Polymerase chain reaction (PCR) tests are commonly used to diagnose many viral infections, including COVID-19. While PCR tests are considered the “gold standard” for detecting viruses, false negative results can sometimes occur. This means that the test fails to detect the virus, even when the person being tested is actually infected.
Why can PCR be false negative?
There are a few reasons why a PCR test may return a false negative result in a person with symptoms:
Sample collection errors
One of the most common reasons for false negative PCR results is improper sample collection. PCR can only detect the virus if infected cells are present in the collected sample. For COVID-19, the sample is usually collected from the nasopharynx using a swab. If the swabbing misses the infected area of the respiratory tract, the sample will not contain the virus.
Timing of sample collection
PCR can only detect a virus when viral levels are high enough. With COVID-19, viral loads tend to peak in the first week of symptom onset. Levels may fall to undetectable levels later on. If the test is done too early or too late, the virus may be missed.
Mutation of the virus
PCR tests detect specific genetic sequences that are unique to the virus. If the target sequence mutates in a patient, the primers may no longer bind, leading to false negative results.
Laboratory errors
Mistakes can occur during sample processing, preparation of the PCR reaction, or analysis of results. This includes issues like cross-contamination, improper storage conditions, or instrument malfunctions.
Low overall viral load
Some people may have a low overall viral load, even with symptoms. If the viral levels are beneath the detection limit of the PCR test, it may return a false negative.
How common are false negative PCR results?
Estimates vary on the false negative rate of PCR tests for COVID-19. Some studies have reported false negative rates between 2-37%. However, a meta-analysis of 29 studies estimated the overall false negative rate to be around 14%.
False negative rates appear to be higher early in infection. One study found PCR sensitivity was only 63% 1-2 days before symptom onset, increasing to 83% on the first day of symptoms. After 4 days, sensitivity reached near 100%.
What are the implications of a false negative PCR test?
There are a few important implications of false negative PCR test results:
Delayed diagnosis and treatment
A false negative PCR may lead to a delay in diagnosis and appropriate treatment for the patient. This could potentially worsen outcomes in severe infections like COVID-19.
Ongoing viral transmission
Patients with false negative results may assume they are uninfected and take fewer precautions against spreading the virus. A missed diagnosis allows continued community and household transmission of the virus.
Repeat testing required
Given the chance of false negatives, patients with persisting symptoms may need to be re-tested to rule out infection. This increases costs and burdens on the healthcare system.
Decreased confidence in PCR
Frequent false negative results could decrease trust in PCR as a reliable diagnostic method. However, when performed correctly, PCR remains one of the most accurate methods for detecting viruses.
How can false negatives be minimized?
Here are some ways to help reduce the chances of false negative PCR results:
Proper sample collection technique
Adequate training of healthcare workers to ensure proper swabbing of the nasopharynx can help maximize chances of capturing infected cells.
Repeat swabbing
Collecting multiple swab samples from the same patient may catch the virus if initial sampling missed the infected area.
Testing at optimal time
Testing during the first week of symptom onset captures peak viral levels, optimizing chances of detection.
Using multiple PCR targets
Running PCR assays for multiple viral genes reduces chances of mutation-related false negatives.
Follow-up testing
Retesting patients with persisting symptoms increases chances of catching the infection on subsequent attempts.
Lab quality control measures
Strict protocols and quality checks in the lab minimize errors that could lead to false negatives.
Conclusion
While PCR is a powerful technique to diagnose viruses, false negatives remain possible. Improper sample collection, low viral loads, mutations, and errors can all prevent detection of the virus. For COVID-19, false negative rates for PCR are estimated around 14%, but may be higher early on. False negatives delay diagnosis and treatment, allow ongoing transmission, and decrease confidence in PCR. Careful specimen collection, testing at peak viral levels, repeat testing, and lab quality control help maximize PCR accuracy.
In summary, PCR tests can sometimes be falsely negative, even when someone has symptoms. However, PCR remains one of the most reliable methods for viral detection when performed correctly. Repeat testing and proper timing of specimen collection are key to reducing occurrences of false negatives.
| Reasons for False Negative PCR | Strategies to Reduce False Negatives |
|---|---|
| Poor sample collection | Adequate staff training on proper sampling technique |
| Testing too early or late | Test during peak viral levels in first week of symptoms |
| Viral mutation | Use PCR assays targeting multiple genes |
| Lab errors | Implement rigorous quality control procedures |
| Low viral load | Repeat testing of symptomatic patients |
Despite the potential for false negatives, PCR remains a highly useful diagnostic test when done correctly. Cases of suspected false negatives should prompt repeat testing to rule out infection. With proper sampling, timing, and lab techniques, the incidence of PCR false negatives can be minimized.
Frequently Asked Questions
How accurate is PCR testing?
PCR testing is highly accurate, with sensitivity and specificity over 90% under optimal conditions. However, there is still a small chance of false positive and false negative results.
Can I still have COVID-19 with a negative PCR test?
It is possible to have COVID-19 but still have a negative PCR test result, especially early or late in infection. False negatives are estimated to occur in 2-37% of COVID-19 PCR tests.
Should I get retested if PCR is negative but I have symptoms?
Yes, it is recommended to repeat PCR testing after 1-2 days if you have persisting COVID-19 symptoms but an initial negative test. This helps minimize chances of a false negative result.
Does PCR detect all variants and mutated strains?
Standard PCR tests may fail to detect newer viral variants if the mutations affect the target genetic sequences. Using multiple PCR targets helps improve detection of mutated strains.
Can poor sample collection cause a false negative PCR?
Yes, improper nasopharyngeal swabbing technique is one of the top reasons for false negative PCR results. Adequate staff training is key to proper specimen collection.
Conclusion
PCR tests are a powerful tool for diagnosing COVID-19 and other viral infections. However, false negatives are possible due to issues like improper sampling, lab errors, viral mutations, and low viral loads. Estimates suggest PCR false negatives occur in about 14% of COVID-19 cases. Repeat testing of symptomatic patients, proper sampling methods, and testing during peak viral levels can help minimize PCR false negatives.