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Viral Population (viral + population)
Selected AbstractsEvidence of occult HCV genotypes in haemophilic individuals with unapparent HCV mixed infectionsHAEMOPHILIA, Issue 4 2008C. PARODI Summary., Individuals with haemophilia who received non heat-treated factor concentrates were likely to undergo multiple exposures to the hepatitis C virus (HCV). Therefore, HCV mixed-genotype infections might be more frequent in these patients than in the general population. Their prevalence is extremely variable in similar groups of patients tested by different assays due to the fact that currently available genotyping techniques are not suitable to detect multiple HCV genotypes in a viral population. As an HCV viral reservoir, the peripheral blood mononuclear cell (PBMC) might harbor viral variants distinct from the genotypes detected in plasma. We investigated the presence of HCV genotypes in a group of chronically infected haemophilic patients in the PBMC compartment using a non-stimulated cell culture system that allows the detection of the HCV genome in culture supernatants. We compared them to the HCV genotypes found in plasma samples. Cell culture experiments performed with PBMC demonstrated the presence of additional HCV genotypes that were undetected in the corresponding plasma samples with the same genotyping technique. Although mixed infections at HCV genotype level became evident in 5.6% of the patients (16/288), the culture methodology increased the number of HCV infections with multiple genotypes to 62.5% (10/16) (P < 0.0001). Once more, the role of mononuclear cells as HCV viral reservoirs is emphasized. Considering minor strains could influence the outcome of treatment, detection of covert HCV mixed-genotype infections might be essential for choosing the adequate therapeutic regimen. [source] Genetic and catalytic efficiency structure of an HCV protease quasispecies,HEPATOLOGY, Issue 4 2007Sandra Franco The HCV nonstructural protein (NS)3/4A serine protease is not only involved in viral polyprotein processing but also efficiently blocks the retinoic-acid,inducible gen I and Toll-like receptor 3 signaling pathways and contributes to virus persistence by enabling HCV to escape the interferon antiviral response. Therefore, the NS3/4A protease has emerged as an ideal target for the control of the disease and the development of new anti-HCV agents. Here, we analyzed, at a high resolution (approximately 100 individual clones), the HCV NS3 protease gene quasispecies from three infected individuals. Nucleotide heterogeneity of 49%, 84%, and 91% were identified, respectively, which created a dense net that linked different parts of the viral population. Minority variants having mutations involved in the acquisition of resistance to current NS3/4A protease inhibitors (PIs) were also found. A vast diversity of different catalytic efficiencies could be distinguished. Importantly, 67% of the analyzed enzymes displayed a detectable protease activity. Moreover, 35% of the minority individual variants showed similar or better catalytic efficiency than the master (most abundant) enzyme. Nevertheless, and in contrast to minority variants, master enzymes always displayed a high catalytic efficiency when different viral polyprotein cleavage sites were tested. Finally, genetic and catalytic efficiency differences were observed when the 3 quasispecies were compared, suggesting that different selective forces were acting in different infected individuals. Conclusion: The rugged HCV protease quasispecies landscape should be able to react to environmental changes that may threaten its survival. (HEPATOLOGY 2007;45:899,910.) [source] A new strategy for studying In Vitro the drug susceptibility of clinical isolates of human hepatitis B virusHEPATOLOGY, Issue 4 2004David Durantel Resistance of hepatitis B virus (HBV) to antivirals has become a major clinical problem. Our objective was to develop a new method for the cloning of naturally occurring HBV genomes and a phenotypic assay capable of assessing HBV drug susceptibility and DNA synthesis capacity in vitro. Viral DNA was extracted from sera and was amplified by polymerase chain reaction, and amplicons were cloned into vectors that enable, after cell transfection, the initiation of the intracellular HBV replication cycle. Single or multiple clones were used to transfect Huh7 cells. The viral DNA synthesis capacity and drug susceptibility were determined by measuring the level of intracellular DNA intermediate, synthesized in absence or presence of antiviral, using Southern blot analysis. We have developed, calibrated, then used this phenotypic assay to determine the drug susceptibility of HBV quasispecies isolated throughout the course of therapy from patients selected according to their mutation profile. A multiclonal and longitudinal analysis enabled us to measure the variation of drug susceptibility of different viral quasispecies by comparison of IC50/IC90s with standards. The presence of famciclovir- or lamivudine-induced mutations in the viral population caused a change in viral DNA synthesis capacity and drug susceptibility in vitro, demonstrating the clinical relevance of the assay. In conclusion, our phenotypic assay enables the in vitro characterization of DNA synthesis capacity and drug susceptibility of HBV quasispecies isolated from patients. This assay should allow a better monitoring of patients undergoing antiviral therapy, as well as the screening of novel drugs on emerging resistant strains. (Hepatology 2004;40:855,864). [source] Non-random reassortment in human influenza A virusesINFLUENZA AND OTHER RESPIRATORY VIRUSES, Issue 1 2008Raul Rabadan Background, The influenza A virus has two basic modes of evolution. Because of a high error rate in the process of replication by RNA polymerase, the viral genome drifts via accumulated mutations. The second mode of evolution is termed a shift, which results from the reassortment of the eight segments of this virus. When two different influenza viruses co-infect the same host cell, new virions can be released that contain segments from both parental strains. This type of shift has been the source of at least two of the influenza pandemics in the 20th century (H2N2 in 1957 and H3N2 in 1968). Objectives, The methods to measure these genetic shifts have not yet provided a quantitative answer to questions such as: what is the rate of genetic reassortment during a local epidemic? Are all possible reassortments equally likely or are there preferred patterns? Methods, To answer these questions and provide a quantitative way to measure genetic shifts, a new method for detecting reassortments from nucleotide sequence data was created that does not rely upon phylogenetic analysis. Two different sequence databases were used: human H3N2 viruses isolated in New York State between 1995 and 2006, and human H3N2 viruses isolated in New Zealand between 2000 and 2005. Results, Using this new method, we were able to reproduce all the reassortments found in earlier works, as well as detect, with very high confidence, many reassortments that were not detected by previous authors. We obtain a lower bound on the reassortment rate of 2,3 events per year, and find a clear preference for reassortments involving only one segment, most often hemagglutinin or neuraminidase. At a lower frequency several segments appear to reassort in vivo in defined groups as has been suggested previously in vitro. Conclusions, Our results strongly suggest that the patterns of reassortment in the viral population are not random. Deciphering these patterns can be a useful tool in attempting to understand and predict possible influenza pandemics. [source] Molecular characterization of the env gene of two CCR5/CXCR4-independent human immunodeficiency 2 primary isolates,JOURNAL OF MEDICAL VIROLOGY, Issue 11 2009Quirina Santos-Costa Abstract Human immunodeficiency virus 2 (HIV-2) infection is characterized by a slower disease progression and lower transmission rates. The molecular features that could be assigned as directly involved in this in vivo phenotype remain essentially unknown, and the importance of HIV-2 as a model to understand pathogenicity of HIV infection has been frequently underestimated. The early events of the HIV replication cycle involve the interaction between viral envelope glycoproteins and cellular receptors: the CD4 molecule and a chemokine receptor, usually CCR5 or CXCR4. Despite the importance of these two chemokine receptors in human immunodeficiency virus 1 (HIV-1) entry into cells, we have previously shown that in some HIV-2 asymptomatic individuals, a viral population exists that is unable to use both CCR5 and CXCR4. The goal of the present study was to investigate whether possible regions in the env gene of these viruses might account for this phenotype. From the molecular characterization of these env genes we could not detect any correlation between V3 loop sequence and viral phenotype. In contrast, it reveals the existence of remarkable differences in the V1/V2 and C5 regions of the surface glycoprotein, including the loss of a putative glycosilation site. Moreover, in the transmembrane glycoprotein some unique sequence signatures could be detected in the central ectodomain and second heptad repeat (HR2). Some of the mutations affect well-conserved residues, and may affect the conformation and/or the dynamics of envelope glycoproteins complex, including the SU,TM association and the modulation of viral entry function. J. Med. Virol. 81:1869,1881, 2009. © 2009 Wiley-Liss, Inc. [source] Detection of human bocavirus in hospitalised childrenJOURNAL OF PAEDIATRICS AND CHILD HEALTH, Issue 3 2009Julia Dina Aim: The objectives of this study are to assess the frequency of human bocavirus (HBoV) infection in hospitalised children and to study the clinical symptoms associated with the detection of HBoV. Methods: Two groups of hospitalised children were included in this study: group 1 consisted of 1946 children hospitalised from 1st September 2004 to 30th May 2005, and group 2 consisted of 448 children hospitalised from 1st November 2003 to 30th March 2004. The respiratory specimens were tested by polymerase chain reaction. Results: In the first group, HBoV was detected by polymerise chain reaction in 11/828 (1.3%) of nasal specimens that tested negative for other respiratory viruses. One child tested positive for HBoV in both a nasal aspirate and stool sample. In the second group, nasal specimens were tested for all respiratory viruses, including HBoV. The presence of HBoV infection was detected in seven children (1.6%). Detection of a mixed viral population was observed in four of these children. The main symptoms in children infected with HBoV were rhinitis (50%), cough (45%), dyspnoea (28%), wheezing (28%), fever (23%) and diarrhoea (22%). The final clinical diagnoses were bronchiolitis (seven children), rhinopharyngitis (five children), the exacerbation of asthma (two children) and pneumonia (one child). Moreover, four children have associated gastroenteritis. Conclusion: These results contribute to the interest in the HBoV detection in children. HBoV detection in hospitalised children with or without any other respiratory virus detection was essentially associated with lower respiratory tract infection and in a lower score with upper respiratory tract infection and gastroenteritis. [source] Freshwater and marine virioplankton: a brief overview of commonalities and differencesFRESHWATER BIOLOGY, Issue 6 2008STEVEN W. WILHELM Summary 1. Viruses are a pervasive component of microbial food webs in both marine and freshwater systems. The abundance of viruses in individual aquatic systems appears to be independent of salinity but related to the biomass of primary and secondary producers as well as seasonal effects. Burst size, virus production rate and the percentage of microbial cells carrying a viral burden also appear to be more closely correlated to trophic status than to salinity. 2. In marine environments, the roles of planktonic viruses as regulators of carbon and nutrient cycling as well as microbial community structure have been a focus of numerous studies, yet the roles of freshwater virioplankton remain much less studied. Nevertheless, a survey of published freshwater studies demonstrates that virioplankton recycle important quantities of growth-limiting nutrients from hosts via generation of dead particulate and dissolved organic matter during cell lysis, and suggests that both the chemical speciation and concentration of these organic compounds and nutrients may have important influences on the microbial community. 3. Parallel observations on the spatial patterns and dynamics of microbial mortality due to viruses or grazing are more advanced in freshwaters than in marine environments. However, the constraints that determine whether virus- or grazer-mediated mortality dominates are not yet understood in either environment. 4. Application of molecular approaches has facilitated the examination of the diversity and ecological dynamics of specific viral populations and entire communities. The depth of detail achieved in marine environments towards characterizing these populations and communities is just beginning to be matched in freshwater systems. The few available data suggest that viruses targeting-related hosts in freshwater and marine systems may be genetically distinct. 5. Although the role of viruses in aquatic systems is complex and remains insufficiently studied, our survey of the literature indicates that, despite some differences, many of the controls on virioplankton activity and diversity are similar in marine and freshwater environments. [source] The selection and evolution of viral quasispecies in HIV-1 infected childrenHIV MEDICINE, Issue 1 2002P Nowak Objectives To analyse the diversity and divergence of the viral populations in three mother,child pairs in longitudinally obtained samples for up to 7 years. Methods Peripheral blood mononuclear cells were obtained from three mothers at delivery and three to four samples were obtained from each of their children from 1.5 months up to 78 months of age. The V3 region of HIV-1 was amplified by polymerase chain reaction, cloned and sequenced. HIV-1 DNA sequence comparisons were performed by phylogenetic analysis. Results The viral population was initially homogenous in two children but highly heterogeneous in one child. Three patterns of vertical transmission seemed to have occurred: transmission of the most prevalent maternal strain, of a minor maternal strain and of multiple maternal strains. In one child, a possible reappearance of a maternal sequence was observed at 34 months of age. Conclusions Children may become infected with the most prevalent maternal strain, a minor maternal variant or multiple maternal quasispecies. Maternal viral variants may reappear in children after several years of infection and could possibly be derived from a reservoir of founder quasispecies established during the children's primary HIV-1 infection. [source] Concordance between semen-derived HIV-1 proviral DNA and viral RNA hypervariable region 3 (V3) envelope sequences in cases where semen populations are distinct from those present in bloodJOURNAL OF MEDICAL VIROLOGY, Issue 1 2002Rebecca Curran Abstract Sequence analysis of the third hypervariable region (V3) of the envelope gene of the HIV-1 was carried out on HIV proviral and viral populations present in blood and semen. Phylogenetically distinct populations of virus were observed in three of the 10 patients analysed. Although the majority of the viruses were predicted to have an R5 phenotype, amino acid differences between blood and semen-derived virus and provirus sequences were observed at sites previously shown to affect cell tropism. Importantly, the semen proviral population was representative of that observed for cell-free virus. This indicates that seminal fluid mononuclear cells are possible sources for the cell-free virus in found in semen. J. Med. Virol. 67:9,19, 2002. © 2002 Wiley-Liss, Inc. [source] Field trial of serially passaged isolates of BYDV-PAV overcoming resistance derived from Thinopyrum intermedium in wheatPLANT BREEDING, Issue 3 2006F. Chain Abstract Barley yellow dwarf disease (BYDD) is one of the main viral diseases of small grain cereals. This disease, reported on numerous plant species of the Poaceae family, is caused by a complex of viral species including the species Barley yellow dwarf virus -PAV (BYDV-PAV, family Luteoviridae, genus Luteovirus), frequently found in western Europe. Resistance sources towards BYDD are scarce. Indeed, breeding-resistant genotypes is a long and expensive process. Thus, estimating the durability of the resistance genes before the achievement of selection would be an asset for breeders. One isolate of BYDV-PAV has been serially passaged on two hosts, ,Zhong ZH' and ,TC14', carrying a gene for partial resistance. The resulting viral population showed an increase of the speed of development of the infection in controlled conditions. In this study, these viral populations were evaluated in a 3-year field trial, including a susceptible host, ,Rendezvous', and a host carrying the resistance gene of ,TC14' in a ,Rendezvous' background, to assess the effect of serial passages in field conditions. Results indicate that isolates issued from serial passages on hosts carrying a gene for partial resistance induced increased damage in field conditions when compared with the initial isolate. Yield losses are mainly due to a decrease of the number of kernels per square metre. The interest on using partial resistance gene to control BYDD is discussed. [source] Comparison of viral RNA populations of pathogenically distinct isolates of Citrus tristeza virus : application to monitoring cross-protectionPLANT PATHOLOGY, Issue 3 2002A. Sambade The population of sequence variants of Citrus tristeza virus (CTV) isolates of different geographic origins and pathogenicity properties was characterized by single-strand conformation polymorphism (SSCP) analysis of cDNA of the genes p18, p13, p20 and p23. The mild isolates analysed here usually yielded a SSCP profile with two DNA bands, suggestive of a predominant sequence variant, whereas the SSCP profile of the most virulent isolates contained more than two DNA bands, indicating that their viral populations are likely to be more complex. The set of SSCP profiles of the four genes allowed identification of individual isolates, but no profile characteristic of a geographic area or a biogroup was found. Sweet orange plants singly inoculated with a mild or with a severe isolate yielded the SSCP profile characteristic of each isolate, whereas the SSCP profile of plants successively inoculated with both isolates was a composite of the two individual profiles. The SSCP profile of plants singly inoculated remained constant, but the profile of doubly inoculated plants varied with time. Plants in which the SSCP profile of the severe isolate became predominant showed stem pitting, and those in which the predominant profile corresponded to the mild isolate remained symptomless. The results indicate that SSCP analysis can be used to study changes in RNA populations of doubly inoculated plants and to monitor cross-protection between mild and severe isolates. [source] | |||||||||||||