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Spit for freedom

Is it time to ditch the PCR?

Artillery Row

Should we gob before we swab, if you will pardon the expression? Why do tests for Covid-19 require an unpleasant swab up the nose rather than a less invasive spit-in-a-pot?

Covid-19 tests will continue for the foreseeable future. But the easier and quicker they are, the faster society can reopen. Last year, Heathrow airport offered a saliva test for £80 with results guaranteed within the hour, while saliva tests with over 1,000 volunteers produced results perhaps good enough for widespread rollout. Even Superdrug is offering saliva tests.

In January, the Department for Health and Social Care announced that an evaluation conducted by NHS trusts and universities has confirmed the LamPORE test, produced by Oxford Nanopore, to be accurate and sensitive enough to detect the virus in people with or without symptoms. While LamPORE used swab samples in the same way as a PCR (polymerase chain reaction) test, it also showed high performance with saliva.

LamPORE is both mobile and scalable. On swab samples from asymptomatic patients, the LamPORE assay with RNA extraction returned sensitivity (the ability to correctly identify those with the virus) of 99.6 per cent and specificity (the ability to correctly identify those without the virus) of 99.4 per cent, while on saliva samples from asymptomatic patients it returned sensitivity of 98.9 per cent and specificity of 99.4 per cent. LamPORE technology combines LAMP (loop-mediated isothermal amplification) and nanopore sequencing.

PCR has a turnaround time which makes it less effective for crowded venues

Late last year, the same department confirmed the OptiGene RT-LAMP tests to be accurate and sensitive enough for Covid-19 testing, including for those without symptoms. The test was found to have sensitivity of 79 per cent and specificity of 100 per cent. OptiGene RT-LAMP tests were used to test NHS staff, and in asymptomatic testing in Southampton. RNA RT-LAMP on swabs showed sensitivity of 95 per cent and specificity of 99 per cent, while RNA RT-LAMP on saliva showed sensitivity of 80 per cent and specificity of 100 per cent. Direct RT-LAMP on swabs showed sensitivity of 70 per cent and specificity of 100 per cent, while Direct RT-LAMP on saliva showed sensitivity of 79 per cent and specificity 100 per cent. With a higher viral load, sensitivity increased to 94 per cent for saliva and 100 per cent for swabs.

According to Professor Dame Sue Hill, Chief Scientific Officer for England in NHS Test and Trace, “we’ve shown through carefully conducted studies that the OptiGene LAMP test is fast, reliable and easy to use and dependent on testing format can work directly with saliva samples as well as with swabs.” Professor Keith Godfrey of the University of Southampton MRC Lifecourse Epidemiology Unit believes that, “the saliva LAMP project in Southampton has proved to be very easy for students to use, and is extremely popular with parents and staff.” He added that, “with regular testing and participation rates exceeding 80 per cent among the school staff and students, there has been no evidence of any transmission of infection within the schools involved.”

Regarding the Hampshire and Isle of Wight Saliva Testing Programme, participants only needed to provide a 2ml sample. The saliva test used the LAMP technique, whereas swab samples are using PCR or lateral flow testing. Unlike PCR tests, LAMP tests do not require sequential changes of temperature and can produce test results faster. According to Southampton City Council, “in validation studies across multiple laboratories in the UK and in other countries, positive samples from LAMP tests have been ‘double tested’ against PCR tests and shown to be highly accurate.”

Some researchers even believe saliva tests could be more accurate than swabs

Lateral flow tests are used with swab samples. While these test results can be read in 10 to 30 minutes, current evidence suggests they have more false positives and false negatives than LAMP tests, while evidence suggests saliva samples are as good as swab samples. LAMP has been shown to be highly accurate in detecting active infections (over 95 per cent sensitive and 100 per cent specific), meaning false positives are extremely rare while false negatives can occur but are uncommon. Some researchers even believe saliva tests could be more accurate than swabs.

In October, the Independent reported on one Japanese study which found saliva tests are as effective as swabs in asymptomatic carriers. The study – which tested and compared swab and saliva samples of nearly 2,000 people – was found to have a very similar false positive rate to the PCR test, with both tests able to identify those without the infection in more than 99.9 per cent of subjects, while the amount of virus detected in the two tests was also similar. Researchers at Hokkaido University got results within 30 minutes. RT-LAMP tests were among those trialled at Heathrow while saliva tests have been approved in Japan, with their use being discussed for the Tokyo Olympics.

By contrast to the saliva test, the PCR test requires more resources, is unpleasant, and has a turnaround time which makes it less effective for crowded venues, crucial for opening-up sectors like hospitality. Common sense dictates that if a quicker, less invasive and more mobile solution than the PCR test exists, enabling the economy to be opened-up faster, then energy should be put into such an option. If it becomes obvious that a saliva test offers virtually the same guarantee as the PCR test, is it not pragmatic to be spitting our way to freedom without relying on PCR tests and mandatory vaccines for what is an evolving virus with a relatively low mortality rate?

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