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One of the most widely used methods to detect an acute viral infection in clinical specimens is diagnostic real-time polymerase chain reaction. However, because of the COVID-19 pandemic, mass-spectrometry-based proteomics is currently being discussed as a potential diagnostic method for viral infections. Because proteomics is not yet applied in routine virus diagnostics, here we discuss its potential to detect viral infections. Apart from theoretical considerations, the current status and technical limitations are considered. Finally, the challenges that have to be overcome to establish proteomics in routine virus diagnostics are highlighted.
This survey will discuss current and emerging isothermal and rapid polymerase chain reaction (PCR) based nucleic acid amplification methods for patient near diagnostics. To assess the clinical need of rapid diagnostics for infectious diseases based on nucleic acid tests (NATs) we performed and analysed a questionnaire among laboratories participating in corresponding INSTAND ring trials for external quality assurance. The questions concerning new amplification technologies like isothermal nucleic acid amplification, potentially suited to significantly decrease turnaround times, were complemented by questions to evaluate the present status of NATs. Besides end-users, companies were also addressed by sending out a manufacturer specific questionnaire. Analysis of the answers from 48 laboratories in 14 European countries revealed that a much shorter turnaround time is requested for selected pathogens compared to about 2 h or longer when applying temperature cycling amplification, i.e. PCR. In this context, most frequently mentioned were MRSA, norovirus, influenza A and B viruses, cytomegalovirus (CMV) as well as hepatitis B virus (HBV) and hepatitis C virus (HCV). At present, 8% of the laboratories having participated in this survey apply isothermal amplification of nucleic acid to identify infectious pathogens.
Driven by recent technological advances and the need for improved viral diagnostic applications, mass spectrometry-based proteomics comes into play for detecting viral pathogens accurately and efficiently. However, the lack of specific algorithms and software tools presents a major bottleneck for analyzing data from host-virus samples. For example, accurate species- and strain-level classification of a priori unidentified organisms remains a very challenging task in the setting of large search databases. Another prominent issue is that many existing solutions suffer from the protein inference issue, aggravated because many homologous proteins are present across multiple species. One of the contributing factors is that existing bioinformatic algorithms have been developed mainly for single-species proteomics applications for model organisms or human samples. In addition, a statistically sound framework was lacking to accurately assign peptide identifications to viral taxa. In this presentation, an overview is given on current bioinformatics developments that aim to overcome the above-mentioned issues using algorithmic and statistical methods. The presented methods and software tools aim to provide tailored solutions for both discovery-driven and targeted proteomics for viral diagnostics and taxonomic sample profiling. Furthermore, an outlook is provided on how the bioinformatic developments might serve as a generic toolbox, which can be transferred to other research questions, such as metaproteomics for profiling microbiomes and identifying bacterial pathogens.