Decreased diversity of hepatitis C virus quasispecies during bone marrow transplantation

Hepatitis C virus (HCV) infections may be initiated by multiple infectious particles, resulting in a genetically heterogeneous viral population, or by a single particle, leading to a clonal population in the initial stage of infection. To determine which of these scenarios is most common, we evaluated the genetic diversity of HCV quasispecies in 12 seronegative subjects with primary infection following community exposures, six acutely infected recipients of HCV-seropositive blood transfusions and six seropositive individuals with infections of undetermined durations. RNA isolated from plasma and a region of the HCV envelope gene including the first hypervariable region (HVR-1) was reverse transcription-PCR amplified and subcloned, and multiple plasmid clones were sequenced. Phylogenetic analysis indicated that all HCV variants clustered by individuals. Genetic distances among HCV variants within recently infected subjects ranged from 1 to 7.8%. On the basis of the estimated mutation rate of HCV in vivo and the Taq polymerase error rate, primary infection viral quasispecies were classified as genetically heterogeneous when the maximum sequence divergence between genetic variants in the same person was >3%. Heterogeneous quasispecies were detected in 4 of 12 preseroconversion subjects, 1 of 6 transfusion recipients, and 4 of 6 seropositive subjects. The high level of viral quasispecies genetic diversity found in at least a third of recently infected individuals is consistent with the transmission of multiple infectious particles. Community-acquired HCV infection, predominantly the result of needle sharing by injection drug users, therefore appears to be frequently initiated by the successful transmission of multiple viral variants.Hepatitis C virus (HCV) in plasma is typically found as a genetically heterogeneous, monophyletic population of viral variants often referred to as a quasispecies (14,18,49). The composition of such quasispecies changes rapidly in immunocompetent hosts, presumably because of the selection of escape variants that evade cellular and humoral immune responses (9,22,31,59,68) or because of superinfection with a divergent strain (25,55). Limited HCV evolution has been reported in immunocompromised chimpanzees and humans, possibly because of reduced immune selective pressures (6,44,47,66). The high mutation rate and short generation time of HCV therefore provide this virus with a high level of genetic adaptability, which may explain why as many as 80% of primary infections result in chronic infection with high-titer viremia (43).Because primary HCV infection is typically asymptomatic, subjects recently infected with HCV through contaminated needle sharing or other community exposures are difficult to identify. Consequently, the genetic diversity of the viral quasispecies during the very early preseroconversion phase of viremia remains largely unknown. The genetic diversity of preseroconversion plasma quasispecies is likely to be closely related to that of the inoculums since they are separated ...

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confidence: 99%

Wide Range of Quasispecies Diversity during Primary Hepatitis C Virus Infection

Herring

Tsui

Peddada

et al. 2005

“…The present data on quasispecies diversity and evolution in coinfected patients are conflicting. However, given that (i) HVR1 responds to immune pressure with increased variability (36,51) and (ii) in other disease models it has been shown that immunosuppression (and thus decreased immune pressure) is associated with a decrease in HCV genetic diversity (2,23,26,29,33), we hypothesized that HAART, via immune restoration and increased immune pressure, might cause an increase in HCV quasispecies diversity. As such, we sought to determine the effect of HAART-associated immune restoration on the HCV quasispecies profile in HIV/HCV-coinfected individuals.…”

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confidence: 99%

Impact of Highly Active Antiretroviral Therapy and Immunologic Status on Hepatitis C Virus Quasispecies Diversity in Human Immunodeficiency Virus/Hepatitis C Virus-Coinfected Patients

Babik

Holodniy

2003

This study analyzes the effect of highly active antiretroviral therapy (HAART), and thus immunologic status, on hepatitis C virus (HCV) load and quasispecies diversity in patients coinfected with the human immunodeficiency virus (HIV) and HCV. Three cohorts of coinfected patients were analyzed retrospectively over a period of 7 to 10 months: group A was antiretroviral drug naïve at baseline and then on HAART for the remainder of the study, group B did not receive antiretroviral therapy at any point, and group C was on HAART for the entire study. HCV quasispecies diversity was analyzed by sequencing hypervariable region 1. In a longitudinal analysis, there was no significant change from baseline in any immunologic, virologic, or quasispecies parameter in any of the three groups. However, in comparison to groups A and B, group C had significantly higher CD4؉ -and CD8 ؉ -cell counts, a trend toward a higher HCV load, and significantly increased number of HCV clones, entropy, genetic distance, and ratio of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site (K a /K s ). In addition, CD4؉ -cell count was positively correlated with HCV load, genetic distance, and K a . Interestingly, patients infected with HCV genotype 2 or 3 had a significantly higher CD4؉ -cell count, HCV load, genetic distance, and K a /K s than those infected with genotype 1. These results suggest that there is no immediate effect of HAART on HCV but that, with prolonged HAART, immune restoration results in an increase in HCV load and quasispecies diversity.

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confidence: 99%

“…Another prediction of the quasispecies model is that the master (or most common) sequence in the quasispecies will not change in a stable environment, while changes in minor variants will continue to occur. Evidence from immunosuppressed individuals, in whom the pace of sequence variation is reduced, suggests that this prediction applies to HCV (7,28,42).If HCV persists by escaping the immune response through sequence variation, then that sequence variation will reveal important characteristics of the immune response. If, however, persistence is due to other factors and sequence variation is simply the random product of an error-prone polymerase and a rapidly replicating virus (47), then sequence variation will always occur when HCV is allowed to replicate, and sequence variation will be uninformative except to define areas tolerant of sequence variation.…”

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confidence: 99%

Hypervariable Region 1 Sequence Stability during Hepatitis C Virus Replication in Chimpanzees

Ray

Mao

Lanford

et al. 2000

The putative envelope 2 (E2) gene of hepatitis C virus (HCV) contains a highly variable region referred to as hypervariable region 1 (HVR1). We hypothesized that this genetic variability is driven by immune selection pressure, rather than representing the accumulation of random mutations in a region with relatively little functional constraint. To test this hypothesis, we examined the E2 sequence of a human inoculum that was passaged through eight chimpanzees, which appear to have a replicative rate (opportunity for chance mutation) similar to that of humans. Acute-phase plasma samples from a human (the inoculum) and six of eight serially infected chimpanzees were studied. For each, 33 cloned cDNAs were examined by a combined heteroduplex-single-stranded conformational polymorphism assay to assess quasispecies complexity and optimize selection of clones with unique gel shift patterns (clonotypes) for sequencing. The sequence diversity of HCV was significantly lower in the chimpanzees than in the humans, and during eight serial passages there was no change in the sequence of the majority clonotype from each animal examined. Similarly, the rates of protein sequence altering (nonsynonymous) substitution were lower in the chimpanzees than in the humans. These findings demonstrate that nonsynonymous mutations indicate selection pressure rather than being an incidental result of HCV replication.An estimated 170 million people worldwide are infected with hepatitis C virus (HCV) (4). More than 80% of infections result in persistent viremia, which may be associated with chronic hepatitis, cirrhosis, liver failure, and hepatocellular cancer (3,41,44). HCV-associated disease is responsible for more than 10,000 deaths each year in the United States alone, and this mortality is expected to rise (8). Because of limitations of in vitro replication systems, studies of HCV pathogenesis have been limited to observation of natural infection of humans and experimental infection of chimpanzees.The chimpanzee is the best experimental model of HCV infection. HCV does not grow efficiently in tissue culture, and the only other candidate model is a tree shrew that is too small to permit adequate sampling with current technology (52). In chimpanzees, HCV replication has been demonstrated within days of experimental infection, and the potential for reinfection has been demonstrated (14,15,37,51). Serum HCV RNA levels and the extent of hepatic HCV involvement are similar in chimpanzees and humans, suggesting that replication rates are similar (1). The chimpanzee has also been used to test the infectivity of HCV clones and vaccine candidates. However, Bassett et al. recently demonstrated that the natural history of HCV infection in a cohort of experimentally infected chimpanzees differed from what is typically found in humans (5, 6). These chimpanzees had a higher rate of clearance of viremia, lower rate of antibody production to envelope proteins, and lower rate of envelope amino acid change. Similarly, others have reported little change in...