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Gene Mapping and Phylogenetic Analysis of the Complete Genome from 30 Single-Stranded RNA Male-Specific Coliphages (Family Leviviridae)
Citation:
FRIEDMAN, S. D., F. J. GENTHNER, J. GENTRY, M. D. SOBSEY, AND J. VINJE. Gene Mapping and Phylogenetic Analysis of the Complete Genome from 30 Single-Stranded RNA Male-Specific Coliphages (Family Leviviridae). JOURNAL OF VIROLOGY. American Society for Microbiology, Washington, DC, 83(21):11233-11243, (2009).
Impact/Purpose:
RARE project to design molecular assay for viral FRNA coliphages. This paper was the result of a genetic database developed on which the molecular assay was designed.
Description:
Male-specific ssRNA (FRNA) coliphages belong to the family Leviviridae. Two genera subdivided into four genogroups (Levivirus, genogroups I and II and Allolevivirus, genogroups III and IV) comprise the lower taxonomic levels. Strains isolated from several continents have been partially characterized; a detailed knowledge of their genetic diversity is, however, lacking. To better characterize the Leviviridae family complete genomic sequences of nineteen FRNA strains (10 Levivirus and 9 Allolevivirus) were determined and compared to eleven genome sequences available in GenBank, for a total of thirty FRNA genomes. Levivirus strains shared 75% - 99% and 83-94% nucleotide similarity for genogroups I and II, respectively. Allolevivirus strains shared a nucleotide similarity range of 70-96% and 75-95% for genogroups III and IV, respectively. Amino acid composition, nucleotide similarities and replicase catalytic domain location contributed to phylogenetic branches. Eight nucleotides at the 3' termini clearly distinguished the Levivirus from the Allolevivirus genera.