The Taiwanese hepatitis C virus genome: sequence determination and mapping the 5' termini of viral genomic and antigenomic RNA.

The complete nucleotide sequence of hepatitis C virus (HCV) cloned from the liver tissue of a Taiwanese patient with post-transfusion type C hepatitis was determined. The 5' end of HCV genomic RNA was located 341 nucleotides upstream from the initiation codon for the viral polyprotein open reading frame. The 5' end of the viral antigenomic RNA was shown to have 13 consecutive As. Thus the 3' terminus of the viral genome is a stretch of U which ends about 50 nucleotides downstream from the stop codon of the large open reading frame. The nucleotide sequence homology between this HCV strain and two Japanese isolates was 90.5 and 90.7%, respectively. Homology with the United States strain, however, was only 77.8%. Accordingly, the indigenous Taiwanese HCV strain is of the same subtype as the Japanese isolates. Novel features of the viral genome termini are possibly relevant to HCV genome replication.     

Cloning and sequence analysis of the hemagglutinin gene of the virulent strain of rinderpest virus

We have cloned the cDNA of the hemagglutinin (HA) gene of the virulent (Kabete O) strain of rinderpest virus and produced a comparative analysis of its sequence with that of the HA genes of rinderpest (lapinized strain) and measles viruses. The gene has an open reading frame of 1827 nucleotides, and the derived protein is 609 amino acids long with a calculated molecular weight of 68,006. The Kabete O HA polypeptide is identical in length to the HA of the lapinized strain of rinderpest virus and has a similar hydropathy profile. The nucleotide divergence between the lapinized and the Kabete O HA genes is 11.4% within the coding region, and 34.3% in the 3' untranslated region. The two rinderpest HA polypeptides differ at 74 amino acid residues for a divergence of 12.2%. Three-way comparison of the two rinderpest HA molecules with the measles virus HA polypeptide indicates that 56.6% of the residues are conserved.     

Nucleotide sequence of the 3' terminal region of plum pox potyvirus RNA

The nucleotide sequence of the 3' terminal 2854 nucleotides of plum pox virus RNA has been determined. There is an open reading frame of 2634 nucleotides upstream from a 220 nucleotide 3' non-coding region followed by a long poly(A) tail. The gene coding for the capsid protein has been mapped adjacent to the 3' non-coding region. The predicted capsid protein is originated by a Gln-Ala cleavage and consists of 330 amino acids; the central and carboxy terminal, but not the amino terminal regions present high sequence similarity with other potyviral capsid proteins. A truncated capsid protein which is present in purified preparations of plum pox virus is originated by a Gln-Thr cleavage and contains the 260 carboxy terminal amino acids of the capsid protein. The predicted plum pox virus RNA-dependent RNA polymerase, 518 amino acids long, has been localized at the 5' end of the open reading frame.     

The complete nucleotide sequence and genome organization of tomato infectious chlorosis virus: a distinct crinivirus most closely related to lettuce infectious yellows virus

The complete nucleotide sequence of tomato infectious chlorosis virus (TICV) was determined and compared with those of other members of the genus Crinivirus. RNA 1 is 8,271 nucleotides long with three open reading frames and encodes proteins involved in replication. RNA 2 is 7,913 nucleotides long and encodes eight proteins common within the genus Crinivirus that are involved in genome protection, movement and other functions yet to be identified. Similarity between TICV and other criniviruses varies throughout the genome but TICV is related more closely to lettuce infectious yellows virus than to any other crinivirus, thus identifying a third group within the genus. The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession numbers (FJ815440 and FJ815441).     

Evidence of duplication and deletion in super short segment 11 of rabbit rotavirus Alabama strain

The complete nucleotide sequence of genome segment 11, of the Alabama strain of rabbit rotavirus, was determined by sequencing dsRNA and mRNA using the dideoxy chain termination method. This strain has a "super short" RNA pattern. Its segment 11 is 1036 bp in length, 369 nucleotides longer than that reported for rotavirus strains with a "long" electropherotype. Sequence analysis indicated that the shift in genome segment 11 of Alabama strain to a "super short" RNA pattern results from a simple duplication followed by a simple deletion. The positive strand of segment 11 contains two non-overlapping open reading frames of 594 bases (198 amino acids) starting at base 22 and a second of 273 bases (91 amino acids) starting at base 712. The polypeptide from the latter reading frame is the result of a partial duplication of the nucleotide sequence encoding amino acids 110 to 198 of gene 11.     

Nucleotide sequence of beet mild yellowing virus RNA

Summary The complete nucleotide sequence of the genomic RNA of beet mild yellowing virus, isolate 2ITB, is reported. The RNA consists of 5722 nucleotides and contains six long open reading frames which conform to the arrangement characteristic of Subgroup 2 luteoviruses. The three 3-proximal open reading frames, which encode the viral coat protein, a putative movement protein and the Readthrough Domain, are highly homologous to the corresponding genes of beet western yellows luteovirus while the three 5-proximal open reading frames are more closely related to the corresponding genes of cucurbit aphid borne yellows luteovirus. The sequence data thus indicate that beet mild yellowing virus should be considered a distinct virus rather than a strain of beet western yellows virus.     

Nucleotide sequence of the ononis yellow mosaic tymovirus genome

The nucleotide sequence of the genome of ononis yellow mosaic tymovirus (OYMV) has been determined. The genome is single-stranded RNA, 6211 nucleotides long, and has three main open reading frames (ORFs), two of them overlapping. The largest ORF (nucleotides 179-5509) encodes a polyprotein of 1776 amino acid residues that has sequence similarities with polymerases of other viruses with RNA genomes. The smaller overlapping ORF (nucleotides 172-1965) encodes a protein of 597 amino acids of unknown function. The third ORF located at the 3' end of the genome (nucleotides 5487-6065) is the virion protein gene, and it overlaps by 20 nucleotides the 3' terminus of the largest ORF. The organization of the OYMV genome, its sequence, and the sequences of the protein it encodes are clearly similar to those of two other tymoviruses, turnip yellow mosaic virus and eggplant mosaic virus. The 5' terminal noncoding region of the OYMV genome is much longer than the same region of other tymoviral genomes and includes a direct duplication of a sequence of 21-23 nucleotides.