Phylogenetic relationships of seven previously unclassified viruses within the family Rhabdoviridae using partial nucleoprotein gene sequences

• Published in: Journal of general virology 2006-08, Vol.87 (8), p.2323-2331
• Main Authors: Kuzmin, I. V, Hughes, G. J, Rupprecht, C. E
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Amino Acid Substitution; Biological and medical sciences; Ephemerovirus; Evolution, Molecular; Fundamental and applied biological sciences. Psychology; Lyssavirus; Microbiology; Miscellaneous; Molecular Sequence Data; Nucleocapsid Proteins - chemistry; Nucleocapsid Proteins - genetics; Oita virus; Phylogeny; Rhabdoviridae; Rhabdoviridae - classification; Rhabdoviridae - genetics; Rhabdovirus; Sequence Analysis, DNA; Sequence Homology, Amino Acid; Tupaia virus; Vesiculovirus; Virology
• ISSN: 0022-1317; 1465-2099
• DOI: 10.1099/vir.0.81879-0

1 Rabies Union, Centers for Disease Control and Prevention, 1600 Clifton Road, MS G-33, Atlanta, GA 30333, USA 2 Laboratory for Clinical and Molecular Virology, The University of Edinburgh, Summerhall, Edinburgh EH9 1QH, UK Correspondence I. V. Kuzmin ibk3{at}cdc.gov Partial nucleoprotein (N) gene sequences of the rhabdoviruses Obodhiang (OBOV), Kotonkon (KOTV), Rochambeau (RBUV), Kern canyon (KCV), Mount Elgon bat (MEBV), Kolongo (KOLV) and Sandjimba (SJAV) were generated and their phylogenetic positions within the family Rhabdoviridae were determined. Both OBOV and KOTV were placed within the genus Ephemerovirus . RBUV was joined to the same cluster, but more distantly. MEBV and KCV were grouped into a monophyletic cluster (putative genus) with Oita virus (OITAV). These three viruses, originating from different regions of the world, were all isolated from insectivorous bats and may be specific for these mammals. African avian viruses KOLV and SJAV were joined to each other and formed another clade at the genus level. Further, they were grouped with the recently characterized rhabdovirus Tupaia virus (TRV). Although the genetic distance was great, the grouping was supported by consistent bootstrap values. This observation suggests that viruses of this group may be distributed widely in the Old World. Non-synonymous/synonymous substitution ratio estimations ( d N / d S ) using a partial N gene fragment (241 codons) for the three rhabdovirus genera revealed contrasting patterns of evolution, where d N / d S values follow the pattern Ephemerovirus > Vesiculovirus > Lyssavirus . The magnitude of this ratio corresponds well with the number of negatively selected codons. The accumulation of d S appears evenly distributed along the gene fragment for all three genera. These estimations demonstrated clearly that lyssaviruses are subjected to the strongest constraints against amino acid substitutions, probably related to their particular niche and unique pathobiology. The GenBank/EMBL/DDBJ accession numbers of the rhabdovirus partial N gene sequences obtained in this study are DQ457098–DQ457104, as outlined in Table 1.