Primary structure of the vesicular stomatitis virus polymerase (L) gene: evidence for a high frequency of mutations.

A consensus sequence of the polymerase (L) gene of vesicular stomatitis virus, derived from three genomic cDNA copies, is presented. This analysis completes the primary structure of the vesicular stomatitis virus genome, totaling 11,162 bases. The L gene alone spans 6,380 nucleotides and codes for a basic 2,109-amino-acid protein with a molecular weight of 241,012. Sixteen point mutations were detected among cDNA clones prepared from viral RNA of the same strain, representing direct evidence for either the high mutability of vesicular stomatitis virus, the infidelity of reverse transcription during cDNA synthesis, or a combination of both. Some mutation, if present in the viral genome, would result in the translation of incomplete L proteins. For example, two out of four cDNA copies which covered the same region of the L gene had a single-base deletion in the exact same position, whereas the other two clones did not, strongly suggesting that a subpopulation of the genomic RNA may contain this lethal mutation. These lethal mutants define a new class of defective and most likely interfering particles which are indistinguishable in size from the parental virus and can be distinguished only by direct sequencing. We suggest that because of its infidelity, the viral polymerase itself introduces mutations and because of its size, most of these mutations are localized within the polymerase gene. In persistently infected cells in which the selective pressures on the polymerase are different, some of these L gene mutations may further erode the accuracy of the polymerase and thereby lead to the increased mutation rate that is characteristic of this type of infection.