis of the viral stocks imported and released as a biocontrol measure in Australia, as well as a global phylogenetic analysis. Importantly, conflicts were identified between the sequences determined here and those previously published that may have affected evolutionary rate estimates. By removing likely erroneous sequences, we show that RHDV emerged only shortly before its initial description in China.
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Shen T, Yan XM, Liu HX, Zhang BX, Li L, Zhang JP, Wang JL, Xiao CJ. Genotype I of hepatitis B virus was found in east Xishuangbanna, China and molecular dynamics of HBV/I. J Viral Hepat 2015; 22:37-45. [PMID: 24548532 DOI: 10.1111/jvh.12231] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 12/01/2013] [Indexed: 02/06/2023]
Abstract
There is a dearth of data about the prevalence of hepatitis B virus (HBV) infection in Mengla, China; and no detailed analysis of the molecular evolution of genotype I in Asia. In this study, 909 serum samples from ethnic minority people in China were obtained. Serological assay and HBV S-gene amplification were carried out, and phylogenetic and evolutionary dynamics analysis of 62 HBV/I S-gene was performed. On this survey, 153 individuals were tested HBsAg-positive. Genotypes of S-gene were classified into three groups: C, B and I. Under the strict model and the relax model, the estimated evolutionary rates for HBV/I were 3.74 × 10(-4) and 6.93 × 10(-4) substitution/site/year, respectively. However, when the geographic origin was taken into account, the mean substitution rates were increased. Estimated time to most recent ancestor of genotype I varied from ~30 to ~70 years ago. The Bayesian sky plot showed a rapid spread of HBV/I at the end of 1980s. Peculiar nucleotides distributed were observed in the subgenotype I1/I2. In conclusion, higher prevalence of HBV infection was observed in Mengla county. Multifactors like timescale and spatial locations should be integrated to provide a better interpretation of the HBV/I evolutionary history in the region.
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Affiliation(s)
- T Shen
- Medical Science College of Yunnan University, Kunming, China; Institute of Basic and Clinical Medicine, Center of Clinical Molecular Biology, Provincial Key Laboratory for Birth Defects and Genetic Diseases, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming Science and Technology University, Kunming, China
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8
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Detection of RHDV strains in the Iberian hare (Lepus granatensis): earliest evidence of rabbit lagovirus cross-species infection. Vet Res 2014; 45:94. [PMID: 25248407 PMCID: PMC4189657 DOI: 10.1186/s13567-014-0094-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/08/2014] [Indexed: 11/10/2022] Open
Abstract
Rabbit hemorrhagic disease virus (RHDV) is a highly lethal Lagovirus, family Caliciviridae, that threatens European rabbits (Oryctolagus cuniculus). Although a related virus severely affects hares, cross-species infection was only recently described for new variant RHDV in Cape hares (Lepus capensis mediterraneus). We sequenced two strains from dead Iberian hares (Lepus granatensis) collected in the 1990s in Portugal. Clinical signs were compatible with a Lagovirus infection. Phylogenetic analysis of the complete capsid gene positioned them in the RHDV genogroup that circulated on the Iberian Peninsula at that time. This is the earliest evidence of RHDV affecting a species other than European rabbits.
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9
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Elsworth P, Cooke BD, Kovaliski J, Sinclair R, Holmes EC, Strive T. Increased virulence of rabbit haemorrhagic disease virus associated with genetic resistance in wild Australian rabbits (Oryctolagus cuniculus). Virology 2014; 464-465:415-423. [PMID: 25146599 DOI: 10.1016/j.virol.2014.06.037] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 06/10/2014] [Accepted: 06/12/2014] [Indexed: 01/14/2023]
Abstract
The release of myxoma virus (MYXV) and Rabbit Haemorrhagic Disease Virus (RHDV) in Australia with the aim of controlling overabundant rabbits has provided a unique opportunity to study the initial spread and establishment of emerging pathogens, as well as their co-evolution with their mammalian hosts. In contrast to MYXV, which attenuated shortly after its introduction, rapid attenuation of RHDV has not been observed. By studying the change in virulence of recent field isolates at a single field site we show, for the first time, that RHDV virulence has increased through time, likely because of selection to overcome developing genetic resistance in Australian wild rabbits. High virulence also appears to be favoured as rabbit carcasses, rather than diseased animals, are the likely source of mechanical insect transmission. These findings not only help elucidate the co-evolutionary interaction between rabbits and RHDV, but reveal some of the key factors shaping virulence evolution.
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Affiliation(s)
- Peter Elsworth
- Robert Wicks Pest Animal Research Centre, Biosecurity Queensland, Department of Agriculture, Fisheries and Forestry, Toowoomba, Queensland, Australia; Invasive Animals Cooperative Research Centre, University of Canberra, Bruce, ACT, Canberra, Australia
| | - Brian D Cooke
- Invasive Animals Cooperative Research Centre, University of Canberra, Bruce, ACT, Canberra, Australia; University of Canberra, Institute for Applied Ecology, ACT, Canberra, Australia
| | - John Kovaliski
- Invasive Animals Cooperative Research Centre, University of Canberra, Bruce, ACT, Canberra, Australia; Biosecurity South Australia, Adelaide, South Australia, Australia
| | - Ronald Sinclair
- Invasive Animals Cooperative Research Centre, University of Canberra, Bruce, ACT, Canberra, Australia; Biosecurity South Australia, Adelaide, South Australia, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases & Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Tanja Strive
- Invasive Animals Cooperative Research Centre, University of Canberra, Bruce, ACT, Canberra, Australia; CSIRO Ecosystem Sciences, Canberra, ACT, Australia; CSIRO Biosecurity Flagship, Canberra, Australia.
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10
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Schwensow NI, Cooke B, Kovaliski J, Sinclair R, Peacock D, Fickel J, Sommer S. Rabbit haemorrhagic disease: virus persistence and adaptation in Australia. Evol Appl 2014; 7:1056-67. [PMID: 25553067 PMCID: PMC4231595 DOI: 10.1111/eva.12195] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 07/10/2014] [Indexed: 12/12/2022] Open
Abstract
In Australia, the rabbit haemorrhagic disease virus (RHDV) has been used since 1996 to reduce numbers of introduced European rabbits (Oryctolagus cuniculus) which have a devastating impact on the native Australian environment. RHDV causes regular, short disease outbreaks, but little is known about how the virus persists and survives between epidemics. We examined the initial spread of RHDV to show that even upon its initial spread, the virus circulated continuously on a regional scale rather than persisting at a local population level and that Australian rabbit populations are highly interconnected by virus-carrying flying vectors. Sequencing data obtained from a single rabbit population showed that the viruses that caused an epidemic each year seldom bore close genetic resemblance to those present in previous years. Together, these data suggest that RHDV survives in the Australian environment through its ability to spread amongst rabbit subpopulations. This is consistent with modelling results that indicated that in a large interconnected rabbit meta-population, RHDV should maintain high virulence, cause short, strong disease outbreaks but show low persistence in any given subpopulation. This new epidemiological framework is important for understanding virus–host co-evolution and future disease management options of pest species to secure Australia's remaining natural biodiversity.
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Affiliation(s)
- Nina I Schwensow
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW) Berlin, Germany ; School of Earth and Environmental Sciences, University of Adelaide Adelaide, SA, Australia
| | - Brian Cooke
- Institute for Applied Ecology, University of Canberra Canberra, ACT, Australia
| | | | | | | | - Joerns Fickel
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW) Berlin, Germany ; Institute for Biochemistry and Biology, Potsdam University Potsdam, Germany
| | - Simone Sommer
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW) Berlin, Germany ; Institute of Experimental Ecology (M25), University of Ulm Ulm, Germany
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11
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Mutze GJ, Sinclair RG, Peacock DE, Capucci L, Kovaliski J. Is increased juvenile infection the key to recovery of wild rabbit populations from the impact of rabbit haemorrhagic disease? EUR J WILDLIFE RES 2014. [DOI: 10.1007/s10344-014-0811-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Cell tropism predicts long-term nucleotide substitution rates of mammalian RNA viruses. PLoS Pathog 2014; 10:e1003838. [PMID: 24415935 PMCID: PMC3887100 DOI: 10.1371/journal.ppat.1003838] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 11/04/2013] [Indexed: 02/05/2023] Open
Abstract
The high rates of RNA virus evolution are generally attributed to replication with error-prone RNA-dependent RNA polymerases. However, these long-term nucleotide substitution rates span three orders of magnitude and do not correlate well with mutation rates or selection pressures. This substitution rate variation may be explained by differences in virus ecology or intrinsic genomic properties. We generated nucleotide substitution rate estimates for mammalian RNA viruses and compiled comparable published rates, yielding a dataset of 118 substitution rates of structural genes from 51 different species, as well as 40 rates of non-structural genes from 28 species. Through ANCOVA analyses, we evaluated the relationships between these rates and four ecological factors: target cell, transmission route, host range, infection duration; and three genomic properties: genome length, genome sense, genome segmentation. Of these seven factors, we found target cells to be the only significant predictors of viral substitution rates, with tropisms for epithelial cells or neurons (P<0.0001) as the most significant predictors. Further, one-tailed t-tests showed that viruses primarily infecting epithelial cells evolve significantly faster than neurotropic viruses (P<0.0001 and P<0.001 for the structural genes and non-structural genes, respectively). These results provide strong evidence that the fastest evolving mammalian RNA viruses infect cells with the highest turnover rates: the highly proliferative epithelial cells. Estimated viral generation times suggest that epithelial-infecting viruses replicate more quickly than viruses with different cell tropisms. Our results indicate that cell tropism is a key factor in viral evolvability. RNA viruses are the fastest evolving human pathogens, making their treatment and control difficult. Compared to DNA viruses, RNA viruses replicate with much lower fidelity, which can explain why RNA viruses evolve significantly faster than most DNA viruses. However, there is tremendous variation among the evolutionary rates of different RNA viruses, which is not explained by variation in mutation rates. Here we present a survey of mammalian RNA virus rates of evolution, and a comprehensive comparison of these rates to different properties of virus genomic architecture and ecology. We found that cell tropism is the most significant predictor of long-term rates of mammalian RNA virus evolution. For instance, viruses targeting epithelial cells evolve significantly faster than viruses that target neurons. Our results provide mechanistic insight into why viruses that infect respiratory and gastrointestinal epithelia have been difficult to control.
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Kovaliski J, Sinclair R, Mutze G, Peacock D, Strive T, Abrantes J, Esteves PJ, Holmes EC. Molecular epidemiology of Rabbit Haemorrhagic Disease Virus in Australia: when one became many. Mol Ecol 2013; 23:408-20. [PMID: 24251353 DOI: 10.1111/mec.12596] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 11/06/2013] [Accepted: 11/13/2013] [Indexed: 12/20/2022]
Abstract
Rabbit Haemorrhagic Disease Virus (RHDV) was introduced into Australia in 1995 as a biological control agent against the wild European rabbit (Oryctolagus cuniculus). We evaluated its evolution over a 16-year period (1995-2011) by examining 50 isolates collected throughout Australia, as well as the original inoculum strains. Phylogenetic analysis of capsid protein VP60 sequences of the Australian isolates, compared with those sampled globally, revealed that they form a monophyletic group with the inoculum strains (CAPM V-351 and RHDV351INOC). Strikingly, despite more than 3000 rereleases of RHDV351INOC since 1995, only a single viral lineage has sustained its transmission in the long-term, indicative of a major competitive advantage. In addition, we find evidence for widespread viral gene flow, in which multiple lineages entered individual geographic locations, resulting in a marked turnover of viral lineages with time, as well as a continual increase in viral genetic diversity. The rate of RHDV evolution recorded in Australia -4.0 (3.3-4.7) × 10(-3) nucleotide substitutions per site per year - was higher than previously observed in RHDV, and evidence for adaptive evolution was obtained at two VP60 residues. Finally, more intensive study of a single rabbit population (Turretfield) in South Australia provided no evidence for viral persistence between outbreaks, with genetic diversity instead generated by continual strain importation.
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Affiliation(s)
- John Kovaliski
- NRM Biosecurity, Biosecurity South Australia, PO Box 1671, Adelaide, SA, 5001, Australia.,Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601, Australia
| | - Ron Sinclair
- NRM Biosecurity, Biosecurity South Australia, PO Box 1671, Adelaide, SA, 5001, Australia.,Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601, Australia
| | - Greg Mutze
- NRM Biosecurity, Biosecurity South Australia, PO Box 1671, Adelaide, SA, 5001, Australia.,Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601, Australia
| | - David Peacock
- NRM Biosecurity, Biosecurity South Australia, PO Box 1671, Adelaide, SA, 5001, Australia.,Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601, Australia
| | - Tanja Strive
- Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601, Australia.,CSIRO Ecosystem Sciences, Black Mountain Laboratories, Clunies Ross Street, Black Mountain, ACT, 2601, Australia
| | - Joana Abrantes
- CIBIO/UP Centro de Investigação em Biodiversidade e Recursos Genéticos/Universidade do Porto, InBio, Laboratório Associado, Campus Agrário de Vairão, R. Padre Armando Quintas, 4485-661, Vairão, Portugal.,INSERM, U892, Université de Nantes, Nantes, France
| | - Pedro J Esteves
- INSERM, U892, Université de Nantes, Nantes, France.,CITS, Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, Gandra, Portugal
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
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Le Gall-Reculé G, Lavazza A, Marchandeau S, Bertagnoli S, Zwingelstein F, Cavadini P, Martinelli N, Lombardi G, Guérin JL, Lemaitre E, Decors A, Boucher S, Le Normand B, Capucci L. Emergence of a new lagovirus related to Rabbit Haemorrhagic Disease Virus. Vet Res 2013; 44:81. [PMID: 24011218 PMCID: PMC3848706 DOI: 10.1186/1297-9716-44-81] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 08/28/2013] [Indexed: 11/10/2022] Open
Abstract
Since summer 2010, numerous cases of Rabbit Haemorrhagic Disease (RHD) have been reported in north-western France both in rabbitries, affecting RHD-vaccinated rabbits, and in wild populations. We demonstrate that the aetiological agent was a lagovirus phylogenetically distinct from other lagoviruses and which presents a unique antigenic profile. Experimental results show that the disease differs from RHD in terms of disease duration, mortality rates, higher occurrence of subacute/chronic forms and that partial cross-protection occurs between RHDV and the new RHDV variant, designated RHDV2. These data support the hypothesis that RHDV2 is a new member of the Lagovirus genus. A molecular epidemiology study detected RHDV2 in France a few months before the first recorded cases and revealed that one year after its discovery it had spread throughout the country and had almost replaced RHDV strains. RHDV2 was detected in continental Italy in June 2011, then four months later in Sardinia.
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Affiliation(s)
- Ghislaine Le Gall-Reculé
- Anses, French Agency for Food, Environmental and Occupational Health & Safety, Ploufragan-Plouzané Laboratory, Avian and Rabbit Virology, Immunology and Parasitology Unit, BP 53, 22440 Ploufragan, France.
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Abrantes J, Lopes AM, Dalton KP, Parra F, Esteves PJ. Detection of RHDVa on the Iberian Peninsula: isolation of an RHDVa strain from a Spanish rabbitry. Arch Virol 2013; 159:321-6. [PMID: 23942953 DOI: 10.1007/s00705-013-1808-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 05/29/2013] [Indexed: 10/26/2022]
Abstract
Rabbit haemorrhagic disease virus (RHDV), genus Lagovirus, family Caliciviridae, causes a large number of deaths in wild and domestic adult European rabbits (Oryctolagus cuniculus). The first documented outbreak dates from 1984 in China, but the virus rapidly dispersed worldwide. In 1997, an antigenic variant was detected in Italy and designated RHDVa. Despite causing symptoms similar to those caused by classic RHDV strains, marked antigenic and genetic differences exist. In some parts of Europe, RHDVa is replacing classic strains. Here, we report the presence of RHDVa on the Iberian Peninsula, where this variant was thought not to contribute to viral diversity.
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Affiliation(s)
- Joana Abrantes
- CIBIO/UP, Centro de Investigação em Biodiversidade e Recursos Genéticos/Universidade do Porto, InBio, Laboratório Associado, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr. 7, 4485-661, Vairão, Portugal,
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Rice yellow mottle virus in Madagascar and in the Zanzibar Archipelago; island systems and evolutionary time scale to study virus emergence. Virus Res 2012; 171:71-9. [PMID: 23123216 DOI: 10.1016/j.virusres.2012.10.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 10/19/2012] [Accepted: 10/22/2012] [Indexed: 11/23/2022]
Abstract
Rice yellow mottle virus (RYMV), of the genus Sobemovirus, is a major threat to rice cultivation in Africa. Long range transmission of RYMV, difficult to study experimentally, is inferred from a detailed analysis of the molecular diversity of the virus in Madagascar and in the Zanzibar Archipelago (Zanzibar and Pemba Islands; Tanzania) compared with that found elsewhere in Africa. A unique successful introduction of RYMV to Madagascar, which is ca. 400 km from mainland Africa, contrasted with recurrent introductions of the virus to the Zanzibar Archipelago, ca. 40 km from the East African coast. Accordingly, RYMV dispersal over distances of hundreds of kilometers is rare whereas spread of the virus over distances of tens of kilometers is relatively frequent. The dates of introduction of RYMV to Madagascar and to Pemba Island were estimated from three sets of ORF4 sequences of virus isolates collected between 1966 and 2011. They were compared with the dates of the first field detection in Madagascar (1989) and in Pemba Island (1990). The estimates did not depend substantially on the data set used or on the evolutionary model applied and their credible intervals were narrow. The estimated dates are recent - 1978 (1969-1986) and 1985 (1977-1993) in Madagascar and in Pemba Island, respectively - compared to the early diversification of RYMV in East Africa ca. 200 years ago. They predated by 5-10 years the first field detections in these islands. The interplay between virus sources, rice cultivation and long range dispersal which led to RYMV emergence and spread is enlightened.
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