The DeepChek® PR/RT Assay is intended to be used for amplifying relevant portions of the human immunodeficiency virus type one (HIV-1) protease and reverse transcriptase genes from input RNA extracted from plasma, serum or whole blood samples.
The entire protease gene (1-99) and codons spanning positions 1 to 320 of the reverse transcriptase (RT) gene in the pol open reading frame are amplified.
This nucleic acid amplification method might aid in the determination of antiviral resistance in clinical samples from HIV-infected patients.
This nucleic amplification test is indicated for use on previously diagnosed HIV patients ONLY.
This test is NOT intended to be used as a screening or confirmation test for the detection, confirmation and quantification in human specimens of markers of HIV infection (HIV 1 and 2).
Indication of Use
The amplified RNA might be used as input material in validated laboratory procedures for genomic variability testing (genotyping) potentially affecting HIV-1 susceptibility to current antiretroviral drugs including protease inhibitors (PI) and reverse transcriptase inhibitors (NRTIs, NNRTIs).
The DeepChek® PR/RT Assay has been validated in laboratories for Sanger sequencing or next generation sequencing (NGS).
Physicians then may use the related genotyping data in conjunction with patient clinical data to make treatment (drug therapy) decisions.
Characteristics and performances
Compatibility with Capillary Electrophoresis (SANGER) platforms
Applicable for any Sanger Sequencing technology-based instrument which can work with Big Dye Terminator v3.1 labeling (standard laboratory consumables, e.g. DeepChek® SANGER SEQUENCING REACTION V1 (24 or 48 reactions) (ABL)
Compatibility with Next Generation Sequencing platforms
Validated with iSeq100 (Illumina, USA; One-Channel SBS Chemistry, iSeq100 Flow Cell) and Illumina Sequencing Analysis Viewer (instrument software version 2.4.5) and standard laboratory consumables, e.g.ABL NGS Library Preparation kit (references 116A96 and 124A96)
CE-IVD for European Economic Area (EEA) and countries with a mutual recognition of this conformity assessment
Research Use Only for other territories
Types of samples
Input RNA extracted from plasma, serum or whole blood samples
PR: codons 1 to 99, RT: codons 1 to 320
RT-PCR & Nested-PCR reagents (enzymes, master mixes, primers, dNTPs...)
Validated on HIV-1 subtype B.
The assay is designed to detect HIV-1 subtype B but can also detect other HIV-1 Group M subtypes and recombinant viral sequences. However, as the HIV-1 genome is highly mutable, there will always be a small possibility that some strains of HIV-1 will react poorly with the assay, especially if random mutations occur within the primer binding sites.
Repeatability / Reproducibility
100% of samples with an optimal median coverage at a concentration of 1000 cp/mL (assay cut-off)
Median coverage per sample for the three amplicons (PR/RT and INT) was 13’237 reads (downstream sequencing with NGS)
From sample to result in ~15 hours for SANGER and ~30 hours for NGS (depending on the platform)
Compatible extraction and PCR
RNA extraction: general laboratory device (i.e. Roche MagNa Pure)
Amplification with any thermal cycler with enough ramp rate of ≥ 1°C/s (i.e. ProFlex PCR System 3x32-Well and 96-Well, Life Technologies)
Compatibility with CE-IVD downstream sequencing software
- DeepChek software (CE-IVD) HIV module (NGS outputs)
- ViroScore Suite (CE-IVD) HIV module (Sanger sequencing outputs)
Examples of reports
For SANGER sequencing
For NGS sequencing
DeepChek® Assay PROTEASE / REVERSE TRANSCRIPTASE Genotyping and Drug Resistance V1 (CE-IVD)
(old reference : K-16-H2-RTPR24)
DeepChek® NGS Library preparation (GLP)(RUO)
DeepChek® Assay Adapters (1-96) (NGS) (GLP)(RUO)
(old ref K-17-NGS-LP1)
DeepChek® Assay PROTEASE / REVERSE TRANSCRIPTASE Sequencing V1 (CE-IVD)
Accessory for use only with the DeepChek® Assay Protease/Reverse Transcriptase (REF 121A24) - For use with Sanger sequencing instruments
(old reference K-17-SR)
DeepChek® SANGER SEQUENCING REACTION V2 (48 reactions) (GLP)(RUO)
(old reference K-17-SR)
IFU REF 121A24
IFU REF 125A24
Zip file MSDS