Coordinated evolution of the hepatitis C virus

Abstract

Hepatitis C virus is a genetically heterogeneous RNA virus that is a major cause of liver disease worldwide. Here, we show that, despite its extensive heterogeneity, the evolution of hepatitis C virus is primarily shaped by negative selection and that numerous coordinated substitutions in the polyprotein can be organized into a scale-free network whose degree of connections between sites follows a power-law distribution. This network shares all major properties with many complex biological and technological networks. The topological structure and hierarchical organization of this network suggest that a small number of amino acid sites exert extensive impact on hepatitis C virus evolution. Nonstructural proteins are enriched for negatively selected sites of high centrality, whereas structural proteins are enriched for positively selected sites located in the periphery of the network. The complex network of coordinated substitutions is an emergent property of genetic systems with implications for evolution, vaccine research, and drug development. In addition to such properties as polymorphism or strength of selection, the epistatic connectivity mapped in the network is important for typing individual sites, proteins, or entire genetic systems. The network topology may help devise molecular intervention strategies for disrupting viral functions or impeding compensatory changes for vaccine escape or drug resistance mutations. Also, it may be used to find new therapeutic targets, as suggested in this study for the NS4A protein, which plays an important role in the network.complex systems ͉ scale-free network ͉ covariation ͉ natural selection ͉ epistasis H epatitis C virus (HCV) is a major cause of liver disease worldwide. The global prevalence of HCV infection is estimated to be 2.2%, representing 130 million people (1). HCV causes chronic infection in 70-85% of infected adults (2). There is no vaccine against HCV and current antiviral therapy is relatively toxic, being effective in 50-60% of patients treated (3). HCV is a single-stranded RNA virus of Ϸ9.4 kb belonging to the Flaviviridae family (4). The positive-sense genome of HCV contains one large ORF that encodes a polyprotein that can undergo proteolytic cleavage into 10 mature proteins (C-E1-E2-P7-NS2-NS3-NS4A-NS4B-NS5A-NS5B). The structural proteins, the core (C) and envelope glycoproteins E1 and E2, are present in the N-terminal part of the polyprotein and presumably self-assemble to form the virion. The nonstructural (NS) proteins have various functions and form the replication complex (5).The HCV genome continually mutates during virus replication. Although a high rate of mutation significantly contributes to the enormous adaptability of RNA viruses, it also limits the size of viral genomes by causing error catastrophe (6). The small size of viral genomes imposes strong evolutionary constraints on their organization, as a result of which each genomic region may encode multiple and often conflicting functions. Such genomic organization requires a tight coor...

Genome-wide hepatitis C virus amino acid covariance networks can predict response to antiviral therapy in humans

“…Genome-wide covariance analysis has very recently been used by Campo and colleagues to assess coordinated evolution of residues throughout the HCV genome (37). This work was performed independently of our analysis and used a different method to identify the covariances, but the results from the 2 studies were very similar.…”

Divergent adaptation of hepatitis C virus genotypes 1 and 3 to human leukocyte antigen-restricted immune pressure

“…27 The fact that viral adaptation is highly constrained may help to explain why persistent infection is not always established following HCV infection, and also suggests that viral adaptation to HLA-restricted CTL could frequently incur costs to viral replicative capacity.…”

Epistatic connectivity among HCV genomic sites as a genetic marker of interferon resistance

“…Pervasive epistatic connectivity among viral genomic sites is frequently detected in the form of compensatory substitutions [45,46]. This widespread connectivity is organized into a network of coordinated substitutions, reflecting extensive global coevolution among sites across the entire HCV genome [47]. The network has a very specific topology, with only a few sites being connected to many other sites and many sites having only a few connections.…”

“…However, the extensive epistatic connectivity discovered among HCV genomic sites [47][48][49] suggests that coevolution among sites in any genomic region reflects selection pressures acting on the entire HCV genome in an infected host. Indeed, it was recently reported that each HCV protein [48,49] or small genomic region, such as hypervariable region 1 (HVR1) and a segment of the NS5A gene [50], has a strong association with IFN resistance.…”

“…As mentioned previously, coordinated evolution among HCV genomic sites reflects many host selection pressures, including innate and adaptive immune responses [47][48][49][50], thus associating host and viral genetic factors. Analysis of individual genomic sites without consideration of their interrelationships is inefficient for the detection of this association.…”