Hepatitis C Virus Dynamics during Natural Infection Are Associated with Long‐Term Histological Outcome of Chronic Hepatitis C Disease

The intrahost evolution of hepatitis C virus (HCV) holds keys to understanding mechanisms responsible for the establishment of chronic infections and to development of a vaccine and therapeutics. In this study, intrahost variants of two variable HCV genomic regions, HVR1 and NS5A, were sequenced from four treatment-naïve chronically infected patients who were followed up from the acute stage of infection for 9 to 18 years. Median-joining network analysis indicated that the majority of the HCV intrahost variants were observed only at certain time points, but some variants were detectable at more than one time point. In all patients, these variants were found organized into communities or subpopulations. We hypothesize that HCV intrahost evolution is defined by two processes: incremental changes within communities through random mutation and alternations between coexisting communities. The HCV population was observed to incrementally evolve within a single community during approximately the first 3 years of infection, followed by dispersion into several subpopulations. Two patients demonstrated this pattern of dispersion for the rest of the observation period, while HCV variants in the other two patients converged into another single subpopulation after ϳ9 to 12 years of dispersion. The final subpopulation in these two patients was under purifying selection. Intrahost HCV evolution in all four patients was characterized by a consistent increase in negative selection over time, suggesting the increasing HCV adaptation to the host late in infection. The data suggest specific staging of HCV intrahost evolution.Hepatitis C virus (HCV) infection is a major cause of liver disease in the world. It is estimated that ϳ130 million people are infected with HCV globally (2). HCV is a heterogeneous single-stranded (plus-strand) RNA virus belonging to the Flaviviridae. The HCV genome contains one large open reading frame that encodes a polyprotein which can be processed into 10 mature proteins (34). HCV causes chronic infection in 70 to 85% of infected adults. There is no vaccine against HCV, and current antiviral therapy is effective in only 50 to 70% of chronically infected patients (18).HCV intrahost evolution is frequently compared to an "arms race," implying that the HCV genome constantly changes in order to escape from neutralizing adaptive immunoresponses (53). This concept of constant change is seemingly different from the HIV model, according to which intrahost evolution slows down with CD4 ϩ T-cell depletion and quasispecies diversity decreases with the development of AIDS (48). Our limited understanding of the dynamics of HCV intrahost evolution impedes the development of efficient therapeutic and prophylactic interventions.Analysis of HCV longitudinal evolution is significantly hindered by difficulties with identifying and with long-term follow-up of patients, starting from the acquisition of infection. In the present study, we explored HCV evolutionary processes during long-term chronic infection in four treatment-...

Section: Discussionmentioning

confidence: 99%

Temporal Variations in the Hepatitis C Virus Intrahost Population during Chronic Infection

Ramachandran

Campo

Dimitrova

et al. 2011

“…These replacements may begin with a cloud of closely related virus strains (i.e., intrahost viral diversity), generated in part by the error-prone RNA-dependent RNA polymerase of DENV (15,16). The intrahost diversity of viruses is typically described in chronic infections, such as those caused by HIV and hepatitis C virus (17)(18)(19), but has also been found in acute infections with DENV and other RNA viruses (20)(21)(22)(23). During arbovirus infections, such populations are subject to natural selection in both the mosquito and the human host.…”

mentioning

confidence: 99%

Increased Replicative Fitness of a Dengue Virus 2 Clade in Native Mosquitoes: Potential Contribution to a Clade Replacement Event in Nicaragua

Quiner

Parameswaran

Ciota

et al. 2014

The four dengue virus (DENV) serotypes (DENV serotype 1 [DENV-1] to DENV-4) are transmitted by Aedes aegypti and A. albopictus mosquitoes, causing up to 390 million DENV infections worldwide each year. We previously reported a clade replacement of the DENV-2 Asian-American genotype NI-1 clade by the NI-2B clade in Managua, Nicaragua. Here, we describe our studies of the replicative ability of NI-1 and NI-2B viruses in an A. aegypti cell line (Aag2) and A. aegypti mosquitoes reared from eggs collected in Managua. In coinfection experiments, several different pairs of NI-1 and NI-2B clinical isolates were used to infect Aag2 cells or blood-fed A. aegypti mosquitoes. Results consistently showed a significant replicative advantage of NI-2B over NI-1 viruses early after infection in vitro, and in mosquitoes, NI-2B viruses attained a higher replicative index than NI-1 isolates 3 to 7 days postinfection (dpi). At 7 dpi, NI-2B viruses displayed a significantly higher replicative index in legs and salivary glands; however, this advantage was lost by 14 and 21 dpi. We also found that the percentage of mosquitoes in which NI-2B viruses were dominant was significantly higher than that in which NI-1 viruses were dominant on day 7 but not at later time points. Taken together, these data demonstrate that clade NI-2B holds a replicative advantage over clade NI-1 early in infection that wanes at later time points. This early fitness advantage of NI-2B viruses over NI-1 viruses in the native vector, A. aegypti, suggests a shorter extrinsic incubation period for NI-2B viruses, which could have contributed to the clade replacement event in Managua. IMPORTANCEDengue virus (DENV), one of the most medically important arthropod-borne viruses, is transmitted to humans by Aedes aegypti and A. albopictus mosquitoes in tropical and subtropical regions worldwide. Dengue epidemics continue to increase in frequency, geographic range, and severity and are a major public health concern. This is due to globalization, unplanned urbanization, and climate change, as well as host genetics and immune responses and viral genetic changes. DENV consists of four serotypes, in turn composed of genotypes and genetically distinct clades. What drives the frequent replacement of a previously circulating DENV clade by another is unclear. Here, we investigate the replicative fitness of two clades of DENV serotype 2 in Aedes aegypti cells and mosquitoes collected from the region where the viruses circulated and conclude that increased replicative fitness could have contributed to a DENV clade replacement event in Nicaragua. These findings provide insight into vectordriven evolution of DENV epidemics. Dengue virus (DENV) is an arbovirus of global importance comprised of four phylogenetically related serotypes, DENV serotype 1 (DENV-1) to DENV-4. DENV is transmitted by Aedes aegypti and A. albopictus mosquitoes, which are typically found in tropical and subtropical regions of the world. However, due to a complex combination of factors that include migratio...

“…Studies of mumps virus and poliovirus demonstrated that increases in the genetic heterogeneity of the virus population led to increases in pathogenesis (28,32). In contrast, a high level of variation in the population of hepatitis C virus and WNV has been associated with decreases in pathogenesis (16,31). In addition, studies using a mouse model of foot and mouth disease virus pathogenesis suggested that the overall pathogenic potential of a virus population arises through a complex interplay of viral genomes that differ in their individual potential to cause disease (27).…”

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confidence: 99%

Nonconsensus West Nile Virus Genomes Arising during Mosquito Infection Suppress Pathogenesis and Modulate Virus Fitness In Vivo

Ebel

Fitzpatrick

Lim

et al. 2011

West Nile virus (WNV) is similar to other RNA viruses in that it forms genetically complex populations within hosts. The virus is maintained in nature in mosquitoes and birds, with each host type exerting distinct influences on virus populations. We previously observed that prolonged replication in mosquitoes led to increases in WNV genetic diversity and diminished pathogenesis in mice without remarkable changes to the consensus genome sequence. We therefore sought to evaluate the relationships between individual and group phenotypes in WNV and to discover novel viral determinants of pathogenesis in mice and fitness in mosquitoes and birds. Individual plaque size variants were isolated from a genetically complex population, and mutations conferring a small-plaque and mouse-attenuated phenotype were localized to the RNA helicase domain of the NS3 protein by reverse genetics. The mutation, an Asp deletion, did not alter type I interferon production in the host but rendered mutant viruses more susceptible to interferon compared to wild type (WT) WNV. Finally, we used an in vivo fitness assay in Culex quinquefasciatus mosquitoes and chickens to determine whether the mutation in NS3 influenced fitness. The fitness of the NS3 mutant was dramatically lower in chickens and moderately lower in mosquitoes, indicating that RNA helicase is a major fitness determinant of WNV and that the effect on fitness is host specific. Overall, this work highlights the complex relationships that exist between individual and group phenotypes in RNA viruses and identifies RNA helicase as an attenuation and fitness determinant in WNV.West Nile virus (WNV; Flaviviridae: Flavivirus) is a positivesense, single-stranded RNA (ssRNA) virus belonging to the Japanese encephalitis virus (JEV) serological complex of the flaviviruses. WNV perpetuates in nature in enzootic transmission cycles through alternating replication in (mainly avian) vertebrates and mosquitoes. The specific mosquito and avian hosts that are most important in a particular locality differ but tend to include Culex species mosquitoes and passerine birds (2, 10). WNV infection of mammals, including humans and horses, occurs via spillover from this enzootic cycle. Since its introduction into North America in 1999 (20), molecular epidemiologic studies have clearly demonstrated that the virus has evolved to maximize its transmission potential within local transmission cycles (8,11,23). This finding stimulated subsequent efforts to understand the details of the underlying evolutionary mechanisms that lead to population-level genetic and phenotypic changes in the virus. In brief, these studies demonstrated that WNV populations are genetically diverse within hosts (15), that genetic diversity may be shared between hosts (15), and that mosquito infection drives genetic diversification of the virus population both through relaxation of purifying selection and through selection of rare genotypes resulting from RNA interference (RNAi) (4,16,17). Thus, in the WNV transmission cycle, different...