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formatics pipeline to identify and classify all known viruses present in a metagenomic sample. Viral NGS reads are identified using a protein-based alignment method, DIAMOND, which is substantially faster than the standard BLAST method, and more reliable for viruses. These reads are automatically assembled into contigs using SPAdes, a de novo assembler. The contigs are then used to classify the virus at species level using a pan-viral typing tool based on all available taxonomic reference sequences from the International Committee on Taxonomy of Viruses (ICTV) database. This bioinformatics pipeline is Java-encoded and will include an easy-to-use web interface that is fit-for-purpose for researchers or clinicians. This tool can assemble viral contigs from paired-end reads generated by an Illumina MiSeq sequencer. So far 1865 viruses can be identified at species level resolution and 10 viruses (chikungunya virus, dengue virus, HBV, HCV, HHV8, HIV-1, HPV, HTLV-1, YFV, and Zika virus) at the genotype level. A web version of the panviral typing tool is already available and a web version with extended NGS functionality is currently being evaluated. Eliminating the need for virus-specific laboratory techniques, or targeted sequence capture, means a virome can be profiled in the context of its non-viral microbiome. Preliminary findings suggest our tool offers greater functionality than existing alternatives, with greater sensitivity to known viruses (including bacteriophages), automatic assembly and good quality phylogenetic analyses. A systematic comparison is underway.

A36 Prevalence of HIV-1 subtypes in Slovenia with an emphasis on molecular and phylogenetic investigation of subtype A