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Next Generation Sequencing (NGS) application in Virology

Viral genomes differ in size and structure. As viruses are not self-replicating the encoded genetic information is limited and viral replication depends on genetic information of the host. The viral genome can encode information that are necessary for replication, host specificity and virulence factors. Some important projects that streamline viral genomic information are the INFLUENZA GENOME PROJECT and Virogenesis.

Virus diagnosis is based on the detection of viral proteins, antibodies against viral proteins or viral nucleic acids. Sequencing of the viral genome allows not only the detection and classification of the virus but can also provide information about virulence and phylogenetically relation that help monitoring and combating the spread of viral diseases.

Some important areas of NGS application in virology are: detection of unknown viruses and discovery of new viruses, characterisation of viruses and antiviral drug resistance, viral evolution and variability (quasi species analysis) studies, and quality control during vaccine or drug production.

For more detailed information we refer to the publication list.


Virus Discovery

Due to the frequently utilisation of NGS technology in different areas of application and on numerous samples regularly new viruses are discovered. If no information about pathogens is available, random sequencing of complete nucleic acids (meta genome analysis) from a give sample is the best choice to detect and characterise unknown pathogens. This method is not only used in research but becomes more and more popular in the investigation of samples from sick humans or animals were conventional methods do not enable diagnosis. The sequence information obtained by NGS does not only detects the virus but can give additional information about phylogeny, virulence, resistance, and treatment options.


Tumour Virus Characterisation and Drug Resistance Testing

An important field of NGS application is the specific virus characterisation in tumour research and for drug resistance testing. There are numerous viruses associated with the occurrence of different tumours including HCV, HBV, HPV, EBV, HIV, HHV-8, MCV or SV40.

For different viruses e.g. HIV and HCV there is no vaccination available. In these cases treatment is the only chance to help infected people. HCV and HIV are RNA viruses with the characteristics of high mutation rates that is reflected by a high quasi species variability. High mutation rates and high quasi species variability facilitate the escape of multi-drug resistant viruses. In order to enable most effective treatments particular knowledge about the virus is needed.  This knowledge can only be provided by deep sequencing through NGS technology utilisation. Therefore, NGS based virus analysis is becoming more and more applied in HIV and HCV diagnosis for patient treatments.


Viral Evolution and Epidemiology

In order to trace back virus spread and for implementation of effective monitoring and treatment strategies during outbreak situations, knowledge about the viral genome is of outmost importance. Modern technologies such as NGS enable a fast characterisation of viruses and support monitoring and treatment strategies. An important global sequencing project is the Influenza Genome Project that investigates the influenza evolution.

Furthermore, excessive vaccination programs in animal health can lead to recombination or viral escape mutants reverting to wild type viruses (e.g. PRRSV). These viral escape mutants often cannot be discriminated from field viruses by conventional diagnostics. Additionally, NGS will enable the discrimination of marker vaccines from field viruses as this is important in some instances for export regulations in the food industry.


Quality Control in Vaccine Production

During the last decades different scandals about virus contaminated vaccines and drugs were reported. The NGS technology enables an effective batch control and monitoring during production of vaccines or drugs.  Any contamination with nucleic acids of viruses or other pathogens such as bacteria can be detected by meta genome analysis of each batch. Furthermore, the stability and functionality of vaccine viruses can be controlled by sequencing of vaccine batches.

NGS based quality control is not only suitable for vaccine or drug production but can also be used in other fields such as blood transfusion or organ transfer.


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