13 September 2020

COVID-19: SALIVA versus SWAB TESTS

The SARS-COV-2 (SARS2) virus causes the COVID-19 disease.  The current primary method of testing whether someone has the disease is to use a swab to collect a sample of cells from the throat, near the tonsils, and up the nose.

In broad terms, the swab sample is subject to a process called RT-PCR which involves the sample being treated and 'replicated' 2-4-8-16 etc until there is enough material to detect.

So why hasn't saliva been used?  Presumably because it does not produce enough of a sample of the viral RNA.  Indeed poor swabbing can produce 'false negatives' of over 30%.

So why is testing using saliva in the news?  It is the basis for the new tests that are the foundation for PM Johnson's "Operation Moonshot".

Nonehteless this study suggests "saliva represents a promising tool in COVID-19 diagnosis".

There was a saliva test trial in Southampton that I saw launched in June.  Then it went quiet.  Apparently it was 'successful', but still no results made public.  Successful enough to now extend the trial in Southampton and Hampshire, with a major trial in Salford.  This was announced a few days before PM Johnson made it a key part of his Downing Street briefing alongside announcing the 'rule of six'.


PURPOSE OF A MASS TESTING PROGRAMME

In the absence of a vaccine, something else must be done to reduce transmission.  A lockdown was used in March, but that has several adverse 'side-effects', as we have experienced.

The Office for National Statistics (ONS) has a programme of random testing, but that is only sufficient to identify the general level of infections in an area.

The idea is to be doing enough testing of people who are asymptomatic to identify those infected at the earliest possible opportunity, get them to self-isolate, and trace all their contacts to do likewise.

This idea was covered a month ago when we looked at The Value Of Testing, where I said:

"To tackle this problem needs ‘Got It’ testing every day, ideally, with immediate results.  Even once every 5 days until (or if) someone tests positive would initially require some 11 million tests a day.  Clearly impractical and horrendously expensive using current testing technology.

We therefore need alternative ‘Got it’ tests that are:

  • Simpler
  • Quicker
  • Cheaper
  • Preferably more reliable, by not being based on swabbing
  • Yet clearly identify all variants of SARS-COV-2 without counting other coronaviruses"

That list is fundamentally the aims of Operation Moonshot.


IS THIS LEVEL OF TESTING PRACTICAL WITH ANY KNOWN TESTING PROCEDURE?

Apparently a similar approach was suggested back in April, but rejected from a practical perspective.  I still think the concept is worth pursuing, as technology develops.

A month ago we looked at the various technologies for testing, including those using different technologies.  Most notable was RT-LAMP technology, using which several tests have been developed.  These offer much shorter result times with much simpler, cheaper equipment.

There have also been advances in paper tests, which at least give a cheap indication of whether someone is infected, though require confirmation by a better test.


There is concern though that at millions of tests, the number of 'false positives' would hugely outnumber true positives.  That could be as damaging as the high level of 'false negatives' using swabs commonly affecting the current RT-PCR tests.

So whilst RT-LAMP offered a way forward it isn't the answer. These tests are also horrendously expensive, with a total cost suggested of some £100 billion.  Simply unsustainable.   Operation Moonshot needs to be looking beyond the tests available today.  We may need them for months if not years.


WHAT SPECIFIC TESTS ARE BEING USED?

The Press Release from the Department for Health and Social Care mentions two specific technologies that we had covered in the Test Test 1-2-3 blogpost:

  • "New rapid LamPORE tests, processing swab and saliva samples to detect the presence of COVID-19 in 60 to 90 minutes".  These are indeed using RT-LAMP technology, and produced by Oxford Nanopore
  • "5,000 DNA ‘Nudgebox’ machines, supplied by DnaNudge, to be rolled out across NHS Hospitals in the UK to analyse DNA in nose swabs, providing a positive or negative result for COVID-19 in 90 minutes, at the point of care".
But PM Johnson talked in terms of tests giving results in 20 minutes.  Whether that was his usual bluster and hopeless optimism, or whether there are other tests in the pipeline, remains to be seen. 


ALTERNATIVE APPROACHES

If asymptomatic people are to be tested, then the level of testing will be independent of the infection rate.  The logistics and cost will become very important.  Though where a second more accurate test is then called upon as confirmation, the quantity will be dependent on infection rates.

As it is, the amount of RT-PCR testing required is overwhelming the system, and that is only when testing symptomatic people.  Not necessarily their contacts who may be self-isolating  when not infected, nor people entering the country from abroad and needing to self-isolate.

The only viable approach is to get infections down to a very low level, which provides so many other benefits too.  Saving lives, livelihoods and improving the economy.  We need to follow a #NearZero strategy regardless.

Will the new 'Rule of Six' be sufficient to get ot #NearZero?  I doubt it with schools re-opening and students now returning for university.

There should have been a second national lockdown earlier in the summer to get infections down to very low levels nationwide.  The downsides would have been far less than the negatives of what we can now expect.  Then we would have been in a stronger position for the winter, when conditions will be easier for the virus than the summer.


IN CONCLUSION

The Operation Moonshot objectives are laudable, but appear to be based on technology that doesn't yet exist.  In the meantime, technology is being used that is slower and more expensive than intended.

This is using saliva samples rather than swabs.  Whether they are found to work adequately remains to be seen as a result of these forthcoming trials.  Fingers crossed.

In any case the government needs to commit to a #NearZero strategy to get infections down to very low levels, so the existing testing regime has a chance to cope.  It would also provide a host of other benefits.  Lives, livelihoods and the economy.




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