Tuesday, 31 March 2020

How do we test for Covid-19 ?

(Yet again, IANAE. Below is information I have gleaned from various sources for my own interest. Any mistakes are my own.)

In all the information being written about Covid-19, there seem to be few resources that highlight the test's methodology and its limitations. It has become a black box 'the test', and many - sadly including journalists - seem to be treating it as an all-conquering miracle.

In reality, whilst it's the best we've got, it's awkward.

The current Covid-19 tests have been produced very rapidly, and is a tribute to the companies and organisations that have developed them. They were aided by the fact there have been several close calls over the last couple of decades - for instance SARS in 2002 and MERS from 2012. These earlier diseases proved to be less susceptible to spreading between humans, and gave investigators a target to concentrate on. The Covid-19 tests are built on that earlier work, which is why we got test for Covid-19 within a couple of weeks of the outbreak starting.

The current commonly-used Covid-19 test are variants of a PCR test.

So (deep breath), what is a PCR test?

A polymerase chain reaction (PCR) test detects viral particles in bodily fluids, such as blood. It is essentially molecular photocopying: small amounts of a pathogen's DNA or RNA are copied many times (amplified) to a level where they can be detected. Without a PCR test, the virus's RNA would be at too low a level for detection. I like to think of it as a gigantic magnifying glass, although perhaps not wielded by Sherlock Holmes.

PCR's inventor, Kary B. Mullis, won a Nobel Prize for Chemistry it in 1993, and it initially proved useful for the Human Genone Mapping Project, although is also used for purposes such as DNA fingerprinting and genetic research (1).

So, what is the testing procedure?

  1. A swab is taken from the patient, or a sample taken from the back of the throat.
  2. The sample is sealed into a tube and sent to a lab for processing.
  3. In the lab, the sample's RNA is extracted.
  4. Chemicals are mixed with the sample in different combinations.
  5. These mixtures are tested in a PCR machine.
  6. The result is given as positive, negative, or uncertain (a catch-all for various errors and problems, for instance the presence of similar viruses).

There are many issues with the test:

  • The PCR tests can only tell if you currently have the disease; not if you have had it and have recovered. For that, we need an antibody test.
  • The test is not instant; samples have to be sent to labs (often distant) for testing.
  • It is not just a case of having enough testing kits: you also need the downstream laboratory to process the samples. It is pointless having a test that you do not get a result from for weeks or months. Tales of countries or organisations ordering tens of thousands of kits seem to neglect the downstream processing. This processing means it is perfectly possible for (say) 10,000 tests to be performed in a day, but for results of only 8,000 to come through, as there is a lag between tests and results - especially if the labs are inundated with tests.
  • The test takes time. Getting samples to a lab takes time. Extracting the RNA takes time. Mixing it with the chemicals takes time. Performing the PCR test itself takes time. Even when samples are batched up, it can tale many hours for a sample to be tested, and that does not include transport from patient to lab.
  • The tests require consumables: from reagents to protective equipment for the lab workers. These consumables and workers are in short supply at a time when every country in the world is demanding them.
  • The tests may be inaccurate. False positives (a patient reported to have the disease when they do not), is less important, as the patient will then be treated with caution, e.g. self-isolation. The big problem is with false negatives: where a patient is reported to be clear of the disease when, in fact, they have it. Some reports give the current test an accuracy of about 70%: in other words, it will only detect Covid-19 within a patient 70% of the time.

Why might false negatives be reported? (2)

  1. In the early stages of the illness, the patient may have too low a viral load to be detected.
  2. The swabs are taken from the nose and/or the back of the throat, and if the patient's respiratory illness is not too severe, not much of the virus may not make it up the respiratory tract.
  3. The sample may be simply incorrectly taken.
  4. The samples may have been poorly handled.
  5. There might be technical issues in the test.

PCR is a tool, and as with any tool, it needs using with care, and with a deep understanding of the tool's limitations.

As an aside, PCR tests are used in Low Copy Number (LCN) DNA fingerprinting techniques, which allow tiny amounts of DNA to be fingerprinted in criminal cases. This is particularly useful in cold cases, where DNA might have degraded over time. The LCN technique proved somewhat controversial a little over a decade ago (3).

Hopefully we will get better, more immediate tests that do not require such a complex process. But in the meantime, thanks to all the companies, organisations and people who are working their socks off to increase the availability of testing kits and increase the testing capability.

(1): https://www.genome.gov/about-genomics/fact-sheets/Polymerase-Chain-Reaction-Fact-Sheet
(2): https://ourworldindata.org/covid-testing
(3): https://en.wikipedia.org/wiki/Low_copy_number#Criticism

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