Detection of a new emerging strain of rabbit haemorrhagic disease virus 2 (GI.2) in China

1Abrantes J., van der Loo W., Le Pendu J., Esteves P.J.: Rabbit haemorrhagic disease (RHD) and rabbit haemorrhagic disease virus (RHDV): a review. Vet Res 2012, 43, 12, doi: 10.1186/12979716-43-12. Abrantes J. van der Loo W. Le Pendu J. Esteves P.J. Rabbit haemorrhagic disease (RHD) and rabbit haemorrhagic disease virus (RHDV): a review Vet Res 2012 43 12 10.1186/12979716-43-12Open DOISearch in Google Scholar

2Bankevich A., Nurk S., Antipov D., Gurevich A.A., Dvorkin M., Kulikov A.S., Lesin V.M., Nikolenko S.I., Pham S., Prjibelski A.D., Pyshkin A.V., Sirotkin A.V., Vyahhi N., Tesler G., Alekseyev M.A., Pevzner P.A.: SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012, 19, 455–477, doi: 10.1089/cmb.2012.0021. Bankevich A. Nurk S. Antipov D. Gurevich A.A. Dvorkin M. Kulikov A.S. Lesin V.M. Nikolenko S.I. Pham S. Prjibelski A.D. Pyshkin A.V. Sirotkin A.V. Vyahhi N. Tesler G. Alekseyev M.A. Pevzner P.A. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing J Comput Biol 2012 19 455 477 10.1089/cmb.2012.0021Open DOISearch in Google Scholar

3Camarda A., Pugliese N., Cavadini P., Circella E., Capucci L., Caroli A., Legretto M., Mallia E., Lavazza A.: Detection of the new emerging rabbit haemorrhagic disease type 2 virus (RHDV2) in Sicily from rabbit (Oryctolagus cuniculus) and Italian hare (Lepus corsicanus). Res Vet Sci 2014, 97, 642–645, doi: 10.1016/j.rvsc.2014.10.008. Camarda A. Pugliese N. Cavadini P. Circella E. Capucci L. Caroli A. Legretto M. Mallia E. Lavazza A. Detection of the new emerging rabbit haemorrhagic disease type 2 virus (RHDV2) in Sicily from rabbit (Oryctolagus cuniculus) and Italian hare (Lepus corsicanus) Res Vet Sci 2014 97 642 645 10.1016/j.rvsc.2014.10.008Open DOISearch in Google Scholar

4Capucci L., Cavadini P., Schiavitto M., Lombardi G., Lavazza A.: Increased pathogenicity in rabbit haemorrhagic disease virus type 2 (RHDV2). Vet Rec 2017, 180, 426, doi: 10.1136/vr.104132. Capucci L. Cavadini P. Schiavitto M. Lombardi G. Lavazza A. Increased pathogenicity in rabbit haemorrhagic disease virus type 2 (RHDV2) Vet Rec 2017 180 426 10.1136/vr.104132Open DOISearch in Google Scholar

5Coil D., Jospin G., Darling A.E.: A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 2015, 15, 587–589, doi: 10.1093/bioinformatics/ btu661. Coil D. Jospin G. Darling A.E. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data Bioinformatics 2015 15 587 589 10.1093/bioinformatics/btu661Open DOISearch in Google Scholar

6Dalton K.P., Nicieza I., Abrantes J., Esteves P.J., Parra F.: Spread of new variant RHDV in domestic rabbits on the Iberian Peninsula. Vet Microbiol 2014, 21, 169, 67–73, doi: 10.1016/j.vetmic.2013.12.015. Dalton K.P. Nicieza I. Abrantes J. Esteves P.J. Parra F. Spread of new variant RHDV in domestic rabbits on the Iberian Peninsula Vet Microbiol 2014 21 169 67–73 10.1016/j.vetmic.2013.12.015Open DOISearch in Google Scholar

7Dalton K.P., Nicieza I., Balseiro A., Muguerza M.A., Rosell J.M., Casais R., Álvarez Á.L., Parra F.: Variant rabbit hemorrhagic disease virus in young rabbits, Spain. Emerg Infect Dis 2012, 18, 2009–2012, doi: 10.3201/eid1812.120341. Dalton K.P. Nicieza I. Balseiro A. Muguerza M.A. Rosell J.M. Casais R. Álvarez Á.L. Parra F. Variant rabbit hemorrhagic disease virus in young rabbits, Spain Emerg Infect Dis 2012 18 2009 2012 10.3201/eid1812.120341Open DOISearch in Google Scholar

8Hu B., Wei H., Fan Z., Song Y., Chen M., Qiu R., Zhu W., Xu W., Xue J., Wang F.: Emergence of rabbit haemorrhagic disease virus 2 in China in 2020. Vet Med Sci 2021, 7, 236–239, doi: 10.1002/vms3.332. Hu B. Wei H. Fan Z. Song Y. Chen M. Qiu R. Zhu W. Xu W. Xue J. Wang F. Emergence of rabbit haemorrhagic disease virus 2 in China in 2020 Vet Med Sci 2021 7 236 239 10.1002/vms3.332Open DOISearch in Google Scholar

9König M., Thiel H.-J., Meyers G.: Detection of viral proteins after infection of cultured hepatocytes with rabbit hemorrhagic disease virus. J Virol 1998, 72, 4492–4497, doi: 10.1128/JVI.72.5.4492-4497.1998. König M. Thiel H.-J. Meyers G. Detection of viral proteins after infection of cultured hepatocytes with rabbit hemorrhagic disease virus J Virol 1998 72 4492 4497 10.1128/JVI.72.5.4492-4497.1998Open DOISearch in Google Scholar

10Kumar S., Stecher G., Li M., Knyaz C., Tamura K.: MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol 2018, 35, 1547–1549, doi: 10.1093/molbev/msy096. Kumar S. Stecher G. Li M. Knyaz C. Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms Mol Biol Evol 2018 35 1547 1549 10.1093/molbev/msy096Open DOISearch in Google Scholar

11Kurtz S., Phillippy A., Delcher A.L., Smoot M., Shumway M., Antonescu C., Salzberg S.L.: Versatile and open software for comparing large genomes. Genome Biol 2004, 5, R12, doi: 10.1186/gb-2004-5-2-r12. Kurtz S. Phillippy A. Delcher A.L. Smoot M. Shumway M. Antonescu C. Salzberg S.L. Versatile and open software for comparing large genomes Genome Biol 2004 5 R12 10.1186/gb-2004-5-2-r12Open DOISearch in Google Scholar

12Le Gall-Reculé G., Lavazza A., Marchandeau S., Bertagnoli S., Zwingelstein F., Cavadini P., Martinelli N., Lombardi G., Guérin J.-L., 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, 8, 44, 81, doi: 10.1186/1297-9716-44-81. Le Gall-Reculé G. Lavazza A. Marchandeau S. Bertagnoli S. Zwingelstein F. Cavadini P. Martinelli N. Lombardi G. Guérin J.-L. 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 8 44 81 10.1186/1297-9716-44-81Open DOISearch in Google Scholar

13Le Pendu J., Abrantes J., Bertagnoli S., Guitton J-S., Le Gall-Reculé G., Lopes A.M., Marchandeau S., Alda F., Almeida T., Célio A.P., Bárcena J., Burmakina G., Blanco E., Calvete C., Cavadini P., Cooke B., Dalton K., Delibes Mateos M., Deptuła W., Eden J.S., Wang F., Ferreira C.C., Ferreira P., Foronda P., Gonçalves D., Gavier-Widén D., Hall R., Hukowska-Szematowicz B., Kerr P., Kovaliski J., Lavazza A., Mahar J., Malogolovkin A., Marques R.M., Marques S., Martin-Alonso A., Monterroso P., Moreno S., Mutze G., Neimanis A., Niedźwiedzka-Rystwej P., Peacock D., Parra F., Rocchi M., Rouco C., Ruvoën-Clouet N., Silva E., Silvério D., Strive T., Thompson G., Tokarz-Deptuła B., Esteves P.: Proposal for a unified classification system and nomenclature of lagoviruses. J Gen Virol 2017, 98, 1658–1666, doi: 10.1099/jgv.0.000840. Le Pendu J. Abrantes J. Bertagnoli S. Guitton J-S. Le Gall-Reculé G. Lopes A.M. Marchandeau S. Alda F. Almeida T. Célio A.P. Bárcena J. Burmakina G. Blanco E. Calvete C. Cavadini P. Cooke B. Dalton K. Delibes Mateos M. Deptuła W. Eden J.S. Wang F. Ferreira C.C. Ferreira P. Foronda P. Gonçalves D. Gavier-Widén D. Hall R. Hukowska-Szematowicz B. Kerr P. Kovaliski J. Lavazza A. Mahar J. Malogolovkin A. Marques R.M. Marques S. Martin-Alonso A. Monterroso P. Moreno S. Mutze G. Neimanis A. Niedźwiedzka-Rystwej P. Peacock D. Parra F. Rocchi M. Rouco C. Ruvoën-Clouet N. Silva E. Silvério D. Strive T. Thompson G. Tokarz-Deptuła B. Esteves P. Proposal for a unified classification system and nomenclature of lagoviruses J Gen Virol 2017 98 1658 1666 10.1099/jgv.0.000840Open DOISearch in Google Scholar

14Liu S.J., Xue H.P., Pu B.Q., Qian N.H., Xu W.Y., Du N.X.: A New Viral Disease in Rabbits (in Chinese). Animal Husb Vet Med 1984, 16, 253–255. Liu S.J. Xue H.P. Pu B.Q. Qian N.H. Xu W.Y. Du N.X. A New Viral Disease in Rabbits (in Chinese) Animal Husb Vet Med 1984 16 253 255Search in Google Scholar

15Lopes A.M., Correia J., Abrantes J., Melo P., Ramada M., Magalhães M.J., Alves P.C., Esteves P.J.: Is the new variant RHDV replacing genogroup 1 in Portuguese wild rabbit populations? Viruses 2015, 7, 27–36, doi: 10.3390/v7010027. Lopes A.M. Correia J. Abrantes J. Melo P. Ramada M. Magalhães M.J. Alves P.C. Esteves P.J. Is the new variant RHDV replacing genogroup 1 in Portuguese wild rabbit populations? Viruses 2015 7 27 36 10.3390/v7010027Open DOISearch in Google Scholar

16Lopes A.M., Dalton K.P., Magalhães M.J., Parra F., Esteves P.J., Holmes E.C., Abrantes J.: Full genomic analysis of new variant rabbit hemorrhagic disease virus revealed multiple recombination events. J Gen Virol 2015, 96, 1309–1319, doi: 10.1099/vir.0.000070. Lopes A.M. Dalton K.P. Magalhães M.J. Parra F. Esteves P.J. Holmes E.C. Abrantes J. Full genomic analysis of new variant rabbit hemorrhagic disease virus revealed multiple recombination events J Gen Virol 2015 96 1309 1319 10.1099/vir.0.000070Open DOISearch in Google Scholar

17Martin D.P., Varsani A., Roumagnac P., Botha G., Maslamoney S., Schwab T., Kelz Z., Kumar V., Murrell B.: RDP5: a computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets. Virus Evol 2021, 7 veaa087, doi: 10.1093/ve/veaa087. Martin D.P. Varsani A. Roumagnac P. Botha G. Maslamoney S. Schwab T. Kelz Z. Kumar V. Murrell B. RDP5: a computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets Virus Evol 2021 7 veaa087 10.1093/ve/veaa087Open DOISearch in Google Scholar

18McIntosh M.T., Behan S.C., Mohamed F.M., Lu Z., Moran K.E., Burrage T.G., Neilan J.G., Ward G.B., Botti G., Capucci L., Metwally S.A.: A pandemic strain of calicivirus threatens rabbit industries in the Americas. Virol J 2007, 4, 96, doi: 10.1186/1743-422X-4-96. McIntosh M.T. Behan S.C. Mohamed F.M. Lu Z. Moran K.E. Burrage T.G. Neilan J.G. Ward G.B. Botti G. Capucci L. Metwally S.A. A pandemic strain of calicivirus threatens rabbit industries in the Americas Virol J 2007 4 96 10.1186/1743-422X-4-96Open DOISearch in Google Scholar

19Neimanis A., Larsson Pettersson U., Huang N., Gavier-Widén D., Strive T.: Elucidation of the pathology and tissue distribution of Lagovirus europaeus GI.2/RHDV2 (rabbit haemorrhagic disease virus 2) in young and adult rabbits (Oryctolagus cuniculus). Vet Res 2018, 49, 46, doi: 10.1186/s13567-018-0540-z. Neimanis A. Larsson Pettersson U. Huang N. Gavier-Widén D. Strive T. Elucidation of the pathology and tissue distribution of Lagovirus europaeus GI.2/RHDV2 (rabbit haemorrhagic disease virus 2) in young and adult rabbits (Oryctolagus cuniculus) Vet Res 2018 49 46 10.1186/s13567-018-0540-zOpen DOISearch in Google Scholar

20Nyström K., Le Gall-Reculé G., Grassi P., Abrantes J., Ruvoën-Clouet N., Le Moullac-Vaidye B., Lopes A.M., Esteves P.J., Strive T., Marchandeau S., Dell A., Haslam S.M., Le Pendu J.: Histo-blood group antigens act as attachment factors of rabbit hemorrhagic disease virus infection in a virus strain-dependent manner. PLoS Pathog 2011, 7, e1002188, doi: 10.1371/journal.ppat.1002188. Nyström K. Le Gall-Reculé G. Grassi P. Abrantes J. Ruvoën-Clouet N. Le Moullac-Vaidye B. Lopes A.M. Esteves P.J. Strive T. Marchandeau S. Dell A. Haslam S.M. Le Pendu J. Histo-blood group antigens act as attachment factors of rabbit hemorrhagic disease virus infection in a virus strain-dependent manner PLoS Pathog 2011 7 e1002188 10.1371/journal.ppat.1002188Open DOISearch in Google Scholar

21Parra F., Prieto M.: Purification and characterization of a calicivirus as the causative agent of a lethal hemorrhagic disease in rabbits. J Virol 1990, 64, 4013–4015, doi: 10.1128/JVI.64.8.4013-4015.1990. Parra F. Prieto M. Purification and characterization of a calicivirus as the causative agent of a lethal hemorrhagic disease in rabbits J Virol 1990 64 4013 4015 10.1128/JVI.64.8.4013-4015.1990Open DOISearch in Google Scholar

22Silvério D., Lopes A.M., Melo-Ferreira J., Magalhães M.J., Monterroso P., Serronha A., Maio E., Alves P.C., Esteves P.J., Abrantes J.: Insights into the evolution of the new variant rabbit haemorrhagic disease virus (GI.2) and the identification of novel recombinant strains. Transbound Emerg Dis 2018, 65, 983–992, doi: 10.1111/tbed.12830. Silvério D. Lopes A.M. Melo-Ferreira J. Magalhães M.J. Monterroso P. Serronha A. Maio E. Alves P.C. Esteves P.J. Abrantes J. Insights into the evolution of the new variant rabbit haemorrhagic disease virus (GI.2) and the identification of novel recombinant strains Transbound Emerg Dis 2018 65 983 992 10.1111/tbed.12830Open DOISearch in Google Scholar

23Vinjé J., Estes M.K., Esteves P., Green K.Y., Katayama K., Knowles N.J., L’Homme Y., Martella V., Vennema H., White P.A., ICTV Report Consortium.: ICTV Virus Taxonomy Profile: Caliciviridae. J Gen Virol 2019, 100, 1469–1470, doi: 10.1099/jgv.0.001332. Vinjé J. Estes M.K. Esteves P. Green K.Y. Katayama K. Knowles N.J. L’Homme Y. Martella V. Vennema H. White P.A. ICTV Report Consortium. ICTV Virus Taxonomy Profile: Caliciviridae J Gen Virol 2019 100 1469 1470 10.1099/jgv.0.001332Open DOISearch in Google Scholar

24Walker B.J., Abeel T., Shea T., Priest M., Abouelliel A., Sakthikumar S., Cuomo C.A., Zeng Q., Wortman J., Young S.K., Earl A.M.: Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014, 9, e112963, doi: 10.1371/journal.pone.0112963. Walker B.J. Abeel T. Shea T. Priest M. Abouelliel A. Sakthikumar S. Cuomo C.A. Zeng Q. Wortman J. Young S.K. Earl A.M. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement PLoS One 2014 9 e112963 10.1371/journal.pone.0112963Open DOISearch in Google Scholar

25Yang Z.-X., Li L.-R., Wang Y., Yao X.-P., Han X.-Q., Yang Z.-Q., Zhou B., Wang K.Y., Zhang Y.-M.: Development of a RT-PCR for the detection of European brown hare syndrome virus. Adv Mater Res 2011, 271–273, 410–416, doi: 10.4028/www.scientific.net/amr.271-273.410. Yang Z.-X. Li L.-R. Wang Y. Yao X.-P. Han X.-Q. Yang Z.-Q. Zhou B. Wang K.Y. Zhang Y.-M. Development of a RT-PCR for the detection of European brown hare syndrome virus Adv Mater Res 2011 271–273 410–416 10.4028/www.scientific.net/amr.271-273.410Open DOISearch in Google Scholar