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

Friday, 20 March 2020

Critical workers

Following on from yesterday's post, the government has published their list of critical workers on the gov.uk website:


So, how did I do? I think fairly well. I missed off police (annoyingly, as I had them on my written list), and totally missed off prison officers, and the military.

In fact, the list is broader than I expected, with categories like 'essential financial services provision'.

I'd also hope that companies can apply for exemptions for their staff, e.g. if a company is working making ventilators (or components thereof), or scientists working on vaccines and tests, or companies making tests.

All in all, I think it's a good, comprehensive list. I wonder how many people it covers? Five to ten million, at a guess.

Thursday, 19 March 2020

What is a 'critical worker' ?

With the shutdown caused by Covid-19 slowly rushing towards us like a particularly laggardly iceberg, it has been announced that special measures are being put in place to help 'critical workers' - such as creche schools for their children allowing them to still go to work.

This leads to a question: what is a 'critical worker' ?

Firstly, it probably depends from crisis to crisis: in a war situation, anything to do with the military, logistics, and wartime production would be critical.

But we are facing a health emergency, and therefore doctors, nurses, and all the frontline staff are undoubtedly critical.

In trying to work out how we as a family will cope with an extended stay in our home, I made two assumptions:
1) We will continue having power (i.e. gas, electricity).
2) Water / sewage will not be interrupted.

In my view, both of these are critical. A population left without power, water or sanitation for any length of time will soon see deaths occurring regardless of Covid-19. People need power, even in the milder weather of a UK spring. Much food will be frozen, and all that dried pasta needs cooking. And to ensure these services, people need to be working on maintaining them. If not serviced, things break. And when things break anyway, we need people to fix them.

Then there is telecoms. We are being told to work from home where possible, and it can be argued that this is not critical. However people rely on the Internet nowadays, and being able to keep in contact with family and friends far away will be a boon, and in many cases a lifesaver. Your elderly friend has run out of food? With communications, you have a hope of getting some to her. Likewise, our son's school is understandably leaning heavily on online resources to teach during this extended break. And the Internet could be a great morale raiser to people trapped in their homes.

Another example: food and logistics. Many people I know are relying on online grocery deliveries for their food. This has meant they have done little or no hoarding, and will rely on as much of their deliveries making it through as possible. This is probably a good, centralised way of restricting social contact. If this was to be a prolonged situation, you could use logistics and central distribution instead  to 'fairly' dole out essentials rather than ration cards, although that's admittedly a very rocky road.

Finally, there is what I would call the essential support staff - a good example in this crisis being the teachers who will look after the children of all the critical workers.

So, I'd create a rank of essential services for this outbreak:
1) Medical and related.
2) Essential services (gas, electric, water, sewage)
3) Logistics / deliveries
4) Telecoms
5) Assorted support (e.g. teachers, planners, decision makers)

I am almost certainly missing some. for instance, how long can society last without bins being emptied? For individual households, that might be less problematic. For many communal spaces, it might be. How about postal services (i.e. Royal Mail) ?

It will be interesting to see what the government comes up with later.

 Any thoughts?

Friday, 13 March 2020

Okay, I thought I'd put my tuppence forwards on the current Covid-19 crisis, and the decisions that the government have to make. I am not an expert; I have no particular knowledge on medical matters or pandemics - so I'm in the same boat as most of us!

Feel free to disagree, but these are my current thoughts, and please forgive the length:

1) We are working on incomplete data, and are having to make decisions based on assumptions. This is always risky. Just a relatively small change in one piece of data might invalidate one approach, whilst validating another. For instance, if a working vaccine is not developed before the end of the year, then isolating everyone now becomes a less valid approach. If a working vaccine is developed by mid-year, then isolating everyone now makes more sense.

Likewise, the number of asymptomatic cases (that means, the people who get Covid and are not recognised as such because they don't get major symptoms) is important. As we don't have a reliable mass antibody test yet, this is a major unknown that again has a major effect on the decision made. If there are a small percentage of asymptomatic cases, then isolating now makes more sense than if there is a high percentage.

Experts and politicians can look at the data and come up with different conclusions. Reasonable people can reasonably differ, especially in the presence of uncertain data.

2) Every country is different: in their stage of the epidemic, the way it is progressing, and in their social mores. In some countries, the epidemic is in only one or two regions, and therefore the rules applied to those regions can be specialised. Here in the UK, we do not have particular hotspots, and no reason to believe it can be contained in particular areas or regions of the country. Likewise, we do not live in a state where (allegedly) doors to apartments can be welded shut to keep them from leaving. We appear to be a week or two behind other countries in the outbreak; what works for them now might not work for us, now; it (or another approach) may work for us in a week.

Blindly comparing our decisions to those of other countries without factoring in such differences is, at best, pointless. This is not about some Union Jack-waving British exceptionalism; it's about the reality that our situation differs - as does every country's.

3) There might not be a 'right' way to handle this. There is a good chance that no approach is perfect, and that even when the current situation has died down, we won't know what the 'right' thing to do was. We are living through a massive experiment.

4) What is 'obvious' is often non-obvious. A common call is for schools to be closed, as has been done in other countries. Yet that can have side effects: children (who, unlike the 1918 flu pandemic, appear to be least affected by the illness) have to be cared for, and that burden will often fall on grandparents - who are most affected. Likewise, Madrid has had to lock shut the gates to playgrounds, as children were just meeting up there instead. What happens with exams? Coursework? A 'simple' decision has massive consequences - and not all in one direction.

5) I'm very glad I'm not the one who has to make these decisions.

In the UK's case, I don't see any reason to believe that Boris Johnson, the government, the Chief Medical Officer, the Chief Science Adviser et al *want* this awful disease to spread and for lots of people to die. They're having to use incomplete data to come to a decision in a terrible situation. I hope they've made a good one.

6) Finally: much of this is up to individuals. If you want to keep you and yours well, don't be silly, and follow the advice. Bulk-buying toilet roll is of little use. Wash your hands. Avoid touching your face. If you feel unwell, rest and isolate yourself as much as possible.

Help your relatives. Help your friends. Help your neighbours.

Wednesday, 4 March 2020

Chris Packham

Apparently Chris Packham is launching a judicial review of HS2, saying it does not take carbon emission targets into account.


Which I found slightly odd, because a little blip in my memory recalled something. So I look on his website, and find nothing under the 'travel' link:

However the wonderful Wayback machine shows the following:

So Chris Packham feels it's perfectly fine to make money out of taking adoring fans on trips to Alaska, Antarctica, the Gambia, Kenya etc - which of course involve environmentally-harmful flights  to and from the ships or locations - but does not want the hoi polloi in the UK to be able to travel.

He also says 'Bakotu Hotel – the base for my first tour – is my second home.' How nice it must be for him to have a second home in the Gambia. I bet he walks there ...