HCV reinfection studies and the door to vaccine development

Genetic susceptibility to infectious diseases: Current status and future perspectives from genome-wide approaches

Genome-wide association studies (GWASs) have been widely applied to identify genetic factors that affect complex diseases or traits. Presently, the GWAS Catalog includes > 2800 human studies. Of these, only a minority have investigated the susceptibility to infectious diseases or the response to therapies for the treatment or prevention of infections. Despite their limited application in the field, GWASs have provided valuable insights by pinpointing associations to both innate and adaptive immune response loci, as well as novel unexpected risk factors for infection susceptibility. Herein, we discuss some issues and caveats of GWASs for infectious diseases, we review the most recent findings ensuing from these studies, and we provide a brief summary of selected GWASs for infections in non-human mammals. We conclude that, although the general trend in the field of complex traits is to shift from GWAS to next-generation sequencing, important knowledge on infectious disease-related traits can be still gained by GWASs, especially for those conditions that have never been investigated using this approach. We suggest that future studies will benefit from the leveraging of information from the host's and pathogen's genomes, as well as from the exploration of models that incorporate heterogeneity across populations and phenotypes. Interactions within HLA genes or among HLA variants and polymorphisms located outside the major histocompatibility complex may also play an important role in shaping the susceptibility and response to invading pathogens.

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Relatively few GWASs for infectious diseases were performed.

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Phenotype heterogeneity and case/control misclassification can affect GWAS power.

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Adaptive and innate immunity loci were identified in several infectious disease GWASs.

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Unexpected loci (e.g., lncRNAs) were also associated with infection susceptibility.

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GWASs should integrate host and pathogen diversity and use complex association models.

Effect of coinfection with hepatitis C virus on survival of individuals with HIV-1 infection

PURPOSE OF REVIEW

Hepatitis C virus (HCV) coinfection is a common and an important comorbidity in HIV infection. We review current trends in mortality and the potential for early combination antiretroviral therapy (cART) and HCV therapy to improve survival in coinfected patients.

RECENT FINDINGS

HIV/HCV coinfection increases risk of death from all causes, and from liver disease and harmful drug use in particular. There is growing evidence for a direct role of HIV in liver fibrogenesis and for cART to decrease the risk of dying from liver disease in coinfected persons. Sustained virologic responses after HCV treatment greatly impact mortality by reducing rates of hepatic decompensation, hepatocellular carcinoma and death from liver-related and nonliver-related causes by at least 50%, but treatment uptake has been low so far. Recent epidemiologic studies do suggest that liver-related mortality is declining in recent calendar periods; however, methodological limitations of currently available studies are important.

SUMMARY

Early cART and wider HCV treatment have the potential to markedly reduce HCV-related mortality and thus increase survival overall for HIV-infected populations. However, HCV treatment will need to be greatly scaled up. Given the complex nature of the populations affected, future studies will need to be carefully designed and controlled to rigorously evaluate the impact of these revolutionary therapies on survival.

Visits to primary care physicians among persons who inject drugs at high risk of hepatitis C virus infection: room for improvement

The role of primary care physicians (PCP) in hepatitis C virus (HCV) prevention is increasingly emphasized. Yet, little is known about the patterns of contacts with PCP among persons who inject drugs (PWID). We sought to assess the 6-month prevalence of PCP visiting among PWID at risk of HCV infection and to explore the associated factors. Baseline data were collected from HCV-seronegative PWID recruited in HEPCO, an observational Hepatitis Cohort study (2004-2011) in Montreal, Canada. An interviewer-administered questionnaire elicited information on socio-demographic factors, drug use patterns and healthcare services utilization. Blood samples were tested for HCV antibodies. Using the Gelberg-Andersen Behavioral Model, hierarchical logistic regression analyses were conducted to identify predisposing, need and enabling factors associated with PCP visiting. Of the 349 participants (mean age = 34; 80.8% male), 32.1% reported visiting a PCP. In the multivariate model, among predisposing factors, male gender [adjusted odds ratio (AOR) = 0.45 (0.25-0.83)], chronic homelessness [AOR = 0.08 (0.01-0.67)], cocaine injection [AOR = 0.46 (0.28-0.76)] and reporting greater illegal or semi-legal income [AOR = 0.48 (0.27-0.85)] were negatively associated with PCP visits. Markers of need were not associated with the outcome. Among enabling factors, contact with street nurses [AOR = 3.86 (1.49-9.90)] and food banks [AOR = 2.01 (1.20-3.37)] was positively associated with PCP visiting. Only one third of participating PWID reported a recent visit to a PCP. While a host of predisposing factors seems to hamper timely contacts with PCP among high-risk PWID, community-based support services may play an important role in initiating dialogue with primary healthcare services in this population.

Many hepatitis C reinfections that spontaneously clear may be undetected: Markov-chain Monte Carlo analysis of observational study data

Hepatitis C virus (HCV) reinfection rates are probably underestimated due to reinfection episodes occurring between study visits. A Markov model of HCV reinfection and spontaneous clearance was fitted to empirical data. Bayesian post-estimation was used to project reinfection rates, reinfection spontaneous clearance probability and duration of reinfection. Uniform prior probability distributions were assumed for reinfection rate (more than 0), spontaneous clearance probability (0-1) and duration (0.25-6.00 months). Model estimates were 104 per 100 person-years (95% CrI: 21-344), 0.84 (95% CrI: 0.59-0.98) and 1.3 months (95% CrI: 0.3-4.1) for reinfection rate, spontaneous clearance probability and duration, respectively. Simulation studies were used to assess model validity, demonstrating that the Bayesian model estimates provided useful information about the possible sources and magnitude of bias in epidemiological estimates of reinfection rates, probability of reinfection clearance and duration or reinfection. The quality of the Bayesian estimates improved for larger samples and shorter test intervals. Uncertainty in model estimates notwithstanding, findings suggest that HCV reinfections frequently and quickly result in spontaneous clearance, with many reinfection events going unobserved.

Virome Analysis of Transfusion Recipients Reveals a Novel Human Virus That Shares Genomic Features with Hepaciviruses and Pegiviruses

To investigate the transmission of novel infectious agents by blood transfusion, we studied changes in the virome composition of blood transfusion recipients pre- and posttransfusion. Using this approach, we detected and genetically characterized a novel human virus, human hepegivirus 1 (HHpgV-1), that shares features with hepatitis C virus (HCV) and human pegivirus (HPgV; formerly called GB virus C or hepatitis G virus). HCV and HPgV belong to the genera Hepacivirus and Pegivirus of the family Flaviviridae. HHpgV-1 was found in serum samples from two blood transfusion recipients and two hemophilia patients who had received plasma-derived clotting factor concentrates. In the former, the virus was detected only in the posttransfusion samples, indicating blood-borne transmission. Both hemophiliacs were persistently viremic over periods of at least 201 and 1,981 days. The 5′ untranslated region (UTR) of HHpgV-1 contained a type IV internal ribosome entry site (IRES), structurally similar to although highly divergent in sequence from that of HCV and other hepaciviruses. However, phylogenetic analysis of nonstructural genes (NS3 and NS5B) showed that HHpgV-1 forms a branch within the pegivirus clade distinct from HPgV and homologs infecting other mammalian species. In common with some pegivirus variants infecting rodents and bats, the HHpgV-1 genome encodes a short, highly basic protein upstream of E1, potentially possessing a core-like function in packaging RNA during assembly. Identification of this new human virus, HHpgV-1, expands our knowledge of the range of genome configurations of these viruses and may lead to a reevaluation of the original criteria by which the genera Hepacivirus and Pegivirus are defined.

More than 30 million blood components are transfused annually in the United States alone. Surveillance for infectious agents in the blood supply is key to ensuring the safety of this critical resource for medicine and public health. Here, we report the identification of a new and highly diverse HCV/GB virus (GBV)-like virus from human serum samples. This new virus, human hepegivirus 1 (HHpgV-1), was found in serum samples from blood transfusion recipients, indicating its potential for transmission via transfusion products. We also found persistent long-term HHpgV-1 viremia in two hemophilia patients. HHpgV-1 is unique because it shares genetic similarity with both highly pathogenic HCV and the apparently nonpathogenic HPgV (GBV-C). Our results add to the list of human viruses and provide data to develop reagents to study virus transmission and disease association and for interrupting virus transmission and new human infections.

Protective immunity against hepatitis C: many shades of gray

The majority of individuals who become acutely infected with hepatitis C virus (HCV) develop chronic infection and suffer from progressive liver damage while approximately 25% are able to eliminate the virus spontaneously. Despite the recent introduction of new direct-acting antivirals, there is still no vaccine for HCV. As a result, new infections and reinfections will remain a problem in developing countries and among high risk populations like injection drug users who have limited access to treatment and who continue to be exposed to the virus. The outcome of acute HCV is determined by the interplay between the host genetics, the virus, and the virus-specific immune response. Studies in humans and chimpanzees have demonstrated the essential role of HCV-specific CD4 and CD8 T cell responses in protection against viral persistence. Recent data suggest that antibody responses play a more important role than what was previously thought. Individuals who spontaneously resolve acute HCV infection develop long-lived memory T cells and are less likely to become persistently infected upon reexposure. New studies examining high risk cohorts are identifying correlates of protection during real life exposures and reinfections. In this review, we discuss correlates of protective immunity during acute HCV and upon reexposure. We draw parallels between HCV and the current knowledge about protective memory in other models of chronic viral infections. Finally, we discuss some of the yet unresolved questions about key correlates of protection and their relevance for vaccine development against HCV.

Hepatitis C virus vaccines among people who inject drugs

Most people who inject drugs (PWID) are infected with hepatitis C virus (HCV), and PWID have the highest risk of HCV infection of any risk group. The incidence of HCV infection is 5%-25% per year, demonstrating continued need for HCV infection prevention in PWID. Existing data in chimpanzees and PWID suggest that protective immunity against persistent HCV infection is achievable. Due to the high incidence of infection, PWID are both the most likely to benefit from a vaccine and a population in which vaccine efficacy could be tested. Challenges to testing a vaccine in PWID are significant. However, the first HCV vaccine trial in at-risk HCV-uninfected PWID was initiated in 2012. The results will likely guide future vaccine development and strategies for vaccination of this and other high-risk populations.

A simple strategy to identify acute hepatitis C virus infection among newly incarcerated injection drug users

Acute hepatitis C virus (HCV) infection is underdiagnosed because most patients are asymptomatic. The majority of new infections occur among people who inject drugs (PWID), many of whom have a history of incarceration. In a previous pilot study, we identified symptomatic HCV cases, mainly among Caucasian inmates. We designed a cross-sectional study to evaluate whether risk factor-based screening of newly incarcerated inmates would enhance identification of asymptomatic acute HCV infection and elucidate any demographic shifts in HCV acquisition. From October 2006 to March 2008, 6,342 inmates underwent health assessments and 3,470 inmates (55%) were screened. The racial distribution was as follows: African American, 24.0%; Caucasian, 49.5%; Hispanic, 22.2%. One hundred seventy-one inmates (4.9%) were classified as high-risk. After further evaluation, 35 (20.5%) inmates were diagnosed with acute HCV with a mean age of 29 years; 62.9% were female and 91% were Caucasian. No African Americans were diagnosed with acute HCV. Our case-finding rate was 1.9 patients/month nearly a three-fold increase compared with our historical control period with a higher proportion of asymptomatic cases. We estimate a prevalence of ∼1.0% (95% confidence interval, 0.7%-1.4%) of acute HCV infections among newly incarcerated inmates.

CONCLUSION

Within the correctional system, systematic screening based on risk factors successfully identifies acute HCV infection among PWID, including asymptomatic patients. Our data also reflect changing nationwide patterns of injection drug use that vary by age, ethnicity, and race, leading to a marked reduction of acute HCV infections among African Americans compared with non-Hispanic whites. The nationwide implementation of this simple low-cost strategy in prison-based settings could identify more than 7,000 acute HCV infections among PWID, provide insight into changing epidemiologic trends, and facilitate appropriate therapeutic and preventive interventions.

Hepatitis C virus clearance, reinfection, and persistence, with insights from studies of injecting drug users: towards a vaccine

Hepatitis C virus (HCV) was discovered more than two decades ago, but progress towards a vaccine has been slow. HCV infection will spontaneously clear in about 25% of people. Studies of spontaneous HCV clearance in chimpanzees and human beings have identified host and viral factors that could be important in the control of HCV infection and the design of HCV vaccines. Although data from studies of chimpanzees suggest that protection against reinfection is possible after spontaneous clearance, HCV is a human disease. Results from studies of reinfection risk after spontaneous clearance in injecting drug users are conflicting, but some people seem to have protection against HCV persistence. To guide future vaccine development, we assess data from studies of HCV reinfection after spontaneous clearance, discuss flaws in the methods of previous human studies, and suggest essential components for future investigations of control of HCV infection.

The more you look, the more you find: effects of hepatitis C virus testing interval on reinfection incidence and clearance and implications for future vaccine study design

INTRODUCTION

Studies have explored whether spontaneous clearance of hepatitis C virus (HCV) infection decreases the likelihood of reinfection or increases the probability of clearance. This analysis investigates whether the conflicting findings from these studies could be due to differences in frequency of HCV RNA testing.

METHODS

A model simulated the dynamics of HCV reinfection and clearance among a cohort of injection drug users. For different reinfection incidence and clearance rates, the model evaluated the accuracy of epidemiological studies that used different HCV testing frequencies.

RESULTS

Experimental estimates for the reinfection incidence and clearance probability will be accurate (<20% error) if the testing interval is less than the reinfection clearance duration. Otherwise, experimental estimates can greatly underestimate the real values (≤66% error if reinfection duration is 1 month and the testing interval is 3 months). Uncertainty in experimental estimates also increases at lower reinfection incidences, whereas for lower clearance probabilities the uncertainty in the estimated clearance probability increases but estimated reinfection incidence decreases.

DISCUSSION

Differences in HCV testing interval could account for most between-study variability in the estimated probability of clearing reinfections and is likely to have biased reinfection incidence estimates. Our findings suggest that a high reinfection clearance probability (>75%) is consistent with data.

Can intranasal drug use reduce HCV infection among injecting drug users?

BACKGROUND

Preventing HCV infection among people who inject drugs is a difficult public health challenge. We examined the potential role of intranasal drug use in reducing HCV acquisition.

METHODS

Subjects were recruited from IDUs entering the Beth Israel drug detoxification program from 2005 to 2010. A structured interview was administered and serum samples were collected for HCV testing.

RESULTS

726 active injecting drug users were recruited from 2005 to 2010. HCV prevalence was 71%, 90% reported recent heroin injection and 44% reported recent intranasal heroin use. In a multiple logistic regression analysis, being HCV seropositive was associated with more years injecting, Latino ethnicity, previous testing for HCV, and recent injection of speedball, and negatively associated with recent intranasal use of heroin (AOR=0.52, 95% CI 0.33-0.82) and intranasal use of speedball (AOR=0.41, 95% CI 0.31-0.80). The association between intranasal heroin use and lower HCV seroprevalance was observed among both new injectors and persons with long injecting histories (16+ years since first injection).

CONCLUSION

Encouraging intranasal use as an alternative to injection among persons currently injecting drugs may be a viable strategy for reducing HCV transmission.

Universal peptide vaccines - optimal peptide vaccine design based on viral sequence conservation

Rapidly mutating viruses such as the hepatitis C virus (HCV), the human immunodeficiency virus (HIV), or influenza viruses (Flu) call for highly effective universal peptide vaccines, i.e. vaccines that do not only yield broad population coverage but also broad coverage of various viral strains. The efficacy of such vaccines is determined by multiple properties of the epitopes they comprise. Beyond the specific properties of each epitope, properties of the corresponding source antigens are of great importance. If a response is mounted against viral proteins with a low copy number within the cell or against proteins expressed very late, this response may fail to induce lysis of the infected cells before budding can take place. We here propose a novel methodology to optimize the epitope composition and assembly in order to induce maximum protection. In order for a peptide vaccine to yield the best possible universal protection, several conditions should be met: (a) an optimal choice of target antigens, (b) an optimal choice of highly conserved epitopes, (c) maximum coverage of the target population, and (d) the proper ordering of the epitopes in the final vaccine to ensure favorable cleavage. We propose a mathematical formalism for epitope selection and ordering that balances the constraints imposed by these different conditions. Focusing on HCV, HIV, and Flu, we show that not all of the conditions can be satisfied for all viruses. Depending on the virus, different constraints are harder to fulfill: for Flu, the conservation constraint is violated first, while for HIV, it is difficult to focus the response at the optimal target antigens. The proposed methodology can be applied to any virus to assess the feasibility of optimally combining the above-mentioned constraints.

A systematic review and meta-analysis of interventions to prevent hepatitis C virus infection in people who inject drugs

INTRODUCTION

High rates of hepatitis C virus (HCV) transmission are found in samples of people who inject drugs (PWID) throughout the world. The objective of this paper was to meta-analyze the effects of risk-reduction interventions on HCV seroconversion and identify the most effective intervention types.

METHODS

We performed a systematic review and meta-analysis of published and unpublished studies. Eligible studies reported on the association between participation in interventions intended to reduce unsafe drug injection and HCV seroconversion in samples of PWID.

RESULTS

The meta-analysis included 26 eligible studies of behavioral interventions, substance-use treatment, syringe access, syringe disinfection, and multicomponent interventions. Interventions using multiple combined strategies reduced risk of seroconversion by 75% (pooled relative risk, .25; 95% confidence interval, .07-.83). Effects of single-method interventions ranged from .6 to 1.6.

CONCLUSIONS

Interventions using strategies that combined substance-use treatment and support for safe injection were most effective at reducing HCV seroconversion. Determining the effective dose and combination of interventions for specific subgroups of PWID is a research priority. However, our meta-analysis shows that HCV infection can be prevented in PWID.

The prevention of infection-associated cancers

Collectively, chronic viral and bacterial infections and trematode infestations have been estimated to be associated with approximately one of five human cancers worldwide. The fraction attributable to each one of the chronic infections caused by hepatitis B and C viruses (HBV and HCV), human papillomaviruses (HPV) and Helicobacter pylori, is ∼5%. These infections are the most important causes of major types of cancer, including hepatocellular carcinoma, cervical cancer and stomach cancer, respectively. Taking into account the mechanisms of infection-related carcinogenesis, integrated approaches are addressed to the control of the associated infection as well as to avoidance of cancer occurrence and progression. Large-scale interventions have been implemented, such as the anti-HBV and anti-HPV routine vaccination programs. The latter has been designed with the specific goal of preventing HPV-associated cancers, which is an outstanding breakthrough in cancer prevention. Intriguingly, not only prevention but even therapy of an infectious disease and eradication of a pathogen become a crucial tool for the primary prevention of these cancers. An important role is also played by secondary prevention (e.g. Pap test and DNA testing for HPV-associated cervical cancers) and by tertiary prevention (e.g. antiangiogenesis in Kaposi's sarcoma). The present article reviews the microbial and parasitic diseases that have been associated so far with human cancers, draws an overview of their burden in cancer epidemiology, deals with applicable prevention strategies and provides examples of co-ordinated approaches to the control of cancers associated with HBV, HCV, HPV, human immunodeficiency virus and H.pylori infections.

Progress in the development of preventive and therapeutic vaccines for hepatitis C virus

Hepatitis C virus (HCV) is a blood borne disease estimated to chronically infect 3% of the worlds' population causing significant morbidity and mortality. Current medical therapy is curative in approximately 50% of patients. While recent treatment advances of genotype 1 infection using directly acting antiviral agents (DAAs) are encouraging, there is still a need to develop vaccine strategies capable of preventing infection. Moreover, vaccines may also be used in future in combination with DAAs enabling interferon-free treatment regimens. Viral and host specific factors contribute to viral evasion and present important impediments to vaccine development. Both, innate and adaptive immune responses are of major importance for the control of HCV infection. However, HCV has evolved ways of evading the host's immune response in order to establish persistent infection. For example, HCV inhibits intracellular interferon signalling pathways, impairs the activation of dendritic cells, CD8(+) and CD4(+) T cell responses, induces a state of T-cell exhaustion and selects escape variants with mutations CD8(+) T cell epitopes. An effective vaccine will need to produce strong and broadly cross-reactive CD4(+), CD8(+) T cell and neutralising antibody (NAb) responses to be successful in preventing or clearing HCV. Vaccines in clinical trials now include recombinant proteins, synthetic peptides, virosome based vaccines, tarmogens, modified vaccinia Ankara based vaccines, and DNA based vaccines. Several preclinical vaccine strategies are also under development and include recombinant adenoviral vaccines, virus like particles, and synthetic peptide vaccines. This paper will review the vaccines strategies employed, their success to date and future directions of vaccine design.

Pathogenesis of hepatitis E virus and hepatitis C virus in chimpanzees: similarities and differences

The chimpanzee is the only animal model for investigating the pathogenesis of viral hepatitis types A through E in humans. Studies of the host response, including microarray analyses, have relied on the close relationship between these two primate species: chimpanzee samples are commonly tested with human-based reagents. In this study, the host responses to two dissimilar viruses, hepatitis E virus (HEV) and hepatitis C virus (HCV), were compared in multiple experimentally infected chimpanzees. Affymetrix U133+2.0 human microarray chips were used to assess the entire transcriptome in serial liver biopsies obtained over the course of the infections. Respecting the limitations of microarray probes designed for human target transcripts to effectively assay chimpanzee transcripts, we conducted probe-level analysis of the microarray data in conjunction with a custom mapping of the probe sequences to the most recent human and chimpanzee genome sequences. Time points for statistical comparison were chosen based on independently measured viremia levels. Regardless of the viral infection, the alignment of differentially expressed genes to the human genome sequence resulted in a larger number of genes being identified when compared with alignment to the chimpanzee genome sequence. This probably reflects the lesser refinement of gene annotation for chimpanzees. In general, the two viruses demonstrated very distinct temporal changes in host response genes, although both RNA viruses induced genes that were involved in many of the same biological systems, including interferon-induced genes. The host response to HCV infection was more robust in the magnitude and number of differentially expressed genes compared to HEV infection.