Scientists have raised concerns about the quality of diagnostic tests performed by government labs, warning that infections could be missed because they are not sensitive enough.

A scientist at Public Health England said the in-house tests that have been in use since February are performing worse than commercial kits, which labs have been advised to switch to by the end of the month.

An internal PHE document, shared with the Guardian, suggests supply chain issues that hampered the UK’s ability to ramp up the numbers of tests performed may also have negatively affected the quality of testing, because labs have had to rely on substandard chemicals and reagents.

The document notes that “discordant results have been identified” and warns laboratories to retest ambiguous results before calling a result negative.

A false negative result is unlikely to radically alter the course of medical treatment, as doctors are already aware that tests miss a proportion of positive cases due to problems taking samples or patients shedding very low levels of the virus.

However, the disclosure raises further questions about the credibility of the UK’s testing operation, which has included labs struggling to source chemicals and equipment, the government purchasing millions of unusable antibody tests and frontline healthcare workers being unable to access testing.

The PHE scientist, speaking anonymously, said that while there are not believed to be any issues with the accuracy of positive results, the in-house tests appear to be less sensitive than commercial kits, such as the one developed by the Swiss company Roche.

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PHE disputed this, with a spokesperson saying: “There is no evidence to support that commercial tests are more accurate than the current PHE test. We believe the performance is comparable to currently available CE-marked assays [tests].”

The internal PHE document, dated 11 April, states that in line with standard practice, laboratories should switch to commercial kits by 23 April, now that such tests are available.

For those labs unable to immediately migrate to commercial kits, the document outlines immediate actions that need to be taken, noting that “discordant results” have been identified between the PHE tests and “new/improved assays”.

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“There is considerable diversity of molecular platforms, reagents, kits and assay performance conditions in PHE and NHS laboratories,” the document states. It goes on to highlight “evidence of quality assurance difficulties for key reagents due to global supply chain issues”, that shortages of swabs may be impacting on the performance of tests and that the performance of enzymes have “degraded compared with original validation performance”.

The document instructs staff to retest ambiguous results with a different kit to avoid incorrectly calling a negative result.

When approached by the Guardian, PHE said a recent back-to-back comparison of its in-house test and commercial tests found 35 differences in results out of 1,165 samples. When PHE updated a component within its own test, the number of discordant results reduced to 15, it said. No information was given on whether these results were classed as false negatives or false positives.

A PHE spokesperson added: “The UK was one of the first countries outside China to develop a testing capability for novel coronavirus. The test is regularly reviewed and compared to commercial tests that are coming on the market and is reliable and effective. The rollout of PHE’s test is the fastest deployment of a novel test in recent history and we continue to make improvements.”

Paul Hunter, a professor of medicine at the University of East Anglia, said doctors were aware of the possibility of false negative results and would typically order a retest in cases where patients were showing clear symptoms. However, he added that it would be unsurprising if quality had been affected by supply chain issues and shortages of qualified testing staff in hospital microbiology labs.

“We almost certainly left it too late to buy a lot of these reagents,” he said. “It’s a bit like the NHS worker who goes to the supermarket to find all the shelves empty. We didn’t expect to be doing anywhere near as much of this stuff.”