An evolutionary divergent pestivirus lacking the N^pro gene systemically infects a whale species

References

• Becher P, Orlich M, Shannon AD, et al. Phylogenetic analysis of pestiviruses from domestic and wild ruminants. J Gen Virol. 1997;78:1357–1366. doi: 10.1099/0022-1317-78-6-1357
   PubMed Web of Science ®Google Scholar
• Becher P, Orlich M, Kosmidou A, et al. Genetic diversity of pestiviruses: identification of novel groups and implications for classification. Virology. 1999;262:64–71. doi: 10.1006/viro.1999.9872
   PubMed Web of Science ®Google Scholar
• Vilcek S, Ridpath JF, Van Campen H, et al. Characterization of a novel pestivirus originating from a pronghorn antelope. Virus Res. 2005;108:187–193. doi: 10.1016/j.virusres.2004.09.010
   PubMed Web of Science ®Google Scholar
• Blome S, Beer M, Wernike K. New leaves in the growing tree of pestiviruses. Adv Virus Res. 2017;99:139–160. doi: 10.1016/bs.aivir.2017.07.003
   PubMed Web of Science ®Google Scholar
• Wu Z, Ren X, Yang L, et al. Virome analysis for identification of novel Mammalian viruses in bat species from Chinese Provinces. J Virol. 2012;86:10999–11012. doi: 10.1128/JVI.01394-12
   PubMed Web of Science ®Google Scholar
• Firth C, Bhat M, Firth MA, et al. Detection of zoonotic pathogens and characterization of novel viruses carried by commensal Rattus norvegicus in New York City. MBio. 2014;5:e01933–14. doi: 10.1128/mBio.01933-14
   PubMed Web of Science ®Google Scholar
• Bekal S, Domier LL, Gonfa B, et al. A novel flavivirus in the soybean cyst nematode. J Gen Virol. 2014;95:1272–1280. doi: 10.1099/vir.0.060889-0
   PubMed Web of Science ®Google Scholar
• Peterhans E, Schweizer M. Pestiviruses: how to outmaneuver your hosts. Vet Microbiol. 2010;142:18–25. doi: 10.1016/j.vetmic.2009.09.038
   PubMed Web of Science ®Google Scholar
• Becher P, Tautz N. RNA recombination in pestiviruses: cellular RNA sequences in viral genomes highlight the role of host factors for viral persistence and lethal disease. RNA Biol. 2011;8:216–224. doi: 10.4161/rna.8.2.14514
   PubMed Web of Science ®Google Scholar
• Tautz N, Tews BA, Meyers G. The molecular biology of pestiviruses. Adv Vir Res. 2015;93:47–160. doi: 10.1016/bs.aivir.2015.03.002
   PubMed Web of Science ®Google Scholar
• Gottipati K, Holthauzen LMF, Ruggli N, et al. Pestivirus Npro directly interacts with interferon regulatory factor 3 monomer and dimer. Diamond MS, editor. J Virol. 2016;90:7740–7747. doi: 10.1128/JVI.00318-16
   PubMed Web of Science ®Google Scholar
• Fiebach AR, Guzylack-Piriou L, Python S, et al. Classical swine fever virus Npro limits type I interferon induction in plasmacytoid dendritic cells by interacting with interferon regulatory factor 7. J Virol. 2011;85:8002–8011. doi: 10.1128/JVI.00330-11
   PubMed Web of Science ®Google Scholar
• Kennedy S, Smyth JA, Cush PF, et al. Viral distemper now found in porpoises. Nature. 1988;336:21–21. doi: 10.1038/336021a0
   PubMed Web of Science ®Google Scholar
• de Graaf M, Bodewes R, van Elk CE, et al. Norovirus infection in harbor porpoises. Emerg Infect Dis. 2017;23:87–91. doi: 10.3201/eid2301.161081
   PubMed Web of Science ®Google Scholar
• van Elk C, van de Bildt M, van Run P, et al. Central nervous system disease and genital disease in harbor porpoises (Phocoena phocoena) are associated with different herpesviruses. Vet Res. 2016;47:28. doi: 10.1186/s13567-016-0310-8
   PubMed Web of Science ®Google Scholar
• van Beurden SJ, IJsseldijk LL, van de Bildt MWG, et al. A novel cetacean adenovirus in stranded harbour porpoises from the North Sea: detection and molecular characterization. Arch Virol. 2017;162:2035–2040. doi: 10.1007/s00705-017-3310-8
   PubMed Web of Science ®Google Scholar
• Endoh D, Mizutani T, Kirisawa R, et al. Species-independent detection of RNA virus by representational difference analysis using non-ribosomal hexanucleotides for reverse transcription. Nucleic Acids Res. 2005;33:e65. doi: 10.1093/nar/gni064
   PubMed Web of Science ®Google Scholar
• Allander T, Emerson SU, Engle RE, et al. A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species. Proc Natl Acad Sci. 2001;98:11609–11614. doi: 10.1073/pnas.211424698
   PubMed Web of Science ®Google Scholar
• Kruppa J, Jo WK, van der Vries E, et al. Virus detection in high-throughput sequencing data without a reference genome of the host. Infect Genet Evol. 2018;66:180–187. doi: 10.1016/j.meegid.2018.09.026
   PubMed Web of Science ®Google Scholar
• Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–359. doi: 10.1038/nmeth.1923
   PubMed Web of Science ®Google Scholar
• Huson DH, Xie C. A poor man’s BLASTX - high-throughput metagenomic protein database search using PAUDA. Bioinformatics. 2014;30:38–39. doi: 10.1093/bioinformatics/btt254
   PubMed Web of Science ®Google Scholar
• Katoh K, Rozewicki J, Yamada KD. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform. 2017.
   PubMed Web of Science ®Google Scholar
• Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33:1870–1874. doi: 10.1093/molbev/msw054
   PubMed Web of Science ®Google Scholar
• Liebler-Tenorio EM, Ridpath JF, Neill JD. Distribution of viral antigen and tissue lesions in persistent and acute infection with the homologous strain of noncytopathic bovine viral diarrhea virus. J Vet Diagnostic Investig. 2004;16:388–396. doi: 10.1177/104063870401600504
   PubMed Web of Science ®Google Scholar
• Cutlip RC, McClurkin AW, Coria MF. Lesions in clinically healthy cattle persistently infected with the virus of bovine viral diarrhea–glomerulonephritis and encephalitis. Am J Vet Res. 1980;41:1938–1941.
   PubMed Web of Science ®Google Scholar
• McClurkin AW, Littledike ET, Cutlip RC, et al. Production of cattle immunotolerant to bovine viral diarrhea virus. Can J Comp Med Rev Can Med Comp. 1984;48:156–161.
   PubMed Web of Science ®Google Scholar
• Brown C, Baker D, Barker I. The alimentary system. In: Maxie G, editor. Pathology of domestic animals. 5th ed. New York: Elsevier; 2007. p. 2340.
   Google Scholar
• King BF. Comparative studies of structure and function in Mammalian placentas with special reference to maternal-fetal transfer of iron. Am Zool. 1992;32:331–342. doi: 10.1093/icb/32.2.331
   Google Scholar
• Tratschin JD, Moser C, Ruggli N, et al. Classical swine fever virus leader proteinase Npro is not required for viral replication in cell culture. J Virol. 1998;72:7681–7684.
   PubMed Web of Science ®Google Scholar
• Gil LHVG, Ansari IH, Vassilev V, et al. The amino-terminal domain of bovine viral diarrhea virus Npro protein is necessary for alpha/beta interferon antagonism. J Virol. 2006;80:900–911. doi: 10.1128/JVI.80.2.900-911.2006
   PubMed Web of Science ®Google Scholar
• Mayer D, Hofmann MA, Tratschin J-D. Attenuation of classical swine fever virus by deletion of the viral Npro gene. Vaccine. 2004;22:317–328. doi: 10.1016/j.vaccine.2003.08.006
   PubMed Web of Science ®Google Scholar
• Lai VCH, Zhong W, Skelton A, et al. Generation and characterization of a hepatitis C virus NS3 protease-dependent bovine viral diarrhea virus. J Virol. 2000;74:6339–6347. doi: 10.1128/JVI.74.14.6339-6347.2000
   PubMed Web of Science ®Google Scholar
• Myers TM, Kolupaeva VG, Mendez E, et al. Efficient translation initiation is required for replication of bovine viral diarrhea virus subgenomic replicons. J Virol. 2001;75:4226–4238. doi: 10.1128/JVI.75.9.4226-4238.2001
   PubMed Web of Science ®Google Scholar
• Meyers G, Ege A, Fetzer C, et al. Bovine viral diarrhea virus: prevention of persistent fetal infection by a combination of two mutations affecting Erns RNase and Npro protease. J Virol. 2007;81:3327–3338. doi: 10.1128/JVI.02372-06
   PubMed Web of Science ®Google Scholar
• Braun BA, Marcovitz A, Camp JG, et al. Mx1 and Mx2 key antiviral proteins are surprisingly lost in toothed whales. Proc Natl Acad Sci. 2015;112:8036–8040. doi: 10.1073/pnas.1501844112
   PubMed Web of Science ®Google Scholar
• Verhelst J, Hulpiau P, Saelens X. Mx proteins: antiviral gatekeepers that restrain the uninvited. Microbiol Mol Biol Rev. 2013;77:551–566. doi: 10.1128/MMBR.00024-13
   PubMed Web of Science ®Google Scholar