Wide Range of Quasispecies Diversity during Primary Hepatitis C Virus Infection

Abstract

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 ...

Optimal targeting of Hepatitis C virus treatment among injecting drug users to those not enrolled in methadone maintenance programs

“…Although viral loads are generally highest at acute HCV infection (Herring et al, 2005;Thimme et al, 2001), they generally do not experience a 100-fold decrease to chronic infection as seen in HIV (Murray et al, 1998). However if acute HCV infection is more infectious than chronic stage disease then it will exacerbate the rise in numbers acutely infected IDU when treatment increases, and will further slow the time taken to reduce HCV prevalence.…”

Selection and Characterization of Replicon Variants Dually Resistant to Thumb- and Palm-Binding Nonnucleoside Polymerase Inhibitors of the Hepatitis C Virus

“…Due to the high genetic heterogeneity of HCV in vivo (17,28,37), the rapid selection of drug-resistant HCV variants upon treatment with antivirals is to be expected when viral suppression is incomplete. Using the replicon system we have selected mutant replicons with reduced susceptibility to a thumb I-binding inhibitor (but not to other nonnucleoside NS5B polymerase inhibitors binding to the palm domain or to nucleoside analogs such as 2Ј-C-Me-C) under different experimental conditions, supporting the conclusion that these resistant variants were selected due to the direct antiviral pressure of the compound on the HCV replicon population.…”

“…HCV is an RNA virus and as such, replicates as a quasispecies, a population of genetically heterogeneous and monophyletic variants (13,17). This high genetic heterogeneity, due to the error-prone nature of its RNA-dependent RNA polymerase, represents an opportunity for the virus to evade antiviral treatment.…”

Mixed genotype transmission bodies and virions contribute to the maintenance of diversity in an insect virus

“…Virus populations are renowned for their diversity, and many viruses adopt infection strategies to ensure that part of that diversity is present in individual infected hosts (Hurst 2000). Within-host diversity may be achieved when inoculum comprises a diverse pool of virus genomes (Lord et al 1997;Bonneau et al 2001;Cory et al 2005;Herring et al 2005;Jerzak et al 2005), when genotypically distinct viruses cooperate to achieve infection, such as the facilitation observed in homologous or heterologous 'helper viruses' (Eckner 1973;Stenger 1998), or when viruses are capable of generating de novo diversity during the replication process in the newly infected host (Domingo et al 1998;Chang et al 2002;Ló pez-Bueno et al 2003). Genotypic diversity within infected hosts can have dramatic repercussions for both host and virus, including alterations in virulence (harm suffered by the host) (Sedarati et al 1988;Brown et al 2002;Schjørring & Koella 2002;Alizon 2008), within-host population dynamics (Miralles et al 2001;Rauch et al 2008), virus fitness (Hodgson et al 2004;Arends et al 2005;Č ičin-Š ain et al 2005;Simó n et al 2006), and if frequent, may favour the evolution of cheating genotypes (Turner & Chao 1999;Frank 2000;Grande-Pérez et al 2005).…”