DeepChek®Assay PR / RT Genotyping and Drug Resistance (HIV) (CE-IVD)

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)

Registration status

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

Format

24 samples/kit

Covered positions

PR: codons 1 to 99, RT: codons 1 to 320

Content

RT-PCR & Nested-PCR reagents (enzymes, master mixes, primers, dNTPs...)

Sensitivity

1000 cp/mL

Specificity

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%

Median coverage

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)

Clinical reproducibility

100%

Clinical sensitivity

99%

Workflow

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

Validated with:
- DeepChek software (CE-IVD) HIV module (NGS outputs)
- ViroScore Suite (CE-IVD) HIV module (Sanger sequencing outputs)

DeepChek® Assay PROTEASE / REVERSE TRANSCRIPTASE Genotyping and Drug Resistance V1 (CE-IVD)

121A24
(old reference : K-16-H2-RTPR24)

DeepChek® NGS Library preparation (GLP)(RUO)
DeepChek® Assay Adapters (1-96) (NGS) (GLP)(RUO)

116A96
124A96
(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

125A24
(old reference K-17-SR)

DeepChek® SANGER SEQUENCING REACTION V2 (48 reactions) (GLP)(RUO)

123B48
(old reference K-17-SR)