A real-time RT-PCR assay is used to detect SARS-CoV-2 in nasopharyngeal swabs. The assay targets the E gene and ORF1ab gene. A sample gives a Ct value of 38 for E gene and is negative for ORF1ab. What does this result most likely represent?

• A Definitive positive result — a single gene target positive is sufficient
• B A negative result — two gene targets must be positive for validity
• C Contamination — Ct >35 is always an artefact
• D A weak positive / inconclusive result warranting repeat testing or clinical correlation ✓

Explanation

Most national and WHO guidelines classify a SARS-CoV-2 PCR as 'inconclusive' or 'weak positive' when only one of two (or more) target genes is detected, especially at a high Ct value (≥35–38), as this may represent very low viral load, early/resolving infection, or borderline contamination. Repeat testing or clinical/epidemiological correlation is required. A single low Ct positive on one target with another target negative usually indicates a true positive, but this combination (high Ct + single target) warrants caution.

Reference: Ananthanarayan & Paniker's Textbook of Microbiology, 11th ed.

High-yield for: NEET PGINI-CETNExTFMGEUSMLEPLABMRCP

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