Nucleotide Sequence Of Genomic RNA Research Articles

Complete genomic sequence of rapidly replicating strain MB-7 of hepatitis a virus and its characterization in comparison with nucleotide sequence of other hepatitis a virus strain

Complete nucleotide sequence of genomic RNA of hepatitis A virus (HAV) rapidly replicating strain MB-7 was determined. Comparison of nucleotide and deduced amino-acid sequences demonstrated the highest level of identity of MB-7 with strain HAS-15 (above 99%) and high homology with other HAV strains (HM 175/7, CR326, and GBM/HFS) used in production of anti-hepatitis A vaccines. MB-7 was classified as subgenotype IA. Phylogenetic analysis showed that MB-7 is most closely related to the strain HAS-15 and the HAV variants circulating in Russia. Comparative analysis of genomic differences between MB-7 and HAS-15 with other HAV strains revealed among changes characteristic of MB-7 those typical of the described earlier rapidly replicating HAV strains (nt. 149-162 in 5'-untranslated region and changes in the VP3 and 2C genes). These results suggest the functional importance of changes in above-mentioned regions of HAV genome for the increased replication level of MB-7 in vitro.

Complete Nucleotide Sequence of Genomic RNA of a Large-Plaque Forming Porcine Reproductive and Respiratory Syndrome Virus PL97-1/LP1

Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most important animal pathogens in swine industry worldwide. In this study, we isolated the large-plaque forming variant virus designated PL97-1/LP1 from the parental strain PL97-1, the first Korean strain of PRRSV, isolated from the serum of an infected pig in 1997. We found that the 15411-nucleotide genome of PL97-1/LP1 consisted of a 189-nucleotide 5' untranslated region (UTR), a 15071-nucleotide protein-coding region, and a 151-nucleotide 3'UTR, followed by a poly (A) tail of about 50~60 nucleotides in size. The 5'-end of PL97-1/LP1 began with ATGACGTAT. Comparison of the PL97-1/LP1 genome with the 11 fully sequenced PRRSV genomes currently available revealed sequence similarity from 99.6~99.7% (the North American VR-2332 and two VR-2332-derived vaccine strains MLV RespPRRS/Repro and RespPRRS MLV) to 62.0% (the Dutch Lelystad strain). Phylogenetc analysis revealed that PL97-1/LP1 is most closely related to the North American genotype VR-2332, two VR-2332-derived vaccine strains, and Chinese BJ-4. It is distantly related to the European genotype Lelystad. The entire nucleotide sequence of PL97-1/LP1 was identical to that of the parental virus PL97-1 except for three silent nucleotide substitutions, one in ORF1a (U4230C), one in ORF1b (C10977U), and one in ORF5 (U13976A). This nucleotide sequence has been submitted to the GenBank database under the accession number AY612613.

Sequencing and analysis for the full-length genome RNA of foot-and-mouth disease virus China/99.

The complete nucleotide sequence of genomic RNA of foot and mouth disease virus (FMDV) strain China/99 from infected bovine tongue epithelium is presented. The nucleotide sequence extending from the 5' end of the genomic RNA to the 5' end of poly (A) tail contains 8173 nucleotides (nt). Its open reading frame, which encodes a single polypeptide of 2332 amino acids, encompasses 6999 nt starting from the initiation codon AUG and terminating at the UAA codon 93 bases upstream from the 5' end of poly (A) tract. The 5' untranslated region (UTR) is composed of 1081 nt. The consensus of the 1d gene of FMDV strain China/99 compared with that of UKG/6/2001, UKG/12/2001, China/99HN4 and China/3/Tibet is over 97%. The result showed the stains belong to the members of the Pan-Asia family. There is a remarkable differentiation in the function-unknown (FUR), p2 and p3 regions between FMDV isolates from infected cattle and swine, especially in 3a gene. No deletion was found in genes I, 1a, 1b, 2a, 2c, 3b, and 3d. These genes might be indispensable to the surviving of FMDV. The secondary structures of small (S) fragments, FUR and an internal ribosome entry site can be classified into three types, and the S fragment and 3' UTR of the positive-sense RNA fold into stem-loop structures similar to the shape of clover.

Sequence of the Genome of Lactate Dehydrogenase-Elevating Virus: Heterogenicity between Strains P and C

The complete nucleotide sequence of genomic RNA (14104 nt) of one strain of lactate dehydrogenase-elevating virus (LDV), LDV-P, is reported. It exhibits only about 80% nucleotide identity with the sequence reported for another LDV strain, LDV-C (Godeny et al., Virology 194, 585-596 (1993), and is 68 nucleotides shorter than the reported LDV-C sequence. The difference in length is largely due to the lack of a 59-nucleotide-long direct repeat in ORF 1a of the reported LDV-C sequence. Sequence analysis of a total of 1.4 kb of ORF 1a of LDV-C via reverse transcription/polymerase chain reaction (RT/PCR) technology failed to confirm 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 genomes and might have represented frameshift mutations. An additional 35 nucleotides in ORF 1a of the RT/PCR LDV-C products were the same as in the LDV-P rather than the reported LDV-C genome. The nucleotide sequences of the 5′ leader and the 3′ noncoding ends of the two genomes and the heptanucleotides involved in joining the 5′ leader to the bodies of the subgenomic mRNAs were highly conserved or identical. The predicted 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 nuoleocapsid protein. All functional motifs of the ORF 1a and ORF 1b proteins were conserved. The ORF 1a protein possesses 11 potential transmembrane segments that flank the serine protease domain.

Molecular cloning and complete nucleotide sequence of genomic RNA of the AIK-C strain of attenuated measles virus

Twelve cDNA clones covering the entire genome of the AIK-C strain of a seed for live measles vaccine were obtained, and the nucleotide sequences were determined. The full viral genomic RNA consists of 15,894 nucleotides. Comparisons of the nucleotide sequence and the deduced amino acid sequence between the AIK-C and other Edmonston strains revealed the following changes: 56 nucleotide differences and one C residue insertion, 31 amino acid changes, and 19 silent mutations.

Nucleotide sequence and organization of potato leafroll virus genomic RNA

The nucleotide sequence of the genomic RNA of potato leafroll virus was determined and its genetic organization deduced. The RNA is 5882 nucleotides long and contains 6 open reading frames (ORFs) encoding proteins of 70, 70, 56, 28, 23 and 17 kDa. The putative genes for the coat protein (23 kDa) and the RNA-dependent RNA polymerase (70 kDa) were identified by interviral amino acid sequence homologies. For expression of the different ORFS, translational frameshift and readthrough events are proposed.