PCR (polymerase chain reaction) testing is now familiar to most people from the pandemic years, but the results are still frequently misread. A positive result does not always mean active infection. A negative result does not always mean absence of the pathogen. And an indeterminate result is not a laboratory error. This article explains how PCR works and how to interpret the results you receive from a molecular diagnostic laboratory.

What PCR Actually Detects

PCR detects the genetic material (DNA or RNA) of a pathogen, not the pathogen itself. The test amplifies a specific target sequence millions of times until it is detectable. This makes PCR extremely sensitive: it can detect very small amounts of genetic material. The implication is that a positive PCR result means the target sequence was present in the sample. It does not, by itself, tell you whether the pathogen is viable (capable of causing infection), whether the person is currently infectious, or whether the infection is active or resolving.

What Ct Values Mean

Quantitative PCR reports often include a Ct (cycle threshold) value. This is the number of amplification cycles required before the target sequence becomes detectable. A lower Ct value means more genetic material was present in the original sample. A higher Ct value means less material was present. In practice, a Ct below 25 typically indicates a high viral or bacterial load; a Ct above 35 may indicate a low-level or resolving infection, or occasionally a contamination event. Ct values should always be interpreted alongside clinical context, not in isolation.

Negative Results and Their Limitations

A negative PCR result means the target sequence was not detected in the sample provided. This can occur because the pathogen is genuinely absent, because the sample was collected too early or too late in the course of infection, or because the sample was collected or transported incorrectly. For respiratory pathogens, nasopharyngeal swabs collected in the first two to four days of symptoms have the highest sensitivity. A negative result in a patient with strong clinical suspicion should prompt discussion with the requesting clinician about whether repeat testing is warranted.

Indeterminate Results

An indeterminate result means the assay produced a signal that was above the background noise but below the validated positive threshold. This is not a laboratory failure. It is an honest representation of an ambiguous finding. Common causes include a very low pathogen load at the margins of detection, sample degradation during transport, or inhibitory substances in the sample matrix. At Pulse Path Lab Core, indeterminate results are reviewed by a senior scientist before reporting, and the report includes a comment recommending whether repeat testing is advisable.

Our respiratory pathogen PCR panel covers eight targets and is run on a Bio-Rad CFX96 platform. Results are available within 6 hours of sample receipt during operating hours. For questions about a specific PCR result, contact our scientific team at enquiries@pulsepathlabcore.com.