During SARS-CoV-2 surveillance, several samples tested on a commercial three-gene RT-PCR platform show amplification of ORF1ab and N genes but repeated failure of the S gene target. What is the most likely explanation?
- A The virus carries a deletion in the S gene region targeted by the probe, classically seen in the Alpha variant (69-70 del) ✓
- B The samples contain a PCR inhibitor affecting the largest amplicon
- C The viral load is too low for all three targets to amplify together
- D This pattern indicates a false positive result and should be reported negative
Correct answer: A. The virus carries a deletion in the S gene region targeted by the probe, classically seen in the Alpha variant (69-70 del)
Explanation
S gene target failure occurs when a deletion removes the probe binding site while other genomic targets still amplify, confirming true infection rather than inhibition or false positivity. The 69-70 deletion in the spike gene of the Alpha (A.1.1.7) variant was widely used as a rapid proxy screen before confirmatory sequencing. Low viral load would weaken all targets equally, and an inhibitor would suppress every target in the reaction.
Reference: Murray's Basic and Medical Microbiology, 9th ed.
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Written and medically reviewed by the StethoPrep medical team.