Editorial overview: Engineering for viral resistance.

Current Opinion in Virology 2015, 14:v–vii

For a complete overview see the

Available online 28th August 2015

1879-6257/© 2015 Elsevier B.V. All rights reserved.

Historically a viral disease killed the host, was cleared by the immune system or evolved into a chronic disease of which after years or decades patients were suffering. Around a hundred years ago, virus infection was to be prevented by vaccination, with the first successful effort against the rabies virus made by Louis Pasteur and Emile Roux in 1885. Vaccination is still today the most effective and potent way for the prevention of viral infections if a vaccine is available and working, which is still not the case for the various herpes viruses, lentiviruses and hepatitis C virus (HCV). Intensive development of specific drugs started with the burden of influenza epidemics and with the world wide spread of the human immunodeficiency virus (HIV) and AIDS.

Recent progress in virology has covered the field of detecting new viruses either in the wake of epidemiologically disturbing outbreaks of recent years, for example, caused by Middle East Respiratory Syndrome coronavirus (MERS-CoV) or H9N7 influenza virus, or by next generation sequencing (NGS), identifying further viruses such as hepacivirus and pegivirus in dogs, horses, and bats. After identification of the structure and genome of key enzymes of new and old viruses, such as polymerase and protease, these are characterized in their three-dimensional structure and inhibitors are designed to hamper the action of the enzyme and to interfere with the replication cycle of the virus, ultimately to find a tool for the treatment of the suffering patient. Analysis of the attachment site and entry receptor of a virus is a further avenue that opens opportunities to interfere with the production of virus and to reduce the burden of viral load in the patient; an example for efficient interference is still the blocking of the chemokine receptor 5 (CCR5) in HIV infection.

Due to the high mutation rate of viruses and the formation of quasispecies, the initiation of therapy leads to a selection of partially resistant and finally totally resistant strains, which implies the need for analyzing the reasons for resistance and changing the drug regimen of the patient. Routine analysis of mutations that are responsible for resistance is done by nucleic acid sequencing either of the active pocket of an enzyme or by the involved binding structures of the drug to target structures of the corresponding protein. Thus a further tool was developed to monitor the effectivity of a drug combination and the outcome in a patient. Besides the viral factors, there are host determinants responsible for replication. The entry receptor was already mentioned, but there are further factors involved, such as the interleukin 28B promoter in hepatitis C (HCV) infection. Each virus needs an activated cell metabolism for replication. One of the plethora of cellular/nuclear factors upregulated during cell activation is the nuclear factor kappa B (NF-κB), which can be inhibited leading to reduced viral replication. Thus the inhibition of the synthesis of virus by antiviral drugs is one side of the coin, to suppress the presence of host factors is another side, which has just started to be a broader target of patient treatment.

So what does genetic engineering for viral resistance mean? In the broadest sense the subject includes the development of new drugs against viral (Direct Acting Antivirals = DAAs) and host (Host-Targeted Agents = HTAs) proteins in competition with virus evolution, as well as the variable design of mutated viruses and host genes, for example, by newest clustered, regularly interspaced, short palindromic repeat (CRISPR) technologies. Latter provides valuable information on the in vitro (cell culture) evaluation of antiviral drugs. In vivo application is certainly limited for various reasons including ethics. Furthermore, Single Nucleotide Polymorphisms (SNPs) of relevant host genes can influence virus infection in a number of diseases. Last but not least, the development of new diagnostic tools to determine, evaluate and predict anti-viral efficacy of therapeutic agents and viral evolution allows for the adaption of therapies giving infected individuals new perspective for life, which could hardly have been envisaged a few years ago.

In this issue of Current Opinion in Virology the most recent developments and progress in selected fields of virology are reviewed and hints for evolving future topics are indicated. T. Watanabe and Y. Kawaoka describe new directly acting antivirals (DAA) against influenza virus, including new sialidase blockers and targets for host cell interference. A summary is given of several approaches to define host factors required for influenza replication allowing for the construction of virus–host interactome maps and aiming at the development of new drugs with much lower risk of resistance emergence. K.K.-W. To and the group of K.-Y. Yuen focus on host genetic variants associated with disease severity in humans after influenza virus infection. Progress will be made by approaches investigating the genome, the proteome, lipidomics of virus and host, and incorporation of all the results of techniques available from bioinformatics. T.F. Baumert and his group discuss new host targets for the inhibition of the replication of hepatitis B virus (HBV) and the possibilities of de-aminating the ccc-DNA (covalently closed circular DNA) to eliminate the HBV genome from all liver cells and to reach the goal of a final cure. A. Stättermayer and P. Ferenci review the publications on the involvement of mutations of SNPs in the promoter region of the IL-28 gene and their influence on chronicity and therapeutic outcome of hepatitis C. They encourage the search for further polymorphisms in the host and viral genome, not only for HCV. They point the way to designing individualized DAAs according to the structure of the drug target and the host factor involved. H. Qi, R. Sun, and colleagues propose high-resolution genetic profiling approaches in order to assess consequences of single nucleotide and amino acid substitutions and to minimize the risk of developing viral resistance mutations. The repertoire for drugs against HCV has been rapidly expanding since 2014, and the three papers discuss the best ways to profit from their application.

Two contributions deal with HIV. K. Allers and T. Schneider's paper gives a summary of the successful elimination of HIV-1 by bone marrow transplantation in the ‘Berlin’ patient by selection of CCR5Δ32 homozygous donor cells. They discuss whether this success is a proof of principle or an exception, but as a consequence they propose to generate an artificial CCR5 deficiency, for example by the drug Maraviroc®, silencing by the use of zinc finger nuclease, modifying the expression of CCR5 and trying to affect not only lymphocytes but also monocytes and dendritic cells. K. Van Laethem and colleagues describe the different methods of HIV-drug resistance testing, their advantages and limitations. Rules for interpretation of occurring mutations are discussed, the possibility and necessity to standardize these rules by user friendly software, as well as the limitations to do these analyses in resource limited settings (RLS), where most of the HIV affected patients live and are in need of drug monitoring.

Y. Sun, G. Li and collaborators describe host genetic variants that play a significant role for susceptibility to HPV infection and their possible use as predictors of HPV infection risk in oral squamous cell carcinomas. K. Tsai and the group of P. Lieberman summarize the current findings on gammaherpesviral vFGARAT tegument proteins essential for viral infection and latency. These proteins interact with different components of cellular subnuclear PML-NB (ProMyelocytic Leukemia Nuclear Body) structures and disrupt the associated intrinsic antiviral response.

The last two papers of this issue reflect the topic of ‘Genetic Engineering for Viral Resistance’ in a special way. They deal with cyclophilin A (CypA) as an essential factor for the replication of several viruses and the in vitro engineering of host factor resistance mutations mimicking natural SNPs. T. von Hahn and S. Ciesek summarize the current knowledge about SNPs of the CypA encoding PPIA gene with emphasis on HIV-1 and HCV replication. A. von Brunn and colleagues describe the effects of these individual SNP mutations on the replication of human coronavirus 229E. The evidence is that SNP mutants around the active site of the enzymatic pocket destabilize CypA and diminish or prevent HCV and coronavirus replication. The low frequency of natural, coding, non-synonymous SNPs in the PPIA gene may encourage the use of non-immunosuppressive Cyp inhibitors to prevent replication of susceptible viruses. Such broad-spectrum host-targeted antivirals are urgently needed, for example, to counteract epidemics caused by emerging viruses like MERS-CoV.

The critical and fruitful chaperonage of Lutz Gürtler during the course of organization of this section is highly appreciated. In the end I would like to thank all the authors for their concise contributions and respecting the limits of time and space, and the Elsevier publisher and editors-in-chief of COVIRO, Mary Estes and Albert Osterhaus, who gave me the chance to edit this special issue. I hope these reviews will contribute to the further progress in handling viral infections, to design specific drug development and thereby help to improve the health of patients.