NS5B Gene Research Articles

Molecular epidemiology of classical swine fever in the Russian Federation.

The ability to discriminate between various classical swine fever virus (CSFV) strains and isolates is a prerequisite for following the spread of the virus after an outbreak. To determine the relatedness between Russian CSFV isolates from different geographical regions, three fragments of the viral genome (5' NTR, the variable region of the E2 gene and a fragment of the NS5B gene) were sequenced and used for genetic typing. Thirty-one field isolates were obtained from CSF outbreaks which occurred between 1994 and 1999. In addition, three attenuated strains were included in the study, namely the LK and CS vaccine strains, and the moderately virulent 238H isolate. The vaccine strains have been used in Russia for more than 30 years. Our results showed that all field isolates are in subgroup 1.1 together with Alfort 187 and with the highly virulent strain Shimen. In contrast, the CS and LK vaccine strains belong to subgroup 1.2. While there is no evidence for the reversion of the two vaccine strains to wild type, it is feasible that the highly virulent Shimen strain, which has been used as a challenge strain for many years, contributed to field strain generation. The Russian field isolates from the 1990s can be distinguished from the CSF virus isolates which occurred in the EU Member States in the same decade, as here all outbreaks were caused by CSF viruses belonging to subgroup 2.

Evolution of hepatitis C virus in blood donors and their respective recipients.

This paper describes the study of hepatitis C virus (HCV) evolution in the largest cohort of HCV-infected blood donors (BDs)/blood recipients (BRs) reported to date (25 pairs). A molecular analysis of partial sequences in the E1 (envelope) and NS5-B (polymerase) genes was performed. Phylogenetic reconstruction showed that the evolution of dominant strains was qualitatively and quantitatively different in BDs and BRs. The evolutionary rate was significantly higher in BRs, in which, in addition, most substitutions observed were antonymous. These findings corroborate the hypothesis that a large part of virus evolution - which was evaluated to be equivalent to approximately 20 years of chronic evolution - is acquired during the early phase of infection. These findings should be taken into account for the modelling of the long-term evolution of HCV and their possible contribution to improve our understanding of HCV natural history is discussed.

Hepatitis C virus infection among pregnant women in Yaounde, Cameroon: prevalence, viremia, and genotypes.

Central Africa is considered to be an area of high endemic hepatitis C infection. To determine the prevalence of anti-HCV antibodies, HCV RNA, and the genotype distribution in Cameroon, 1,494 pregnant women attending antenatal care units in Yaounde, Cameroon were screened for HCV infection. Anti-HCV antibodies were detected with a 3rd generation ELISA (Monolisa anti-HCV plus version 2, BioRad, Richmond, CA). All anti-HCV antibody-positive sera were then tested with another 3rd generation ELISA (AxSYM) HCV version 3, Abbott Laboratories, Abbott Park, IL) and subsequently for HCV RNA (Amplicor HCV, Roche Diagnostics, Basel, Switzerland). Genotype was determined by phylogenetic analysis of the NS5b gene. Seventy-three pregnant women were found to be anti-HCV antibody positive by the first ELISA, but only 28 were anti-HCV positive by both ELISA. The prevalence of anti-HCV antibodies was thus 1.9% (28/1,494) (95% CI: 1.3-2.7%). 21/28 (75%) of the positive samples by both ELISA were HCV RNA positive. The 45 samples that were HCV antibody negative by the second ELISA were also HCV RNA negative. The HCV subtypes identified were 1a (24%), 2f (38%) and 4f (38%). In contrast to previous studies, anti-HCV antibodies were rare among pregnant women in Cameroon. The percentage of HCV seropositive pregnant women who had circulating HCV RNA was similar to that observed in Europe. Several HCV genotypes were found in Cameroon.

Specificity and Mechanism Analysis of Hepatitis C Virus RNA-Dependent RNA Polymerase

The RNA-dependent RNA polymerase encoded by the hepatitis C virus (HCV) NS5B gene has been expressed as a nonfusion protein in bacterial cells and purified to homogeneity using sequential chromatographic columns. The purified NS5B protein exhibited RNA-dependent RNA polymerase activity using poly(A) template and the Km and Vmax were determined as 8.4 μM and 1976 pmol/mg-min, respectively. This full-length NS5B protein exhibited much stronger binding affinity toward the 30-mer poly(G) than other homopolymeric RNAs of the same size. For the first time, we demonstrate that the HCV NS5B was able to bind various ribonucleotides. Using a panel of oligonucleotides varying in length, we studied the NS5B catalytic efficiency and proposed the size of the NS5B active site to be 8–10 nucleotides. The multifunctional nature of NS5B protein is also discussed and compared with other viral RNA polymerases.

Classical swine fever virus: a second ring test to evaluate RT-PCR detection methods.

Six laboratories participated in a study to compare the sensitivity and specificity of RT-PCR tests for the detection of classical swine fever virus (CSFV). Sets of coded samples were prepared by serial dilution of positive samples and then distributed to each of the laboratories. One set comprised 25 samples of random primed cDNA, synthesised from viral RNA representative of different pestiviruses. The other set comprised samples of blood and serum obtained from virus-free or CSFV-infected pigs. Each laboratory tested the samples using PCR/RT-PCR according to a set of standardised protocols that specified the exact conditions and requirements for inclusion of control samples. Two types of test were evaluated. One amplified a part of the 5'-non coding region of the pestivirus genome by means of a closed, one-tube RT-nested PCR. The other amplified a part of the NS5B gene using non-nested RT-PCR. The results of the laboratories were compared with one another, and with those obtained earlier when similar samples were tested by the same laboratories using non-standardised methods [Paton et al., Classical swine fever virus: a ring test to evaluate RT-PCR detection methods, Vet. Microbiol., in press]. Standardisation of the protocols resulted in a more consistent test sensitivity. Three laboratories avoided significant false positive results. Others that did not, could nevertheless recognise that test specificity was inadequate from the results obtained with the control samples. Minimum requirements for the inclusion of adequate controls and periodic proficiency testing are proposed.

Dengue virus structural differences that correlate with pathogenesis.

The understanding of dengue virus pathogenesis has been hampered by the lack of in vitro and in vivo models of disease. The study of viral factors involved in the production of severe dengue, dengue hemorrhagic fever (DHF), versus the more common dengue fever (DF), have been limited to indirect clinical and epidemiologic associations. In an effort to identify viral determinants of DHF, we have developed a method for comparing dengue type 2 genomes (reverse transcriptase PCR in six fragments) directly from patient plasma. Samples for comparison were selected from two previously described dengue type 2 genotypes which had been shown to be the cause of DF or DHF. When full genome sequences of 11 dengue viruses were analyzed, several structural differences were seen consistently between those associated with DF only and those with the potential to cause DHF: a total of six encoded amino acid charge differences were seen in the prM, E, NS4b, and NS5 genes, while sequence differences observed within the 5' nontranslated region (NTR) and 3' NTR were predicted to change RNA secondary structures. We hypothesize that the primary determinants of DHF reside in (i) amino acid 390 of the E protein, which purportedly alters virion binding to host cells; (ii) in the downstream loop (nucleotides 68 to 80) of the 5' NTR, which may be involved in translation initiation; and (iii) in the upstream 300 nucleotides of the 3' NTR, which may regulate viral replication via the formation of replicative intermediates. The significance of four amino acid differences in the nonstructural proteins NS4b and NS5, a presumed transport protein and the viral RNA polymerase, respectively, remains unknown. This new approach to the study of dengue virus genome differences should better reflect the true composition of viral RNA populations in the natural host and permit their association with pathogenesis.

Genetic variation in the 5' end and NS5B regions of classical swine fever virus genome among Japanese isolates.

Sixteen clinical strains of classical swine fever virus (CSFV) isolated in Japan were subjected to analyses of nucleotide sequence variations in the 5' end and NS5B regions of the genome. These isolates were divided into three genovars, CSFV-1, CSFV-2 and CSFV-3, based on palindromic nucleotide substitutions at the three variable loci in the 5' untranslated region (UTR). Phylogenetic trees constructed from nucleotide sequences in the 5'-UTR and NS5B gene indicated that the CSFV strains were divided into three clusters, I, II and III. CSFV strains included in clusters I, II and III were identical to those in the CSFV-1, CSFV-2 and CSFV-3 genovars, respectively.

A Second Outbreak of Hepatitis C Virus Infection from Anti‐D Immunoglobulin in Ireland

Abstract Objective: To investigate the infectivity for hepatitis C virus (HCV) of intravenous anti‐D immunoglobulin batches manufactured in Ireland between 1991 and 1994. Methods: Women who had received anti‐D manufactured between 1991 and 1994 were screened for serological markers of HCV infection and for the presence of HCV RNA by RT‐PCR amplification and virus genotyping. Results: 44 women exposed to anti‐D manufactured between 1991 and 1994 were polymerase chain reaction positive for HCV RNA, 19 of whom were infected with genotype 3a virus shown by phylogenetic analysis of the NS5B gene to be closely related to that from the single implicated donor. Conclusions: Anti‐D manufactured in 1991–1994 transmitted infection of HCV genotype 3a. The prevalence of HCV‐specific antibody in anti‐D recipients was relatively low (0.59%), consistent with the low leve! of virus RNA in these anti‐D batches.

A Second Outbreak of Hepatitis C Virus Infection from Anti–D Immunoglobulin in Ireland

Objective: To investigate the infectivity for hepatitis C virus (HCV) of intravenous anti–D immunoglobulin batches manufactured in Ireland between 1991 and 1994. Methods: Women who had received anti–D manufactured between 1991 and 1994 were screened for serological markers of HCV infection and for the presence of HCV RNA by RT–PCR amplification and virus genotyping. Results: 44 women exposed to anti–D manufactured between 1991 and 1994 were polymerase chain reaction positive for HCV RNA, 19 of whom were infected with genotype 3a virus shown by phylogenetic analysis of the NS5B gene to be closely related to that from the single implicated donor. Conclusions: Anti–D manufactured in 1991–1994 transmitted infection of HCV genotype 3a. The prevalence of HCV–specific antibody in anti–D recipients was relatively low (0.59%), consistent with the low level of virus RNA in these anti–D batches.

Genetic analysis of pestiviruses at the 3' end of the genome.

Specific PCR primers were selected for each pestivirus genotype which flanked the 3'-part of the NS5B gene and more than three quarters of the 3'-UTR. PCR products were sequenced in both directions using an automatic sequencing device and analyzed by computer package program DNASTAR. A comparative analysis of the 3' untranslated region (3'-UTR) of 82 viruses, representing the four genotypes of the Pestivirus genus, provided a similar phylogenetic grouping as other genomic regions. Intertypic recombination was not observed, but Border disease virus (BDV) and Bovine viral diarrhoea virus type I (BVDV I) showed great intragenotypic variability. In most pestiviruses the stop codon is TGA, but BDV isolates were found to have either a TAG or a TAA stop codon. Various deletions and insertions were observed in the 3'-UTR region. Viruses of the BVDV lb group contained a characteristic deletion of 41 nucleotides. Compared to the 5'-UTR, the 3'-UTR was less conserved. The first 50-60 nucleotides were particularly variable, whilst the most conserved part was found at the 3' end of the studied region. All 82 viruses contained AT-rich stretches, the positions and sizes of which differed between the genotypes.

Application of genetic methods to study the relationship between classical swine fever outbreaks

Eleven viruses isolated between 1993 and 1997 from outbreaks of classical swine fever in the neighbouring countries of Slovakia, The Czech Republic and Austria were compared after partial sequencing of the NS5B and E2 genes. Viruses collected from South-Central and West Slovakia were indistinguishable during a period of four years, even when associated with outbreaks of variable severity. Outbreaks that occurred in the Czech Republic in 1996 involved two types of virus, one of which was related to the Slovakian outbreaks, and the other to Austrian outbreaks. The results show that the molecular-genetic approach can reveal epizootiological relationships between outbreaks that would not otherwise be apparent. Furthermore, the relative genetic stability of the classical swine fever virus in the field, means that quite small sequence differences can have epizootiological significance.

Characterization of recombinant hepatitis C virus NS5B gene product (RDRP)

Characterization of recombinant hepatitis C virus NS5B gene product (RDRP)

Expression, Purification, and Partial Characterization of HCV RNA Polymerase

The product of the NS5B gene of Hepatitis C Virus (HCV) has been expressed in Escherichia Coli both as a fusion protein with glutathione-S-transferase (GST) of molecular weight 91KDa and at high level as a single protein of molecular weight 65KDa. The protein was sequestered within inclusion bodies and a variety of procedures designed to minimize inclusion body formation proved unsuccessful. The method finally adopted involved the purification of inclusion bodies followed by the solubilization, purification, and re-folding of the expressed protein. A good recovery and protein purity of the order of 80-90% were achieved. The purified protein was shown to possess RNA polymerase activity in an assay using polyA/oligoU as template. The enzymatic activity is rifampicin resistant, poly A dependent, and requires Mg++. The availability of purified HCV RNA polymerase will allow the study of viral replication and constitute the basis for testing new anti-viral drugs.

The origin of hepatitis C virus genotypes.

For many RNA viruses, relatively recent times of origin of extant viruses are implied by the high rate of substitution observed in longitudinal studies. However, extrapolation of short-term rates of substitution can give misleading estimates of times of divergence. We show here that the common ancestor of different types of hepatitis C virus (HCV) is older than previously thought. The rate of HCV sequence change was measured amongst a cohort of individuals infected following administration of anti-D immunoglobulin. Virus sequences were obtained in the E1 and NS5B genes and compared with each other and with sequences from an infective batch. Taking account of the bias towards synonymous transition substitutions, the time of divergence of variants of subtype 1b is estimated to have occurred 70-80 years ago. The numerous subtypes of HCV are proposed to derive from more than 300 years of endemic infection in certain geographical regions, with recent spread of some subtypes to other parts of the world. Estimation of the time of origin of the major HCV genotypes (types 1-6) is problematic, but our data and analogy with other viruses suggest that divergence occurred at least 500-2000 years ago.

Genetic Variation in Yellow Fever Virus: Duplication in the 3′ Noncoding Region of Strains from Africa

The nucleotide sequences of three regions of the genomes of 13 yellow fever (YF) virus isolates were determined to define genetic variation and evolution of the virus. Phylogenetic trees generated from sequences of either the 5′ terminal 1320 nucleotides of the genome, 754 nucleotides from the NS4A and NS4B genes, or the 3′ terminal 511 nucleotides were very similar and contained minor differences. Overall, these results suggested that there were at least four major genotypes of YF virus, including one in Central/East Africa, one in West Africa, and two in South America. Examination of the 3′ noncoding region (3′NCR) showed that only West African strains had a 3′NCR of 511 nucleotides while strains from Central/East Africa and South America had shorter 3′NCRs (443–469 nucleotides) due to the absence of YF specific repeat sequences (RYFs). Central/East African strains have two RYFs and West African strains have three RYFs while South American strains only have one copy of the RYF. It is speculated that duplication of the RYF took place in West Africa subsequent to the presumed introduction of YF virus into South America. Thus, both tick-borne (Mandlet al., J. Virol.65, 4070–4077, 1991 and Wallneret al., Virology213, 169–178, 1995) and mosquito-borne flaviviruses have variable 3′NCRs.

Classical swine fever virus diversity and evolution.

By analysing the nucleotide sequence data generated from both the E2 (gp55) and the NS5B genes of classical swine fever virus (CSFV), in addition to previously published data from the 5'NCR, we were able to divide 115 CSFV isolates into two major groups, five subgroups and two disparate isolates. Further discrimination was possible by analysis of sequence data from the E2 region. The three sequencing based methods were compared to monoclonal antibody (MAb) typing and to limited restriction enzyme (RE) mapping. Although both MAb and RE methods confirmed the previous classification the resolution was inferior. We estimated an approximate evolution rate for CSFV from an analysis of the virus variation observed in a single geographical area over a 6 year period. Applying this proposed rate to each of our deduced CSFV subgroups enabled us to calculate the approximate dates of divergence for each subgroup.

Expression and characterization of the NS5B (RNA-dependent RNA polymerase) gene of hepatitis C virus: [formula omitted]. Division of Digestive Diseases Emory University School of Medicine and The VA Medical Center, Atlanta

Expression and characterization of the NS5B (RNA-dependent RNA polymerase) gene of hepatitis C virus: [formula omitted]. Division of Digestive Diseases Emory University School of Medicine and The VA Medical Center, Atlanta