COVID-19: the problems with current widely used testing methods

As reported last week, testing methods for COVID-19 have been developed to improve efficiency in terms of speed and accuracy of diagnosis; be it positive or negative.

Until widescale more efficient testing is rolled out, such as through SAMBA II machines, this article looks at the problems with the current qRT-PCR testing method.

More on the SAMBA II machines here: SAMBA II COVID-19 Test

The quantitative Reverse Transcription Polymerase Chain Reaction test, or qRT-PCR for short, is the technique currently being used to identify the presence of COVID-19.

Dr Colin Butter, Associate Professor and Programme Leader in Bioveterinary Science, University of Lincoln, said of the PCR test:

“Strictly speaking it does not detect antigen but viral RNA.”

“Thousands of machines capable of doing the assay exist in the UK and a specific subset of these has now been requisitioned by PHE to be stationed at (I think) three centres including Milton Keynes.” 

“To my knowledge there were 25 machines recruited from the Nottingham area alone so PHE must have, or have access to, hundreds.”

“Given the samples to run and the reagents to do this, each machine can do well over 1,000 tests per day, working 24h.” 

“Each sample needs to be tested in 3 different ways so say 330 samples per day.” 

“100 machines x 330 = 33,000 so why are so few being achieved?” 

“Is this the processing of samples or the logistics of moving them about? Where is the bottleneck?”

As the WHO has stated several times over the course of the pandemic, “test, test, test” should be the modus operandi of governments across the world.

Up to now, there has been very little detail in why testing is taking so long.

Prof Ashley Woodcock, Associate Dean for Clinical Affairs and Professor of Respiratory Medicine, University of Manchester, said on further problems of the PCR test:

“All these tests depend on upper respiratory samples.”

“They are crucially dependent on the quality of samples.” 

“Sputum is better than oropharynx which is better than nasopharynx.”

“Sampling itself is hazardous. People sampling have described having sputum on their arms; They need full PPE.”

“The UK has been using a central laboratory setup of PCR machines for virus tests and is building greater capacity.” 

“In spite of this testing type being the ‘gold standard’, there are a number of issues:

“Capacity: turnaround has been too long – in many places 24-48 hours (but this is getting shorter). 

Patients can still be sat on wards without a firm position on their infectivity for 24 hours.”

“Positive rates for patients with COVID syndrome are ~70%.  This means we have a lot of patients waiting for a repeat virus testing/diagnosis.

“There are many false negatives (maybe 30%) meaning potentially infectious patients could be nursed in COVID negative areas, or sent home thinking they are non-infectious. 

“Reasons for false negatives include low levels of the virus in the early stages of the disease, and especially poor technique in sampling or conducting the test.”

The issues with false negatives are something we reported on last week.

See more on this here:

COVID-19 Testing Misconceptions