We're doing COVID testing wrong

Testing for infectious diseases should be done in portable facilities and homes, not in high-end labs

The COVID-19 pandemic has brought the issue of public health to the forefront of everyone's minds, especially mine. As a high school student in Maryland, I began a two-week-long COVID-induced break last Friday.

Since then I've carried out a frantic and very likely unhealthy deep dive into the world of diagnostic tests, biochemistry, and epidemiology. I've mainly focused on how to improve the capacity or throughput of testing around the world.

Now that I'm writing this, I'm worried it's too late, with states changing strategies to limit testing, and experts telling us that it simply doesn't make sense to test everyone we would want to at the peak of the pandemic.

Nevertheless, testing will be an important tool in finding the "front-lines" of the pandemic, by which I mean the people who seem fine but are asymptomatic carriers.

This will allow us to use contact tracing and traditional public health surveillance techniques to finally beat the virus and prevent second or third waves from occurring.

In the U.S. at least, serious blunders from the start have caused problems with testing.

The issue is not testing large segments of the population, even if large portions of it may become infected.
Even the countries that have tested the most people in the world per capita have only tested less than 0.5% of their population. Like we just described, it is finding the people who may be asymptomatic so they can self-isolate.

Allowing anyone who wants one, however, to get a test, like in South Korea, could allow people with any sense of being sick, even without symptoms, to get tested.

Other testing methods include testing everyone if the population is small enough, like in one Italian town of 3,000 people, and random sampling, which may not work well depending on how and where it is done.

Ok. So enough introduction: we know that scaling testing well and providing it to everyone, early, is one of the most powerful ways to stop an outbreak, but we also know that testing will be increasingly more important to stop the next waves of the virus, and as the virus spreads to the rest of the world, especially resource-limited developing countries.

Findings

What I've found is that using a group of newer testing methods called LAMP instead of the more established method called PCR would enable testing on a scale we have never seen before.

LAMP is faster, less complicated, often less expensive, and often more accurate than it's counterpart PCR. PCR requires a large expensive machine called a thermocycler (which heats and cools the sample over many cycles), and all its supporting laboratory equipment.

This machine alone can cost $2000-$4000 and only delivers results in 8 hours. There are some modified versions of this machine, but the cheapest and fastest cost around $160 and can deliver results in an hour.

Also, labs need to carefully prepare the sample from the patient by extracting the DNA or RNA and performing other processing. This requires reagents and other materials that can be a limiting factor in a pandemic situation that strains the supply chain. Not to mention, all of these healthcare workers need to be trained to do this.

In comparison, LAMP-based methods can work in a single test tube and deliver results in less than 20 minutes. This is why LAMP methods have been deployed widely in developing countries to combat malaria, tuberculosis, and other diseases.

LAMP methods were also used in the U.S. during the Zika virus outbreak. In contrast with PCR methods, some LAMP methods require no sample preparation, including one Zika test which could take an entire dead mosquito in a test tube and then change color depending on the result of the test.

This may sound a little hokey-pokey and unscientific. We can detect a virus just by looking at the color of a test tube? That's crazy!

But the truth is that these tests are just as accurate, if not more accurate, than PCR based methods for detecting COVID-19, even if the only studies so far have been on small sets of patient samples (20-40).

If you want to read in-depth about the comparison between these two methods, feel free to check out my article on it.

The article also goes into possible deployment options for testing facilities based on this technology. I believe we could build facilities that could test tens of thousands of samples per day, and I talk about that a bit more below.

If we were to collaborate with companies that had factories containing industrial ovens that could be set to 60-65° C, that would help expand capacity as well.

Discussion

All the politicians and health administrators I've heard strongly support patient-collected samples in people's own homes, which would reduce the need for medical personnel and personal protective equipment.

Although the public health community seems to embrace drive-thrus and other facilities to collect samples, there seems to be opposition to doing the actual testing in a manner any different from the patchwork of public and private labs around the country.

Maybe this is just a general sluggishness towards adapting new technologies or maybe it's that we've never encountered an outbreak in modern history where our demand for testing outstripped our capabilities.

However, for global outbreaks that have the potential to turn into pandemics, like COVID-19 was in January and February, we need to take a long hard look at building our capabilities for both resource-limited environments and massive rapidly-deployed test processing facilities.

LAMP-based methods are so simple and versatile, requiring only heat and a few chemicals, that they could be deployed virtually anywhere, using a variety of heat sources.

One option would be to send the entire test kit to the patient, which would need to find a way to heat it up properly, which could work in a home.

One study suggests using a thermos with a magnesium reactor to provide the necessary heat. This could be used for testing in remote villages where electricity might not be available.

In developed countries, however, LAMP provides us with an opportunity to build mobile laboratories that could be deployed wherever they are needed.

Just like an assembly line on a factory floor, I believe that we could automate large parts of most laboratory work. An automatic test processing facility could receive patient samples via the mail, automatically run them through the testing system, and upload results electronically to the patient.

Remember, most LAMP tests require virtually no sample processing, thus cutting down on the other lab equipment required, leading to minimal costs.

Also, LAMP tests can be designed to target any strand of DNA or RNA, thus allowing for wide applicability to other types of viruses. These facilities could be shut down, the main components (industrial ovens, test-tube racks, and various mechanical or automated parts) stored, and then quickly rebuilt and used again for other outbreaks, with only the chemicals for the reaction (primers) changing.

Additionally, I would hypothesize, although I haven't even done preliminary research on this, that the cost per sample of a test in a custom-built facility designed to do one and only one diagnostic test would be much cheaper than in a lab that has hundreds of pieces of equipment and possibly entire subsystems just for biocontainment.

The goal would be to have this facility be scalable from a single room in a government building in a developing country, with some or most of the work done by volunteers, to a massive facility in a large factory or warehouse that could be almost completely automated.

I've discussed various other aspects of a possible scalable testing center in my previous article on testing.

Although this is an ambitious project, we need to take it on to help provide testing capabilities to countries around the world battling COVID-19, and to prepare ourselves for any future outbreaks that could occur.

Of course, we should make use of existing laboratory infrastructure, where the initial tests will need to be developed, and many patient samples will need to be sent for research or tracking more advanced properties of the virus. For example, sequencing the RNA of the virus from different locations around the world allows us to determine whether it has mutated.

At this point, having experienced a bold new vision for diagnostic testing, you may be wondering: Who is this guy who thinks everyone is doing COVID-19 testing wrong? Why do we need a completely new system?

Those questions may be partly inspired by the slightly antagonistic and possibly clickbaity title. The truth is that what we are doing right now is not wrong, but that there is a better option out there.

I think in many areas, only outsiders can be real innovators. Maybe it is part naiveté and part childish imagination that allows them to envision things in a new way. Ultimately, these new ideas might not pan out.

But I think it is irresponsible not to consider radically new options when the cost of not doing so could be thousands of human lives.