Complete genomic sequence and phylogenetic analysis of the lactate dehydrogenase-elevating virus (LDV).
The apparently complete sequence of the RNA genome of the neurovirulent isolate of lactate dehydrogenase-elevating virus (LDV-C) has been determined. The LDV-C genome is at least 14,222 nucleotides in length and contains eight open reading frames (ORFs). ORF 1a, which encodes a protein of 242.8 kDa and is located at the 5' end of the genome, contains at least two putative papain-like cysteine protease domains, and one putative chymotrypsin-like serine protease domain. This ORF terminates with a UAG stop codon that can be bypassed if a -1 frameshift occurs. The frameshift region consists of a heptanucleotide "slippery" sequence, 5'-UUUAAAC-3', followed by a putative pseudoknot. ORF 1b encodes a protein of 155.4 kDa containing, in its N-terminal portion, an RNA-dependent RNA polymerase and an RNA helicase domain separated by a Zn finger domain. Another domain of unknown function that is also conserved in coronaviruses and toroviruses is located at the C-terminus of the ORF 1b product. Three cleavage sites in the ORF 1a polyprotein and three in the ORF 1b polyprotein were predicted for the chymotrypsin-like protease and tentatively delimit the mature nonstructural proteins of LDV. Six small, overlapping 3' ORFs (ORFs 2 through 7) encode proteins with calculated sizes of 25.8, 21.6, 19.8, 23.9, 18.9, and 12.3 kDa. ORF 7 encodes the virion nucleocapsid protein Vp-1, while ORF 6 encodes the nonglycosylated envelope protein Vp2. ORFs 5, 4, 3, and 2 each encode glycoproteins which may be virion envelope proteins. LDV is closely related to equine arteritis virus, Lelystad virus (LV), and simian hemorrhagic fever virus. These four viruses belong to a new group of positive-strand RNA viruses and are related to coronaviruses and toroviruses.
Godeny
E K
EK
Department of Biology, Georgia State University, Atlanta 30302.
Chen
L
L
Kumar
S N
SN
Methven
S L
SL
Koonin
E V
EV
Brinton
M A
MA
D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D003001:Cloning, Molecular; D003062:Codon; D017124:Conserved Sequence; D003332:Coronaviridae / Q000235:genetics; D003546:Cysteine Endopeptidases / Q000235:genetics; D007240:Equartevirus / Q000235:genetics; D016679:Genome, Viral; D007772:Lactate dehydrogenase-elevating virus / Q000145:classification* / Q000235:genetics*; D051379:Mice; D008815:Mice, Inbred Strains; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D020365:RNA Helicases; D012316:RNA Nucleotidyltransferases / Q000235:genetics; D012367:RNA, Viral / Q000235:genetics* / Q000302:isolation & purification; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid; D012697:Serine Endopeptidases / Q000235:genetics; D017003:Torovirus / Q000235:genetics; D016335:Zinc Fingers / Q000235:genetics
D003062:Codon; D012367:RNA, Viral; D012316:RNA Nucleotidyltransferases; D012324:RNA-Dependent RNA Polymerase; D012697:Serine Endopeptidases; D003546:Cysteine Endopeptidases; D020365:RNA Helicases