Proficiency Testing for Viral High-throughput Sequencing

High-throughput sequencing (HTS) has enabled the identification of several viruses and is becoming increasingly important in clinical settings and disease outbreaks. The presented virus proficiency test (PT) was designed to contribute to the standardization of HTS “wet lab” and “dry lab” procedures, with the main goal to improve the detection, identification and analysis of viral pathogens in diagnostic samples. The participants’ proficiency in identification and analysis of viral pathogens in complex samples and HTS datasets was evaluated in two general parts of the virus PT: (1) the laboratories’ proficiency to analyze HTS data and identify viral pathogens, (2a) the laboratories’ sample preparation and sequencing procedures and (2b) the laboratories’ HTS performance and output. Therefore, participants of the PT were invited to (1) analyze a complex metagenomics fastq dataset to identify viral sequences of 4 viruses in varying numbers, (2a) perform purification, DNA/RNA extraction, library preparation and sequencing of a virus strain within a complex sample matrix and (2b) perform library preparation and sequencing of viral RNA/DNA. The results summarized in this talk indicate that numerous protocols, tools and different workflows are used for virus HTS and results of such workflows differ in sensitivity and specificity. So far, there are no standard procedures for sample preparation and virome analyses, and sharing and comparing reliable results of such analyses remain difficult.