Personalized Infection Medicine Taking the Example of Hepatitis E Virus Infection

Personalized Medicine in the Field of Virology

  • Daniel Todt. ©Tim Kramer, Ruhr University BochumDaniel Todt. ©Tim Kramer, Ruhr University Bochum
  • Daniel Todt. ©Tim Kramer, Ruhr University Bochum
  • Fig. 1: Identification of virus population in the host. ©Tabea Cubelic, Bundesministerium für Bildung und Forschung.

Nowadays, there are plenty of specific, antiretroviral treatment options for the therapy of HIV-infected patients available. They all inhibit propagation of the virus in the patient and reduce viral loads. However, they differ in the way they act on the virus. Some impede the virus from entering the cell, while some prevent it from influencing cellular processes to its advantage. Others interfere with the release of newly produced viral particles from the infected cell. Clinicians know about the changeableness of HIV and the way that certain changes influence the response to antivirals. Before therapy, the viral genome, the genetic information, is therefore sequenced and analyzed for specific mutations. The combination of antiretroviral drugs is then determined based on the virus for each patient individually.

Hepatitis infection and personalized medicine

The same principle was used until recently when treating patients with chronic Hepatitis C-Virus (HCV) infection. The geno- or subtype of the pathogen had to be determined in order to be able to treat the patient accordingly. Since approval of so-called direct acting antivirals (DAA), which are efficacious against all known HCV subtypes, this differentiation is not important any longer.

HIV and HCV as examples highlight that there are already approaches of personalized medicine in the field of virology, which are implemented in the clinic. With their work, the researcher at the Molecular and Medical Virology at the Ruhr University Bochum aim to broaden the scope of viral infections being treated for each patient individually. In their laboratory, they mainly work with hepatitis viruses. An important focus of their research is the Hepatitis E-Virus (HEV), a relatively new member in the group of pathogens leading to hepatitis. Although it is the main cause of acute viral hepatitides, with over 3,000,000 symptomatic infections and more than 70,000 deaths every year, it has been out of scope of medical professionals in industrial nations until recently [1]. About every sixth person in Germany undergoes a HEV infection in his or her lives. Because infections usually are self-limited in persons with an intact immune system, infections are not recognized in most cases (fig.

1). The main risk factor for an infection are undercooked pork products and contaminated blood transfusion products. In patients with an impaired or suppressed immune system, for example organ transplant recipients or patients suffering from an HIV infection, the infection can take chronic courses. Therapy options for the chronically infected are limited. Reducing the dose of immunosuppressive medication and pegylated interferons (IFNα) are possible treatment options. Nevertheless, unsatisfying therapy success and severe side effects like rejection of the transplant make the use of alternative drugs necessary [2]. The broadly used antiviral Ribavirin is currently considered the treatment option of choice, leading to sustained virological responses in a majority of patients within 3-5 months of treatment. However, there are also patients, in which Ribavirin fails to permanently reduce viral loads. For patients experiencing treatment failure, no further options are available. One of the reasons is the lack of a reliable cell culture model, hampering research on the biology of the virus as well as development of novel antivirals [3]. The complete lifecycle of the virus cannot be represented in culture dishes yet, only certain steps of the replication of the virus can be investigated in the laboratory to date.

Improve hepatitis E treatment

The aim of the work presented here is to tackle three main scientific questions of current HEV research: 1) establishment of a robust cell culture system, making it possible to address questions on the biology of the virus in host cells. 2) Development of alternative treatment approaches for chronically infected patients. 3) Elucidate, why Ribavirin fails to cure some patients from HEV infections.

To clarify, why Ribavirin does not always lead to therapy success, they collected serum samples of patients chronically infected with HEV over prolonged periods. The cohort comprised therapy failures as well as successful therapies. The researcher were particularly interested in the nucleotide sequences of the viral population and how it changes upon Ribavirin treatment [4]. HEV has its genetic information coded in a single RNA strand of about 7,200 nucleotides length. One of the proteins coded for in the RNA is a polymerase responsible for viral replication. It is fast, but error-prone leading to the abundance of a big variety of genetic variants of the virus. By this mechanism, HEV forms a heterogeneous viral population of genetic variants within the host. State-of-the-art deep sequencing technologies allowed them to investigate the dynamics of viral populations in patients under Ribavirin treatment (fig. 1). The researcher observed two main findings: 1) a persistent infection was linked to a high heterogeneity of the viral population. 2) They identified certain variants of the virus in populations isolated from patients with therapy failure. Interestingly, these variants were already present in most patients before the start of the therapy and became dominant during Ribavirin treatment. In contrast, these variants could either not be found in patients achieving sustained virological responses or in significantly lower numbers. These results suggest that the proportion of certain variants within the viral population at the beginning of therapy, or its selection in the first weeks, are predictive for the therapy outcome with Ribavirin (fig. 2). They could show that this method, which can easily be implemented in clinical routine, has the power to identify patients at risk for treatment failure [4].

Currently, they are trying to identify more patients with chronic HEV infections to add them to the cohort. The aim is to deepen the understanding of the selection of certain variants in vivo that confer Ribavirin resistance and want to know, by which mechanism they do so. They expect to increase the ability to predict therapy failures by expanding the database of sequences from chronically infected patients as well as to learn more about the resistance mechanism against Ribavirin. Moreover, a correlation of more variants with a wider variety of clinical outcomes, can facilitate the power of the method to anticipate the risk of a chronic course of the infection.

Translational medicine is an aspect in demand when working scientifically nowadays. In medical research, the way of translationality does not always have to be from bench to bedside but can also work the other way around. The researcher around Daniel Todt were able to use the identified variants to improve the HEV cell culture system, so that in future all steps of the viral lifecycle can be investigated in vitro. This innovation does represent a substantial progress for HEV research and will help to screen natural compounds or FDA-approved drug libraries in a high-throughput setting for their activity against the HEV. First experiences with the new system have already been made, leading to the discovery of the natural compound silvestrol [5]. Silvestrol is extracted from mahogany plants and a potent inhibitor of viral replication.

With their work, the researcher set a basis for a personalized treatment of HEV infections. Using Next Generation Sequencing, they could perform a detailed analysis of viral populations in the patient and predict therapy outcome accordingly. The research on anti-HEV molecules will contribute to the development of alternative treatments for patients with a negative prognosis for a Ribavirin intervention. Furthermore, the researcher of the Ruhr University were able to translationally transfer their in vivo findings to the cell culture system, providing a cornerstone for the development of new therapy options. These new treatment options will in turn help to fully exploit the diagnostic potential of their approach.

Author
Dr. Daniel Todt
Abteilung für Molekulare und Medizinische Mikrobiologie
Medizinische Fakultät
Ruhr-Universität Bochum
Bochum, Germany
daniel.todt@ruhr-uni-bochum.de

Hepatitis E
The Hepatitis E Virus encodes its genetic information as RNA. RNA Viruses have in common that they produce errors in their genome during replication cycles in the host, slightly changing its own genetic information. Because several billions of viruses are produced within a single host each day, so-called virus populations emerge, which are characterized by a certain degree of heterogeneity regarding their genetic information. Classical sequencing methods can only identify the genetic information, which is the most abundant. However, often minor variants in the viral population are decisive for success or failure of the therapy. Depp sequencing technologies help to overcome this restriction, making it possible to identify more rare variants.

Daniel Todt 
born 1981, finished his Bachelor studies in bioinformatics 2011 in Bingen and his master 2014 at the Medizinische Hochschule Hannover in biomedicine in 2014. He earned his doctoral degree in 2017 and relocated with his supervisor Prof. Dr Eike Steinmann to the institute of Molecular and Medical Virology at the Ruhr-Universität Bochum. In November 2018, he received the “Best Practice in Personalized Medicine” Award by the International Consortium for personalized Medicine (ICPerMed) for his work on the Hepatitis E Virus. ICPerMed brings together 42 international partners from 28 countries. Members are ministries, funding agencies and the European commission. The ministry for research and education (BMBF) as well as the ministry for health (BMG) represent Germany.

References

[1] Wedemeyer H, Pischke S, Manns MP: Pathogenesis and treatment of hepatitis e virus infection. Gastroenterology,142(6):1388-1397.e1 (2012)
[2] Todt D, François C, Anggakusuma, et al.: Antiviral Activities of Different Interferon Types and Subtypes against Hepatitis E Virus Replication. Antimicrobial agents and chemotherapy, 60(4):2132-2139 (2016)
[3] Todt D, Walter S, Brown RJP, Steinmann E.: Mutagenic Effects of Ribavirin on Hepatitis E Virus-Viral Extinction versus Selection of Fitness-Enhancing Mutations. Viruses, 8 (10) (2016)
[4] Todt D, Gisa A, Radonic A, et al.: In vivo evidence for ribavirin-induced mutagenesis of the hepatitis E virus genome. Gut, 65:1733-1743 (2016)
[5] Todt D, Moeller N, Praditya D, et al.: The natural compound silvestrol inhibits hepatitis E virus (HEV) replication in vitro and in vivo. Antiviral research. 2018;157:151-158.
[6] Todt D, Meister TL, Steinmann E: Hepatitis E virus treatment and ribavirin therapy: Viral mechanisms of nonresponse. Current opinion in virology, 32:80-87 (2018)

 

 

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