Abstract
Next-generation sequencing (NGS) technologies have revolutionised our ability to sample species' genomes due to the massively parallel nature of the sequencing reactions. Different groups have now demonstrated the ability of NGS to perform HLA typing in a cost-effective manner supporting a shift in technology platform from current Sanger-based sequence typing to NGS. However, the use of NGS is not restricted to host genomes and is currently used to identify clinically relevant low frequency viral strains in the setting of drug resistance and host/viral interactions. In this presentation, I will discuss the advantages and limitations of NGS in HLA genotyping and show how NGS can help to better understand the critical interaction between the host's immune response (driven by HLA-restricted T-cell responses) and viral adaptation to this response and its impact on viral infection outcome.