PCR testing is a double-edged sword

In order to avoid blind reliance on the result for COVID-19, clinical diagnosis by specific criteria should be popularised

Updated - July 01, 2020 12:32 am IST

Published - July 01, 2020 12:02 am IST

The government has allowed SARS-CoV-2 polymerase chain reaction (PCR) testing in many government and private laboratories. In January there was one laboratory (National Institute of Virology, Pune) but today there are 1,000. Test validity depends on laboratory quality. Mechanisms to ensure internal quality control and external quality assessment are urgently required.

The boon and bane of PCR testing are in its capacity to amplify even one viral gene segment in the sample to generate a detectable signal — a positive test; it is a boon because it accurately detects the presence of virus but a bane because it is prone to false negative and false positive results.

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Follow protocol

When a laboratory handles several samples, cross-contamination must be avoided. During sample preparation for testing, if even one gene segment falls into the tube from the laboratory environment, it will be amplified and the test will be positive — but, false positive. It points to the lack of meticulous attention to protocol while processing samples, some with and others without the viral genes. A laboratory technician’s proficiency is integral to quality assurance. In reliable laboratories, a positive result means that the person whose sample was tested was indeed infected. For reliability, only laboratories under quality assurance should do testing.

Ensure quality

Here is an example. A conscientious professional in Vellore, Tamil Nadu, scrupulously practising personal protective procedures, had to get the mandatory PCR test to get an e-pass for an important meeting in a neighbouring city. The authorised laboratory for voluntary testing, a private laboratory in another town, sent a technician to his house to collect a nasopharyngeal swab. Two days later he gets a “positive for COVID-19” test report.

The laboratory informed the health authorities who wanted him admitted in a COVID-19 quarantine centre, despite pleas for home isolation. With great difficulty he bought time for two days to get admitted in a reputed hospital for two tests on consecutive days, in the hospital’s nationally accredited lab. You can imagine his personal anxiety and his family’s anguish, apart from the expenses incurred. Both tests were negative; he returned home, missed his meeting, and lost faith in the epidemic management system. Had he been admitted in a COVID-19 quarantine centre, he might have been exposed to infected persons, the story turning tragic for no fault of his.

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The first test result was false positive, which should not occur in any quality-assured laboratory. The selection of private laboratories has not been careful. There have been newspaper reports recently of a private laboratory in Amritsar turning out four false positive PCR results in as many days. After selection, quality checks of laboratories have been found to be woefully inadequate.

We wonder how many laboratories produce similar false positive results. How many of reported positive tests in asymptomatic subjects nationwide are false positives? And how many lead to a misfortune similar to that experienced by the gentleman in Vellore? There is urgent need to ensure quality assurance from all laboratories testing for the coronavirus infection. Erring laboratories must be disqualified at least until quality assurance is certified.

A false negative PCR means that a person with infection was missed by the test, but that is in the very nature of PCR. The viral load is lower in the throat than in the nasopharynx. Hence throat swabs are falsely negative in 60% of tests and nasopharyngeal swabs in 30%, according to published studies. An incorrectly taken nasal swab may miss the virus altogether and lead to a false negative test.

The relatively high frequency of false negative results leads to gross underestimation of the epidemic’s magnitude. Moreover, traced contacts with false negative tests will not be quarantined but allowed to spread the virus, augmenting the epidemic.

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Doctors should not be misled by false negative tests when COVID-19 is clinically diagnosed with specific criteria. The patient must be treated as COVID-19, and the PCR repeated. Globally, many patients with COVID-19 pneumonia who are PCR negative on the first swab have typical appearances of COVID-19 in a chest x-ray or CT scan. They turn PCR positive on repeat testing. Missing a diagnosis of COVID pneumonia just because of a negative PCR test is medical negligence.

Terms and differences

Contrary to the pervasive misconception that PCR alone diagnoses COVID-19, it detects only virus infection, not the disease. Most of the media report PCR positive persons incorrectly as cases. In medical parlance, case is “patient with disease”. PCR positive but asymptomatic subjects during contact tracing are infections, not cases.

False PCR results highlight that blind faith in the laboratory test misleads the government, underestimates the real extent of spread and, at the individual level, it is a recipe for personal tragedy.

When a false positive result is suspected, the doctor should alert the authorities, who in turn should get the subject re-tested in an accredited laboratory. In case of discrepancy, the laboratory concerned must be closed and checked for compliance with protocols and record-keeping.

In order to avoid blind reliance on the PCR test result, clinical diagnosis by specific criteria, which is the only way to diagnose COVID, (D for disease), should be popularised among doctors. Whether or not a confirmatory PCR test is done depends on circumstances. During the rural wave of the epidemic, doctors should be confident to diagnose COVID-19 even without a PCR. If we fail to implement these correctly, we are rendering disservice to unsuspecting society and its members.


M.S. Seshadri is retired Professor of Medical Endocrinology, Christian Medical College (CMC), Vellore and now Medical Director, Thirumalai Mission Hospital, Ranipet, Tamil Nadu. T. Jacob John is retired Professor of Clinical Virology, CMC, Vellore and past president of the Indian Academy of Pediatrics

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