Evolutionary dynamics of hepatitis C virus envelope genes during chronic infection

Abstract

Hepatitis C virus (HCV) envelope glycoproteins E1 and E2 are important targets for the host immune response. The genes encoding these proteins exhibit a high degree of variability that gives rise to differing phenotypic traits, including alterations in receptor-binding affinity and immune recognition and escape. In order to elucidate patterns of adaptive evolution during chronic infection, a panel of full-length E1E2 clones was generated from sequential serum samples obtained from four chronically infected individuals. By using likelihood-based methods for phylogenetic inference, the evolutionary dynamics of circulating HCV quasispecies populations were assessed and a site-by-site analysis of the d N /d S ratio was performed, to identify specific codons undergoing diversifying positive selection. HCV phylogenies, coupled with the number and distribution of selected sites, differed markedly between patients, highlighting that HCV evolution during chronic infection is a patient-specific phenomenon. This analysis shows that purifying selection is the major force acting on HCV populations in chronic infection. Whilst no significant evidence for positive selection was observed in E1, a number of sites under positive selection were identified within the ectodomain of the E2 protein. All of these sites were located in regions hypothesized to be exposed to the selective environment of the host, including a number of functionally defined domains that have been reported to be involved in immune evasion and receptor binding. Dated-tip methods for estimation of underlying HCV mutation rates were also applied to the data, enabling prediction of the most recent common ancestor for each patient's quasispecies. INTRODUCTIONHepatitis C virus (HCV) is a positive-sense RNA virus and is the sole member of the genus Hepacivirus of the family Flaviviridae (Lindenbach & Rice, 2001). Globally, approximately 170 million people are at risk of liver disease due to chronic HCV infection, with an estimated 3 million individuals newly infected per annum (WHO, 1999). Of those infected, a reported 80 % fail to clear the virus, a significant number of whom will go on to develop severe liver disease, including cirrhosis and hepatocellular carcinoma (Alter et al., 1992;Muller, 1996;Saito et al., 1990).HCV circulates within an infected host as a heterogeneous viral population containing genetically distinct, but closely related variants, known as quasispecies (Bukh et al., 1995;Martell et al., 1992). The propensity for genetic change is associated primarily with the error-prone nature of the RNA-dependent RNA polymerase, together with the high HCV replicative rate in vivo (Fukumoto et al., 1996; Neumann et al., 1998;Ramratnam et al., 1999;Zeuzem, 2000). Chronic infection arises, at least in part, through the outgrowth of immune-escape mutants (Farci et al., 2000;Frasca et al., 1999; Majid et al., 1999;Ray et al., 1999;Wang & Eckels, 1999). The envelope glycoprotein genes display some of the highest levels of HCV genetic heterogeneity, with E2 exh...

Mutations within a Conserved Region of the Hepatitis C Virus E2 Glycoprotein That Influence Virus-Receptor Interactions and Sensitivity to Neutralizing Antibodies

“…In contrast, the region of interest has only a single site detected as positively selected-that at position 416 (9). Consistent with this, the survey of 1311 E2 sequences reported here shows that 182 of them are variants (ca.…”

“…Together, the different infection systems, viral isolates and/or cell lines used in each study likely account for these inconsistencies. T416A is one of seven variants at a locus subject to positive selection (9), and although occurring 13 times in our sample, is only a minor component (7% of substitutions) of the extensive variability in this position.…”

Influence of quasispecies on virological responses and disease severity in patients with chronic hepatitis C

“…Several conflicting reports about a possible correlation of therapy response and disease severity with the presence of quasispecies have been published [15,20,[24][25][26][27] . The genes encoding HVR protein exhibit a high degree of variability, giving rise to differing phenotypic traits, including alterations in receptorbinding affinity and escape from immune recognition [28] . Substitutions in the NS5B gene of HCV may correlate with the virological response to interferon-based therapy [29][30][31] .…”

Intensive temporal mapping of hepatitis C hypervariable region 1 quasispecies provides novel insights into hepatitis C virus evolution in chronic infection

“…A number of studies investigating hypervariable region 1 (HVR1), a 27 aa segment encoding part of the virus envelope, have demonstrated an association between low HVR1 QS complexity, or high QS diversity, and sustained virologic response (SVR) with dual pegylated IFN and ribavirin treatment. Although HVR1 has been extensively studied in a number of differing conditions [acute HCV infection (Chen & Wang, 2002;Farci et al, 2000;Kuntzen et al, 2007;Liu et al, 2010), human immunodeficiency virus (HIV) co-infection (Mao et al, 2001;Shuhart et al, 2006), alcoholic liver disease (Sherman et al, 1999), chronic infection (Brambilla et al, 1998;Brown et al, 2005;Cabot et al, 2001;Kumagai et al, 2007;McAllister et al, 1998;Qin et al, 2005;Ray et al, 2005;Sullivan et al, 2007;Wang et al, 2007), during treatment (Abbate et al, 2004;Grahovac et al, 2000) and following transplantation (Doughty et al, 2000;Lyra et al, 2002;Pessoa et al, 1999;Sánchez-Fueyo et al, 2001)], little is known of the natural history of HVR1 QS evolution over short time intervals in subjects with chronic infection.…”