Downloaded from www.microbiologyresearch.org by IP: 54.224.135.207 On: Tue, 10 May 2016 10:04:46 Journal of General Virology (2002), 83, 2475–2483. Printed in Great Britain ................................................................................................................................................................................................................................................................................... Full-length genome analysis of natural isolates of vesicular stomatitis virus (Indiana 1 serotype) from North, Central and South America Luis L. Rodriguez, Steven J. Pauszek, Thomas A. Bunch† and Kate R. Schumann‡ Plum Island Animal Disease Center, Agricultural Research Service, US Department of Agriculture, Orient Point, Long Island, PO Box 848 Greenport, NY 11944-0848, USA Most studies on the molecular biology and functional analysis of vesicular stomatitis virus Indiana 1 serotype (VSV-IN1) are based on the only full-length genomic sequence currently deposited in GenBank. This sequence is a composite of several VSV-IN1 laboratory strains passaged extensively in tissue culture over the years and it is not certain that this sequence is representative of strains circulating in nature. We describe here the complete genomic sequence of three natural isolates, each representing a distinct genetic lineage and geographical origin : 98COE (North America), 94GUB (Central America) and 85CLB (South America). Genome structure and organization were conserved, with a 47 nucleotide 3 leader, five viral genes – N, P, M, G and L – and a 59 nucleotide 5 trailer. The most conserved gene was N, followed by M, L and G, with the most variable being P. Sequences containing the polyadenylation and transcription stop and start signals were completely conserved among all the viruses studied, but changes were found in the non-transcribed intergenic nucleotides, including the presence of a trinucleotide at the M–G junction of the South American lineage isolate. A 102–189 nucleotide insertion was present in the 5 non-coding region of the G gene only in the viruses within a genetic lineage from northern Central America. These full-length genomic sequences should be useful in designing diagnostic probes and in the interpretation of functional genomic analyses using reverse genetics. Introduction Vesicular stomatitis virus (VSV) is the prototype virus of the family Rhabdoviridae, genus Vesiculovirus. Two serotypes, New Jersey (VSV-NJ) and Indiana (VSV-IN1), cause vesicular disease in livestock in North America, Central America and northern South America. Two subtypes of the Indiana serotype, Cocal (VSV-IN2) and Alagoas (VSV-IN3), cause vesicular disease in livestock in Brazil and Argentina (Rodriguez & Nichol, 1999). VSV-IN1 is widely used as an Author for correspondence : Luis L. Rodriguez. Fax 1 631 323 2507. email lrodriguezpiadc.ars.usda.gov †Present address : Advanced Life Science Products, Corning Inc., Corning, NY 14831, USA. ‡Present address : Animal Health and Biomedical Sciences, University of Wisconsin–Madison, WI 53706, USA. The sequences reported in this manuscript have been submitted to GenBank under accession numbers AF473864–AF473866. RNA virus laboratory model because it readily grows to high titres in a variety of tissue culture cells and in laboratory animal models. Due to the high error rate and lack of proofreading activity of its RNA polymerase, VSV has been extensively used as a model for virus evolution (Holland et al., 1982 ; Domingo et al., 1996). The viral genome consists of a linear, single-stranded, negative-sense RNA molecule of approximately 11 kb en- coding five genes : the nucleocapsid protein (N), phos- phoprotein (P), matrix protein (M), glycoprotein (G) and polymerase (L). A 47 nucleotide leader (Le) RNA is transcribed from the 3 genomic terminus. Only 70 nucleotides – two nucleotides at each of the four gene junctions, three nucleotides at the Le–N junction and a 59 nucleotide trailer (Tr) sequence at the 5 terminus – are not transcribed (Gallione et al., 1981). Two additional small proteins (C and C’) are encoded in a second open reading frame within the P gene (Spiropoulou & Nichol, 1993). Transcription of the viral genes occurs in sequential order from a single promoter at the 3 end of the genome resulting in decreasing amounts of each transcript in 0001-8368 CEHF