SEQUENCE OF THE GENOME OF LACTATE DEHYDROGENASE-ELEVATING VIRUS - HETEROGENICITY BETWEEN STRAIN-P AND STRAIN-C

The complete nucleotide sequence of genomic RNA (14104 nt) of one stra in of lactate dehydrogenase-elevating virus (LDV), LDV-P, is reported. It exhibits only about 80% nucleotide identity with the sequence repo rted for another LDV strain, LDV-C (Godeny el al., Virology 194, 585-5 96 (1993), and is 68 nucleotides shorter than the reported LDV-C seque nce. The difference in length is largely due to the lack of a 59-nucle otide-long direct repeat in ORF la of the reported LDV-C sequence. Seq uence analysis of a total of 1.4 kb of ORF 1a of LDV-C via reverse tra nscription/polymerase chain reaction (RT/PCR) technology failed to con firm the presence of this repeat in the LDV-C genome as well as of 24 deletions/insertions of single nucleotides that give rise to apparent transient reading frame differences between the LDV-P and LDV-C genome s and might have represented frameshift mutations. An additional 35 nu cleotides in ORF la of the RT/PCR LDV-C products were the same as in t he LDV-P rather than the reported LDV-C genome. The nucleotide sequenc es of the 5' leader and the 3' noncoding ends of the two genomes and t he heptanucleotides involved in joining the 5' leader to the bodies of the subgenomic mRNAs were highly conserved or identical. The predicte d LDV-P proteins, however, differed from those predicted for the LDV-C proteins between 25% for the ORF 2 protein and 1% for the ORF 7 nucle ocapsid protein. All functional motifs of the ORF la and ORF Ib protei ns were conserved. The ORF 1a protein possesses 11 potential transmemb rane segments that flank the serine protease domain. (C) 1995 Academic Press, Inc.