NAAT Testing Simulator

Chlamydia trachomatis / Neisseria gonorrhoeae nucleic acid amplification test simulation.

Current Stage

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Sensitivity

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Specificity

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False-neg risk

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Retest timing

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Days since exposure0

Collection locusUrine

Target DNA / amplicon

Primer / detection probe

Detection threshold gauge

False-negative risk zone

Swab / sample locus

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Choosing the Collection Site for NAAT Sampling

Placeholder: locus choice shapes sensitivity and specificity outcomes.

87%: Urine sensitivity (Placeholder reference value)
94%: Vaginal sensitivity (Placeholder reference value)
85%: Rectal sensitivity (Placeholder reference value)
80%: Pharyngeal sensitivity (Placeholder reference value)

Locus-dependent yield

Placeholder: each anatomical site yields different bacterial load.

Nucleic Acid Extraction from Swab Material

Placeholder: lysis and purification isolate target DNA/RNA.

Chemical: Lysis method (Placeholder short note)
Bead-based: Purification (Placeholder short note)
~20 min: Yield time (Placeholder short note)
Wash steps: Inhibitor removal (Placeholder short note)

Extraction fidelity

Placeholder: clean extraction lowers inhibition and false negatives.

PCR-like Exponential Amplification of Target Sequence

Placeholder: repeated cycles double the target copy count.

~35: Cycle count (Placeholder short note)
2x: Doubling per cycle (Placeholder short note)
~90 min: Assay time (Placeholder short note)
CT/NG specific: Target genes (Placeholder short note)

Exponential kinetics

Placeholder: low starting copies still amplify to detectable levels.

Detection Threshold and Positive Call Logic

Placeholder: signal crossing threshold cycle confirms detection.

Ct value: Threshold cycle (Placeholder short note)
95-99%: Specificity (Placeholder short note)
Low: Cross-reactivity (Placeholder short note)
Fluorescent probe: Signal type (Placeholder short note)

Threshold calling

Placeholder: earlier threshold crossing means higher starting load.

Interpreting the Post-Exposure False-Negative Window

Placeholder: testing too early after exposure risks missed detection.

~14 days: Window period (Placeholder short note)
High: Early-test risk (Placeholder short note)
Day 14+: Retest advice (Placeholder short note)
Pharyngeal lowest: Locus effect (Placeholder short note)

Retest guidance

Placeholder: repeat testing after the window reduces missed cases.

Placeholder: retest after day 14 if initial test was early.