📄RVOP/RVEK
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
RVEK
Respiratory Virus Enrichment Kit
RVOP
Respiratory Virus Oligo Panel
RUO
For Research Use Only. Not for use in diagnostic procedures.
URL
See https://www.illumina.com/ for additional information.
Quantification
RVOP data analysis using DRAGEN Microbial Enrichment Plus detects 24 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.
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.
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.
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