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The Lyra Direct Strep Assay is a Real-Time PCR in vitro diagnostic test for the qualitative detection and differentiation of Group A ß-hemolytic Streptococcus (Streptococcus pvogenes) and pyogenic Group C and G B-hemolytic Streptococcus nucleic acids isolated from throat swab specimens obtained from patients with signs and symptoms of pharvngitis, such as sore throat. The assay does not differentiate between pyogenic Groups C and G ß-hemolytic Streptococcus.

All negative test results should be confirmed by bacterial culture, because negative results do not preclude Group A, C or G Strep infection and should not be used as the sole basis for treatment.

The assay is intended for use in hospital, reference, or state laboratory settings. The device is not intended for point-of-care use.

The Lyra Direct Strep Assay detects nucleic acids isolated from throat swab specimens obtained from patients with signs and symptoms of pharyngitis. A multiplex Real-time PCR reaction is carried out under optimized conditions in a single tube generating amplicons for Group A B-hemolytic Streptococcus (Streptococcus pyogenes) and pyogenic Group C and G B-hemolytic Streptococcus, and the Process Control (PRC). Identification of Group A, pyogenic Group C/G, and the PRC occurs by the use of target-specific primers and fluorescent-labeled probes that hybridize to conserved regions in the genomes of Group A, pyogenic Group C/G, and the PRC. The assay does not differentiate between Group C and Group G streptococci.

A specimen from a patient's throat swab is transferred to the Process Buffer then heated to lyse the bacteria and expose the DNA. The lysed specimen is then added to a rehydrated Master Mix of targeted oligonucleotide primers, fluorophore and quencher-labeled probes is added to each plate. The plate is placed into the Applied Biosystems® 7500 Fast Dx instrument and the Quidel Molecular Direct Streptococci Assay protocol is initiated.

This assay is based on Taqman® chemistry, and uses an enzyme with DNA polymerase, and 5'-3' exonuclease activities. During DNA amplification, this enzyme cleaves the probe bound to the conserved complementary DNA sequence, separating the quencher dye from the reporter dye. This step generates an increase in fluorescent signal upon excitation by a light source of the appropriate wavelength. With each cycle, additional dye molecules are separated from their quenchers resulting in an increase in the fluorescent signal. If sufficient fluorescence is achieved, the sample is reported as positive for the detected nucleic acid.

{
  "acceptance_criteria_and_study": {
    "acceptance_criteria_table": {
      "headers": [
        "Performance Metric",
        "Acceptance Criteria (Implicit)",
        "Reported Device Performance"
      ],
      "data": [
        [
          "Precision/Repeatability (Group A Strep, High Negative)",
          "Acceptable detection rates",
          "45.8% Detection"
        ],
        [
          "Precision/Repeatability (Group A Strep, Low Positive)",
          "Acceptable detection rates",
          "100% Detection"
        ],
        [
          "Precision/Repeatability (Group A Strep, Moderate Positive)",
          "Acceptable detection rates",
          "100% Detection"
        ],
        [
          "Precision/Repeatability (Group A Strep, Negative)",
          "Acceptable detection rates",
          "0% Detection"
        ],
        [
          "Precision/Repeatability (Pyogenic Group C Strep, High Negative)",
          "Acceptable detection rates",
          "75% Detection"
        ],
        [
          "Precision/Repeatability (Pyogenic Group C Strep, Low Positive)",
          "Acceptable detection rates",
          "100% Detection"
        ],
        [
          "Precision/Repeatability (Pyogenic Group C Strep, Moderate Positive)",
          "Acceptable detection rates",
          "100% Detection"
        ],
        [
          "Precision/Repeatability (Pyogenic Group C Strep, Negative)",
          "Acceptable detection rates",
          "0% Detection"
        ],
        [
          "Reproducibility (Group A Strep, Low Pos, Combined)",
          "Acceptable detection rates (e.g., close to 100% for positive and 0% for negative)",
          "99% (89/89)"
        ],
        [
          "Reproducibility (Group A Strep, Mod Pos, Combined)",
          "Acceptable detection rates (e.g., close to 100% for positive and 0% for negative)",
          "100% (90/90)"
        ],
        [
          "Reproducibility (Group A Strep, Neg, Combined)",
          "Acceptable detection rates (e.g., close to 100% for positive and 0% for negative)",
          "0% (0/90)"
        ],
        [
          "Reproducibility (Pyo Group C Strep, Low Pos, Combined)",
          "Acceptable detection rates (e.g., close to 100% for positive and 0% for negative)",
          "100% (89/90)"
        ],
        [
          "Reproducibility (Pyo Group C Strep, Mod Pos, Combined)",
          "Acceptable detection rates (e.g., close to 100% for positive and 0% for negative)",
          "100% (90/90)"
        ],
        [
          "Reproducibility (Pyo Group C Strep, Neg, Combined)",
          "Acceptable detection rates (e.g., close to 100% for positive and 0% for negative)",
          "0% (0/90)"
        ],
        [
          "Analytical Specificity (Cross-reactivity)",
          "No cross-reactivity with common throat microorganisms",
          "None of the forty-four (44) microorganisms tested cross-react with the assay."
        ],
        [
          "Clinical Sensitivity (Group A Strep, All Sites)",
          "High sensitivity (no explicit numerical criteria, but implied to be high for regulatory acceptance)",
          "96.5% (95% CI: 91.3%-98.6%)"
        ],
        [
          "Clinical Specificity (Group A Strep, All Sites)",
          "High specificity (no explicit numerical criteria, but implied to be high for regulatory acceptance)",
          "98.0% (95% CI: 97.0%-98.6%)"
        ],
        [
          "Clinical Sensitivity (Pyogenic Group C and G Strep, All Sites)",
          "High sensitivity (no explicit numerical criteria, but implied to be high for regulatory acceptance)",
          "95.7% (95% CI: 88.1%-98.5%)"
        ],
        [
          "Clinical Specificity (Pyogenic Group C and G Strep, All Sites)",
          "High specificity (no explicit numerical criteria, but implied to be high for regulatory acceptance)",
          "98.3% (95% CI: 97.4%-98.9%)"
        ]
      ]
    },
    "test_set_sample_size": "1293 prospectively collected fresh throat specimens.",
    "test_set_data_provenance": "United States, prospective.",
    "number_of_experts_ground_truth": "The document does not explicitly state the number of experts used to establish ground truth for the clinical study. However, the ground truth was established by microbiological culture, which typically involves trained laboratory personnel but not necessarily an 'expert consensus' in the sense of multiple independent clinical expert opinions on each case.",
    "qualifications_of_experts": "Not explicitly stated for the clinical ground truth. For culture methods, typically microbiologists or trained laboratory technologists perform and interpret the results.",
    "adjudication_method": "Not applicable in the context of expert consensus. The ground truth was based on a composite culture method: a specimen was considered positive if culture from either the directly plated swab or the transport fluid material was positive for the target streptococci. This is a laboratory-based reference standard, not an adjudication of expert opinions.",
    "mrmc_comparative_effectiveness_study": "No, a multi-reader multi-case (MRMC) comparative effectiveness study was not explicitly mentioned. The study compares the device performance to a reference standard (culture), not to human readers with and without AI assistance.",
    "standalone_performance_study": "Yes, the clinical sensitivity and specificity results 'vs. Composite Cultures' (Tables X and XI) represent the standalone performance of the algorithm/device without human-in-the-loop assistance for interpretation of primary results.",
    "type_of_ground_truth": "Expert reference standard based on **composite bacterial culture** (directly plated throat swabs and culture of transport fluid material). Cultured isolates were typed by latex agglutination, and beta-hemolytic isolates were speciated using MALDI TOF.",
    "training_set_sample_size": "The document does not explicitly state the sample size for a 'training set'. The data presented are for analytical and clinical validation. While the device developers would have utilized data during development, specific training set sizes are not provided in this regulatory submission for a diagnostic device.",
    "ground_truth_for_training_set": "Not explicitly stated. For PCR-based assays, 'training' typically involves optimizing assay parameters (primers, probes, cut-offs) using characterized bacterial strains and spiked samples (e.g., as described in the Analytical Sensitivity and LoD sections), rather than a large clinical training set with expert ground truth in the same way an AI model might be trained."
  }
}

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