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PubMed1995

Serial assay of hepatitis C virus RNA in serum for predicting response to interferon-alpha therapy.

To determine whether the loss of serum hepatitis C virus RNA (HCV-RNA) early in interferon therapy would indicate a sustained response to this agent, we detected serum HCV-RNA successively during and after therapy. Serum samples for detection of HCV-RNA were obtained serially from 36 patients with chronic hepatitis C treated with interferon-alpha. In 28 of these patients, results of the assay were compared with genotypes and quantitative levels of HCV-RNA in serum before therapy. HCV-RNA was detected by a reverse transcription polymerase chain reaction using the 5'-noncoding region as a primer. Genotypes were determined by using type-specific primers, and serum levels of HCV-RNA were determined by a competitive reverse transcription polymerase chain reaction (RT-PCR). HCV-RNA disappeared from serum in eight of 10 responders (80%), but in only one of the 26 nonresponders (3.8%) at the second week of therapy (P < 0.0005). The time until the disappearance of HCV-RNA was correlated with the serum level of HCV-RNA present before therapy (P < 0.05). The early disappearance of HCV-RNA from serum during interferon therapy was useful in predicting a sustained response in patients with chronic hepatitis C.

Adult↗
PubMed1988

The adenovirus tripartite leader sequence can alter nuclear and cytoplasmic metabolism of a non-adenovirus mRNA within infected cells.

All mRNAs encoded by the adenovirus major late transcription unit share a common 5' noncoding region, 200 nucleotides in length, termed the tripartite leader sequence. To assess function of the tripartite leader, recombinant viruses were prepared which carried either a bona fide herpes simplex virus thymidine kinase gene or a modified thymidine kinase gene whose normal 5' noncoding domain was replaced with the adenovirus leader sequence. The tripartite leader simultaneously decreased the nuclear half-life and increased the cytoplasmic half-life of the thymidine kinase-specific mRNA. The tripartite leader stabilized the non-adenovirus mRNA only within the environment of an adenovirus-infected cell during the late phase of the infectious cycle.

Adenoviruses, Human↗
PubMed1997

Hepatitis G virus replication in human cultured cells displaying susceptibility to hepatitis C virus infection.

We recently developed a hepatitis C virus (HCV) replication system using two cultured human cell lines: MT-2C, a human T-cell leukemia virus type I-infected cloned T cell line, and PH5CH, a non-neoplastic human hepatocyte line. In the course of the study, we found evidence that replication of hepatitis G virus (HGV), which has recently been identified, was supported in both MT-2C and PH5CH cells. When these cells were inoculated with serum 1B-3 containing both HCV and HGV obtained from a blood donor, the 5'-noncoding (5'-NC) regions of HCV RNA and HGV RNA were detected by RT-nested PCR in both cell lines more than 30 days postinoculation, and the 3'-noncoding region of HGV RNA was also detected in the both cell lines more than 30 days postinoculation. Sequence analysis of the 5'-NC region of HGV RNA revealed the quasispecies nature of HGV, although the 5'-NC region was highly conserved among HGV isolates. This HGV-infected culture system will be useful for various biological and virological studies of HGV.

Base Sequence↗
PubMed2003

Assessment of development of resistance to antivirals in the ferret model of influenza virus infection.

We attempted to develop in vivo resistance of influenza virus to amantadine and to zanamivir, by use of the ferret model of influenza virus infection. Resistance of influenza virus A/LosAngeles/1/87 (H3N2) to amantadine was generated within 6 days, during a single course of treatment, and mutations in the M2 gene that are characteristic of human infections were observed. In contrast, during an identical single course of treatment with zanamivir, no evidence of reduced susceptibility was demonstrated. Pooled virus shed by zanamivir-treated ferrets was used to infect another group of ferrets. Twenty virus clones grew in plaque assays containing zanamivir, indicating possible reduced susceptibility; however, none exhibited reduced susceptibility to zanamivir in neuraminidase (NA) inhibition assays. Sequencing of the NA gene of these clones revealed only a noncoding nucleotide mutation at position 685. Sequencing of the hemagglutinin gene revealed mutations at positions 53, 106, 138, 145, 166, and 186. Similar to the situation in humans, amantadine use in ferrets rapidly produces antiviral resistance, but zanamivir use does not, although nucleotide changes were observed.

Amantadine↗
PubMed1991

Sendai virus NP gene codes for a 524 amino acid NP protein.

The complete nucleoprotein (NP) gene sequences of the Sendai virus Fushimi and 6/94 strains were determined. For both viruses an open reading frame of 524 amino acids can be predicted for the NP proteins. By comparing the sequences with others reported in the literature, the 5' noncoding region and the middle third of the coding region were found to be highly conserved. The carboxyl terminal part carries nine amino acid changes and a completely different sequence of the carboxyl terminus with a seven amino acid extension. This carboxyl terminus of the Sendai virus NP protein was confirmed using tryptic peptide sequence analysis.

Amino Acid Sequence↗
PubMed1984

Cloning and nucleotide sequence of the simian rotavirus gene 6 that codes for the major inner capsid protein.

The nucleotide sequence of the gene that codes for the major inner capsid protein of the simian rotavirus SA11 has been determined. A DNA copy of mRNA from gene 6 was cloned in the E. coli plasmid pBR322. The full-length gene is 1357 nucleotides long with a 5'-noncoding region of 23 nucleotides and a 3'-noncoding region of 140 nucleotides. The gene contains a single, long, open reading-frame of 1194 nucleotides capable of coding for a protein of 397 amino acids with a molecular weight of 44,816. The predicted protein product is relatively proline-rich with a net charge at neutral pH of -3.5. One stretch of 53 amino acids (encoded by nucleotides 327-485) is basic.

Base Sequence↗
PubMed1989

Attenuation and cell culture adaptation of hepatitis A virus (HAV): a genetic analysis with HAV cDNA.

RNA transcripts of hepatitis A virus (HAV) HM-175 cDNA from attenuated, cell culture-adapted HAV were infectious in cell culture. A full-length HAV cDNA from wild-type HAV (propagated in marmosets in vivo) was constructed. Chimeric cDNAs that contained portions of both wild-type and attenuated genomes were produced. Oligonucleotide-directed mutagenesis was used to engineer a point mutation into the VP1 gene of attenuated HAV cDNA, so that the sequence of this capsid protein would be identical to that of the wild-type virus. Transfection of monkey kidney cells with RNA transcripts from several of the chimeric cDNAs and from the mutagenized cDNA induced production of HAV. Comparison of the growth of attenuated, wild-type, chimeric, and mutant viruses in vitro indicated that the P2-P3 (nonstructural protein) region is important for cell culture adaptation of the virus; the 5' noncoding region may also contribute to adaptation, but to a lesser extent. Inoculation of marmosets with transfection-derived virus also suggested that the P2-P3 region plays an important role in attenuation of HAV HM-175.

Animals↗
PubMed1985

Five pseudoknots are present at the 204 nucleotides long 3' noncoding region of tobacco mosaic virus RNA.

The 104 nucleotides long 3' terminal region of TMV RNA was shown previously to contain two pseudoknotted structures (Rietveld et al. (1984), EMBO J. 3, 2613-2619). We here present evidence for the occurrence, within the 204 nucleotides long 3' noncoding region, of another highly structured domain located immediately adjacent to the tRNA-like structure of 95 nucleotides (Joshi et al. (1985) Nucleic Acids Res. 13, 347-354). A model for the three-dimensional folding of this region, containing three more pseudoknots, is proposed on the basis of chemical modification and enzymatic digestion. The existence of these three consecutive pseudoknots was supported by sequence comparisons with the RNA from the related tobamoviruses TMV-L, CcTMV and CGMMV. Coaxial stacking of the six double helical segments involved gives rise to the formation of a 25 basepair long quasi-continuous double helix. The results show that the three-dimensional folding of the 3' non-translated region of tobamoviral RNAs is largely maintained by the formation of five pseudoknots. The organisation of this region in the RNA of the tobamovirus CcTMV suggests that recombinational events among aminoacylatable plant viral RNAs have to be considered.

Base Sequence↗
PubMed1983

Complete nucleotide sequence of alfalfa mosaic virus RNA 1.

Double-stranded cDNA of alfalfa mosaic virus (AlMV) RNA 1 has been cloned and sequenced. From clones with overlapping inserts, and other sequence data, the complete primary sequence of the 3644 nucleotides of RNA 1 was deduced: a long open reading frame for a protein of Mr 125,685 is flanked by a 5'-terminal sequence of 100 nucleotides and a 3' noncoding region of 163 nucleotides, including the sequence of 145 nucleotides the three genomic RNAs of AlMV have in common. The two UGA-termination codons halfway RNA 1, that were postulated by Van Tol et al. (FEBS Lett. 118, 67-71, 1980) to account for partial translation of RNA 1 in vitro into Mr 58,000 and Mr 62,000 proteins, were not found in the reading frame of the Mr 125,685 protein.

Amino Acid Sequence↗
PubMed1994

Rapid characterization of new pestivirus strains by direct sequencing of PCR-amplified cDNA from the 5' noncoding region.

Reverse transcription coupled with the polymerase chain reaction (RT-PCR) was used for the rapid laboratory diagnosis of pestivirus infections. A direct DNA sequencing method was developed for the analysis of the amplified cDNA from the 5' noncoding region of the viral genome. 70 pestivirus strains were compared in this study. Sequence analysis allowed the characterization of each isolate as either classical swine fever virus (CSFV), bovine viral diarrhea virus, or border disease virus, respectively. The 48 CSFV strains could be further classified into several subgroups, which correlated either with the geographical origin or the date of the first isolation of the respective isolate.

Animals↗
PubMed1984

Nucleotide sequence of avian carcinoma virus MH2: two potential onc genes, one related to avian virus MC29 and the other related to murine sarcoma virus 3611.

The 5.2-kilobase (kb) RNA genome of avian carcinoma virus MH2 has the genetic structure 5'-delta gag (0.2 kb)- mht (1.2 kb)-myc (1.4 kb)-c (0.4 kb)-poly(A) (0.2 kb)-3'. delta gag is a partial retroviral core protein gene, mht and myc are cell-derived MH2-specific sequences, and c is the 3'-terminal retroviral vector sequence. Here we have determined the nucleotide sequence of 3.5 kb from the 3' end of delta gag to the 3' end of molecularly cloned proviral MH2 DNA, in order to elucidate the genetic structure of the virus and to compare it with other mht - and myc-containing oncogenic viruses as well as with the chicken proto-myc gene. The following results were obtained: (i) delta gag- mht forms a hybrid gene with a contiguous reading frame of 2682 nucleotides that terminates with a stop codon near the 3' end of mht . The 3' 969 nucleotides of mht up to the stop codon are 80% sequence related to the onc-specific raf sequence of murine sarcoma virus 3611 (94% homologous at the deduced amino acid level). (ii) The myc sequence is preceded by an RNA splice acceptor site shared with the cellular proto-myc gene, beyond which it is colinear up to a 3'-termination codon and 40 noncoding nucleotides with the myc sequences of avian retrovirus MC29 and chicken proto-myc. Thus, myc forms, together with a 5' retroviral exon, a second MH2-specific gene. (iii) myc is followed by the 3'-terminal c region of about 400 nucleotides, which is colinear with that of Rous sarcoma virus except for a substitution near the 5' end of the long terminal repeat. It is concluded that MH2 contains two genes with oncogenic potential, the delta gag- mht gene, which is closely related to the delta gag-raf transforming gene of MSV 3611, and the myc gene, which is related to the transforming gene of MC29. Furthermore, it may be concluded that the cellular proto-onc genes, which on sequence transduction become viral onc genes, are a small group because among the 19 known onc sequences, 5 are shared by different taxonomic groups of viruses of which the mht /raf homology is the closest determined so far.

Amino Acid Sequence↗
PubMed1994

Sequences of wild Puumala virus genes show a correlation of genetic variation with geographic origin of the strains.

An experimental scheme was developed for direct sequence analysis of Puumala virus-containing specimens from wild rodents (Clethrionomys glareolus). Total RNA isolated from rodent lung tissues was reverse-transcribed in the presence of a universal 11 nucleotide primer complementary to all three viral RNA segments followed by amplification in a PCR with gene-specific primers. A full-length PCR product of approximately 1800 bp from the S segment encoding the viral nucleoprotein and a product of approximately 900 bp from the M segment (encoding the C-terminal two-thirds of the G2 protein and including the 3' non-coding region) of Puumala virus (from C. glareolus trapped in Udmurtia) were prepared and sequenced. No pronounced differences to Vero cell-grown viruses were seen. The Udmurtia/894Cg/91 strain was more closely related to the Bashkiria/CG18-20/84 strain than to the Finnish prototype strain of Puumala virus, Sotkamo/V-2969/81. Thus there is a correlation with the geographic origin of the three strains. The results indicate the occurrence of genetic drift and different selection pressures leading to (i) clustering of mutations, (ii) a lower frequency of nucleotide substitutions in the coding than in the 3' noncoding regions and (iii) a higher frequency of amino acid substitutions in G2 than in the N protein.

Base Sequence↗
PubMed1994

Identification of the third major genotype of hepatitis C virus in France.

We have previously found type I and type II hepatitis C virus (HCV) as the predominant HCV genotypes in France. Here we report on the identification and partial characterization of a third major genotype there. This genotype showed only 93-94% sequence conservation to either type I or type II HCV in the 5' noncoding region. The point mutations changed the small open reading frames but not the proposed secondary structure of this region. Sequence of the structural protein region also differed significantly from other genotypes. The new genotype was found in 12% of HCV infections in France. Rapid method for the identification of this genotype was developed.

Amino Acid Sequence↗
PubMed1988

Genome sequences of a mouse-avirulent and a mouse-virulent strain of Ross River virus.

The nucleotide sequence of the genomic RNA of a mouse-avirulent strain of Ross River virus, RRV NB5092 (isolated in 1969), has been determined and the corresponding sequence for the prototype mouse-virulent strain, RRV T48 (isolated in 1959), has been completed. The RRV NB5092 genome is approximately 11,674 nucleotides in length, compared with 11,853 nucleotides for RRV T48. RRV NB5092 and RRV T48 have the same genome organization. For both viruses an untranslated region of 80 nucleotides at the 5' end of the genome is followed by a 7440-nucleotide open reading frame which is interrupted after 5586 nucleotides by a single opal termination codon. By homology with other alphaviruses, the 5586-nucleotide open reading frame encodes the nonstructural proteins nsP1, nsP2, and nsP3; a fourth nonstructural protein, nsP4, is produced by read-through of the opal codon. The RRV nonstructural proteins show strong homology with the corresponding proteins of Sindbis virus and Semliki Forest virus in terms of size, net charge, and hydropathy characteristics. However, homology is not uniform between or within the proteins; nsP1, nsP2, and nsP4 contain extended domains which are highly conserved between alphaviruses, while the C-terminal region of nsP3 shows little conservation in sequence or length between alphaviruses. An untranslated "junction" region of 44 nucleotides (for RRV NB5092) or 47 nucleotides (for RRV T48) separates the nonstructural and structural protein coding regions. The structural proteins (capsid-E3-E2-6K-E1) are translated from an open reading frame of 3762 nucleotides which is followed by a 3'-untranslated region of approximately 348 nucleotides (for RRV NB5092) or 524 nucleotides (for RRV T48). Excluding deletions and insertions, the genomes of RRV NB5092 and RRV T48 differ at 284 nucleotides, representing a sequence divergence of 2.38%. Sequence deletions or insertions were found only in the noncoding regions and include a 173-nucleotide deletion in the 3'-untranslated region of RRV NB5092, compared with RRV T48. In the coding regions, most of the nucleotide differences are silent; there are 36 amino acid differences in the nonstructural proteins and 12 in the structural proteins. The distribution of amino acid differences between the two RRV strains correlates with the location of domains which are poorly conserved in sequence between alphaviruses. The possible role of amino acid differences in envelope glycoproteins E1 and E2 in determining the different antigenic and biological properties of RRV NB5092 and RRV T48 is discussed.

Alphavirus↗
PubMed1987

Partial nucleotide sequence of St. Louis encephalitis virus RNA: structural proteins, NS1, ns2a, and ns2b.

cDNA clones of the St. Louis encephalitis (SLE) virus genome have been obtained and the nucleotide sequence of 4.7 kb corresponding to the 5' terminal half of the genome determined. The genome contains a 5' noncoding region of 98 nucleotides followed by a single continuous open reading frame that encodes three structural proteins in the order capsid (C), membrane precursor (prM)-membrane (M), and envelope (E). Immediately following the C-terminus of E are located nonstructural proteins NS1 through NS3. The SLE amino acid sequence homology with yellow fever (YF), Murray Valley encephalitis (MVE), West Nile (WN), and dengue-2 (DEN) viruses over the sequenced region is 39, 66, 64, and 43%, respectively. The start of each SLE protein has been assigned on the basis of N-terminal sequence data and potential proteolytic cleavage sites homologous with YF and MVE viruses. Flaviviruses have conserved glycosylation sites in prM and NS1 proteins, although only one of the two glycosylation sites in the SLE E protein is conserved in MVE and DEN viruses. An evolutionary tree showing relationships of SLE, MVE, WN, YF, and DEN-2 flaviviruses is proposed on the basis of the amino acid sequences of the C proteins.

Base Sequence↗
PubMed1993

Characterization of the major locus of immediate-early genes of rat cytomegalovirus.

A major locus of rat cytomegalovirus (RCMV) immediate-early (IE) RNA transcription was identified. A cDNA library from rat embryo fibroblasts infected with RCMV under IE conditions was constructed and screened by using appropriate RCMV DNA probes, revealing at least two IE genes (IE1 and IE2) transcribed from this locus by differential splicing. The first three exons (the first is noncoding) are spliced to exon 4 to form IE1 and to exon 5 to form IE2. The structural organization of the RCMV major IE region is therefore similar to that of human cytomegalovirus (HCMV) and murine cytomegalovirus (MCMV). When we compared the predicted amino acid sequences of the IE1 proteins of RCMV, HCMV, and MCMV, no areas of homology were found across all three proteins, while a few small areas of homology were found between RCMV IE1 and MCMV IE1. In contrast, large areas of homology were found across the carboxyl half of RCMV IE2, HCMV IE2, and MCMV ie3 proteins. In addition, similarities were found at the beginning of exon 5 of RCMV and MCMV. The possible significance of these conserved regions is discussed. Dinucleotide frequency analysis demonstrated a decrease in CpG frequency over the IE region. The IE gene products were able to transactivate heterologous promoters.

Amino Acid Sequence↗
PubMed2005

Synthesis of infectious in vitro transcripts from Cassia yellow blotch bromovirus cDNA clones and a reassortment analysis with other bromoviruses in protoplasts.

Cassia yellow blotch virus (CYBV), genus Bromovirus, was isolated from the Australian native legume, Cassia pleurocarpa, in western Queensland, and its host range was found to be distinct from other bromoviruses. In this study, CYBV was shown to infect systemically and efficiently a model plant species, Arabidopsis thaliana, as we recently reported for another bromovirus, Spring beauty latent virus (SBLV). We constructed full-length cDNA clones of CYBV genomic RNAs from which infectious in vitro transcripts can be transcribed, and determined their complete nucleotide sequences. CYBV RNA3 contains the box B motif in the intercistronic region, but lacks the subgenomic promoter-like sequence in the 5' noncoding region, as does Brome mosaic virus (BMV). To understand relationships among bromoviruses, we generated reassortants between CYBV and three other bromoviruses, BMV, SBLV and Cowpea chlorotic mottle virus. We found that all reassortants between BMV and CYBV accumulated viral RNAs to detectable levels in protoplasts of Nicotiana benthamiana, even when RNAs 1 and 2, which encode the replication proteins 1a and 2a, respectively, were heterologous. Sequence comparison and reassortment experiments of CYBV and other bromoviruses demonstrated that CYBV is closely related to BMV.

Bromovirus↗
PubMed1993

Sequence analysis of the nucleocapsid protein gene of rat coronavirus SDAV-681.

The nucleotide sequence of the 3'-end of the genomic RNA of sialodacryoadenitis virus strain 681 (SDAV-681) was determined. A large open reading frame encoding a 454-amino-acid protein was identified as the nucleocapsid protein (N) gene, since the predicted protein is similar in size, chemical properties, and amino acid sequence to the N proteins of other coronaviruses. The amino acid variance of the N proteins between SDAV and mouse hepatitis virus (MHV) is not markedly different from that among MHV strains. A high degree of genetic relatedness between SDAV and MHV was revealed in the intergenic and 3'-noncoding sequences as well as in the N gene.

Amino Acid Sequence↗