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United States Department of Agriculture

Agricultural Research Service

Title: Full-Length Genome Analysis of Natural Isolates of Vesicular Stomatits Viruses (Indiana 1 Serotype) from North, Central and South America

Authors
item Rodriguez, Luis
item Pauszek, Steven
item Bunch, Thomas - FORMER ARS EMPLOYEE
item Schumann, Kate - FORMER ARS EMPLOYEE

Submitted to: Journal of General Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 20, 2002
Publication Date: October 1, 2002
Citation: RODRIGUEZ,L.L., PAUSZEK,S.J., BUNCH,T.A., SCHUMANN,K.R., FULL-LENGTH GENOME ANALYSIS OF NATURAL ISOLATES OF VESICULAR STOMATITS VIRUSES (INDIANA 1 SEROTYPE) FROM NORTH, CENTRAL AND SOUTH AMERICA, JOURNAL OF GENERAL VIROLOGY, V83:2475-2483, 2002

Interpretive Summary: Only one full-length genomic sequence of vesicular stomatitis virus Indiana serotype (VSV-IN1) is currently deposited in GenBank. Most studies on the molecular biology and functional analyses of the VSV-IN1 genome are based on this sequence, which is a composite of several VSV-IN1 laboratory strains passaged extensively in tissue culture over the years. It is not certain that this sequence is representative of strains circulating in nature. We describe for the first time, complete genomic sequences of three natural isolates, each representing a distinct genetic lineage and geographic origin. Genome structure and organization were conserved among the three viruses. The most conserved gene was N, followed by genes M,L,G and the most variable was P. Since N is the both the most conserved gene and the most abundant transcript, it shows the most potential as a target for molecular probes. As we expected sequences containing the transcription and replication control signals were completely conserved among all viruses but changes were found in the intergenic nucleotide at the M-G junction of the South American lineage. An insertion of variable length (100-187 nucleotides) was present in the non-coding region of the glycoprotein gene only in viruses from a genetic lineage from northern Central America. By comparing the viral genes we identified variable as well as conserved areas related to functional and antigenic domains. These full-length genomic sequences should be useful in designing diagnostic probes and on the interpretation of functional genomic analyses using reverse genetics.

Technical Abstract: We describe the complete genomic sequence of three natural isolates, each representing a distinct genetic lineage and geographic origin: 98COE (North America lineage), 94GUB (Central America lineage), and 85CLB (South America lineage). Genome structure and organization were conserved among the three viruses, with a 47-nucleotide 3' leader (3'Le); five viral genes: N, P, M, G, L and a 59-nucleotide 5' trailer sequence (5'Tr). The small, highly basic C-C' proteins, coded in a second open reading frame within the P gene, were highly variable in sequence but maintained high pI values for all viruses. The most conserved gene was N followed by M, L, G and the most variable was the P gene. Sequences containing the polyadenylation and transcription stop and start signals (3'AUACU7NN(N)UUGUC5') were completely conserved among all viruses, but changes were found in the intergenic dinucleotide, including the presence of a trinucleotide at the M:G junction nof the South American lineage. A nucleotide insertion composed primarily of imprecise reiterations of the sequence (3'UUAAAAA5'), was present in the 5' non-coding region of G only in viruses from a genetic lineage from northern Central America. By comparing the viral genes we identified variable as well as conserved areas related to functional and antigenic domains. These full-length genomic sequences should be useful in designing diagnostic probes and on the interpretation of functional genomic analyses using reverse genetics.

Last Modified: 4/18/2014