A Phylogenomic Study of the Genus Alphavirus Employing Whole Genome Comparison.pdfVIP

Comparative and Functional Genomics Comp Funct Genom 2005; 6: 217–227. Published online in Wiley InterScience (). DOI: 10.1002/cfg.478 Research Article A phylogenomic study of the genus Alphavirus employing whole genome comparison ´ 1 1 2 1 Aimee J. Luers , Sandra D. Adams , John V. Smalley and James J. Campanella * 1 Montclair State University, Department of Biology and Molecular Biology, 1 Normal Avenue, Montclair, NJ 07043, USA 2 Bergen Community College, Department of Science and Technology, 400 Paramus Road, Paramus, NJ 07652, USA *Correspondence to: Abstract James J. Campanella, Montclair State University, Department of The phylogenetics of the genus Alphavirus have historically been characterized using Biology and Molecular Biology, 1 partial gene, single gene or partial proteomic data. We have mined cDNA and Normal Avenue, Montclair, NJ amino acid sequences from GenBank for all fully sequenced and some partially 07043, USA. sequenced alphaviruses and generated phylogenomic analyses of the genus Alphavirus E-mail: genus, employing capsid encoding structural regions, non-structural coding regions james.campanella@ and complete viral genomes. Our studies support the presence of the previously reported recombination event that produced the Western Equine Encephalitis clade, and confirm many of the patterns of geographic radiation and divergence of the multiple species. Our data suggest that the Salmon Pancreatic Disease Virus and Sleeping