SARS-CoV-2 RT-PCR
SARS-CoV-2
Last reviewed 2026-08-13
Public health significance
Still the backbone of respiratory situational awareness. Variant context now lives in surveillance, not in every diagnostic report.
Specimen types
Nasopharyngeal swab, saliva, lower respiratory
Method
NAA with probe detection
CLIA / validation
High complexity. Verification of an FDA-authorized assay, or full validation if run as an LDT.
Interpretation
Prefer Detected / Not detected. Ct values, if reported, are numeric plus UCUM and never a substitute for the coded flag.
Reflex / referral
Unexpected positives in low-prevalence settings may reflex to a second target or a reference method.
Quality control
External positive and negative controls each run. Proficiency testing per CLIA. Lot-to-lot checks on new reagent lots.
Reportability
Reportable in most jurisdictions. Outbreak clusters escalate to epidemiology the same day.
HL7 / ELR
OBX-3 LOINC 94500-6. OBX-5 SNOMED 260373001 / 260415000. Do not put a panel LOINC in every OBX-3.
Sources
CDC LIVD SARS-CoV-2 mappings; US Realm ELR IG.