📄VSP V2

Abbreviation	Definition
AMR	antimicrobial resistance
mL	milliliter
NAI	neuraminidase inhibitor
NGS	next-generation sequencing
PAI	polymerase acidic endonuclease inhibitor
pangolin	phylogenetic assignment of named global outbreak lineages
RPKM	targeted Reads mapped Per Kilobase of targeted sequence per Million quality-filtered reads
VSP	Viral Surveillance Panel

Category	Test information
RUO	For Research Use Only. Not for use in diagnostic procedures.
URL	See https://www.illumina.com/ for additional information.
Quantification - when a quantitative Internal Control {ic_name} and concentration {ic_concentration} is specified	VSP (generation 2) data analysis using DRAGEN Microbial Enrichment Plus detects 200 viruses and 238 AMR markers based on target enriched next-generation sequencing (NGS) of viral DNA and cDNA sequences. Sequencing data are interpreted by the DRAGEN software platform and viruses that pass detection thresholds are reported. Absolute quantification assumes use of {ic_name} as an Internal Control spiked at {ic_concentration} copies/mL of sample. Relative abundance is calculated based on absolute quantities and is expressed as proportion of absolute quantities. If RPKM for the Internal Control is zero, no absolute quantification is provided, and relative abundance is expressed as proportion of RPKM values.
Quantification - when a quantitative Internal Control is NOT specified	VSP (generation 2) data analysis using DRAGEN Microbial Enrichment Plus detects 200 viruses and 238 AMR markers based on target enriched next-generation sequencing (NGS) of viral DNA and cDNA sequences. Sequencing data are interpreted by the DRAGEN software platform and viruses that pass detection thresholds are reported. Relative abundance is expressed as proportion of RPKM values. Internal Control not specified; no absolute quantification provided.
AMR	This test detects 238 antimicrobial resistance (AMR) markers associated with resistance to Influenza virus neuraminidase inhibitor (NAI) and polymerase acidic protein inhibitor (PAI) in Influenza A virus (H1N1pdm09), Influenza A virus (H1N1), Influenza A virus (H5N1), Influenza A virus (H3N2), Influenza A virus (H3N2; swine-like), Influenza A virus (H7N9), and Influenza B virus. AMR markers and drug associations are based on the World Health Organization (WHO) Influenza virus NAI and PAI Reduced Susceptibility Marker Tables (07 March 2023 version). Detection of an AMR marker is reported if the marker passes a minimum detection threshold and if the Influenza virus associated with the marker is also detected. Reported AMR markers have been associated with antimicrobial resistance but may not always indicate phenotypic resistance. Failure to detect AMR variants does not always indicate phenotypic susceptibility. Results should be interpreted in the context of all available information.
AMR	Mutations connected with a '+' form an epistatic group. Epistatic groups are two or more mutations that need to be present concurrently to confer the associated resistance.
Read classification	This test differentiates sequencing reads classified to microorganism and Internal Control regions that are targeted by capture probes (“Targeted Microbial” and “Targeted Internal Control”) from those that are not targeted (“Untargeted”), are low complexity (“Low Complexity”), cannot be unambiguously assigned to one category (“Ambiguous”), or cannot be classified with confidence (“Unclassified”).
Pango lineage	The most likely Pango (phylogenetic assignment of named global outbreak) lineage is assigned to the majority consensus SARS-CoV-2 genome sequence using pangolin 4.3.1 (Áine O'Toole & Emily Scher et al. 2021 Virus Evolution DOI:10.1093/ve/veab064).
Limitations	Non-detected results do not rule out the presence of viruses and AMR markers. Contamination is possible during specimen collection, transport, and processing. Closely related viruses may be misidentified based on sequence homology to viruses present in the database. The identification of cDNA or DNA sequences from a virus does not confirm that the identified virus is causing symptoms, is viable, or is infectious. Recombinant viral strains may not be reported or may be reported as one or more individual viruses. Should one or more individual viruses be reported for a recombinant viral strain, antiviral resistance results may be inaccurate. In viral strains containing insertion-deletion mutations (indels), there is a risk of false positive or false negative results for other resistance mutations within a region of 100 nucleotides around the indel.
Limitations	Information provided by DRAGEN Microbial Enrichment Plus is based on scientific knowledge and has been curated; however, scientific knowledge evolves and reported information may not always be complete and/or correct. Results should be interpreted in the context of all available information. Other sources of data may be required for confirmation.