Unexpectedly Intriguing!
September 29, 2020

Getting the results of coronavirus tests has been a chronic problem throughout much of the 2020 pandemic.

Mufid Majnun: Laboratory worker takes a swab test, via Unsplash at https://unsplash.com/photos/oI20ehIGNd4

Early on, simply getting things like an adequate supply of nasal swabs to collect samples for all those seeking COVID tests was a huge problem. Later, testing labs entrusted with determining whether a person either tested positive for the SARS-CoV-2 coronavirus infection or not became a problem when many couldn't keep up with the demand for tests.

The answer to the first challenge was to increase the supply of the test kit components that were in short supply. Engineers deployed 3-D printing technology to make the nasopharyngeal swabs used in COVID test kits. Earlier this month, a study found that one of the more widely used 3-D printed swabs that was developed to cope with the shortage "work as well, and safely, as the standard synthetic flocked nasal swabs".

The answer to the second challenge has been more difficult. The standard answer for the testing labs has been to add more testing equipment to process test results. Unlike nasal swabs however, this equipment cannot be easily produced using 3-D printers, and the supply of qualified equipment and related testing supplies has also come to be in short supply.

That shortage can be seen in the experience of testing labs in states coping with surges in coronavirus infections. Many have had to wait weeks to get new equipment they ordered, only to then face further delays as they needed more time to clear the huge backlogs of past test results after it arrived.

These delays have made it difficult for testing labs to get caught up enough to make testing an effective way to monitor and control the rate of spread of coronavirus infections as envisioned by public health officials. In the absense of sufficient testing capacity, many politicians have stepped in to impose restrictions on commerce and other activities in a bid to slow the spread of infections, but their reactionary policies have wrought considerable damage.

Damage that might be avoided if only COVID-19 testing can be done in a much more timely manner.

That's where the idea of pooling test samples makes a lot of sense. Take a portion of the individual test samples that have been collected and combine them together to perform a single test. If the test on the combined sample comes back negative, then all the individuals whose samples were pooled together this way can be cleared in the time it takes to perform a single test. If the combined test samples comes back positive, then individual tests might be performed to identify the individuals who are infected.

The following diagram provides an example of how pooled testing works in the case of testing for HIV infections in multiple individuals using collected blood samples.

Horemheb-Rubio et al (September 2017). Figure 1. Diagram of pooling method for serum samples from blood donors

In this example, we can see how pooling test samples can reduce the number of required tests from 20, one for each individual sample, down to as few as 9 tests, a 55% reduction. Applied to COVID-19, pooled testing could greatly amplify the capacity of testing labs while reducing their immediate needs to add expensive equipment.

That's the promise of pooled testing, but the reality hinges on a number of factors. How prevalent are coronavirus infections among the population being tested? How many people's tests can be batched and usefully processed and tracked together using this testing method? What's the optimal size of a testing subgroup?

Fortunately, if you have an idea of what the answer for the first two of these questions might be, there's math to answer the third question! Math that we've deployed in the following tool. If you're accessing this article on a site that republishes our RSS news feed, please click through to our site to access a working version.

Testing Parameters
Input Data Values
Total Number of Individual Samples in Testing Pool
Probability of a Positive Sample in the Tested Population

Optimal Subgroup Size for Pooled Testing
Calculated Results Values
Optimal Size of Pooled Testing Subgroup
Benefits of Using Pooled Testing
Expected Number of Tests with Pooled Testing
Percentage of Tests Saved Using Pooled Testing

Without pooled testing, the number of tests that would otherwise need to be performed would be equal to the total number of individual samples.

For the default scenario in the tool, that would be 20 tests. With pooled testing, and assuming that 10% of the population would test positive, the required number of tests to identify all those with positive results would drop to 9, a 55% reduction. That was to be expected, seeing as the default scenario presented in the tool matched the example in the diagram.

But how might the results change if you increased the number of individual samples? What would happen if the expected test positivity rate was 5% instead of 10%? Being able to answer questions like those is why we built this tool!

For what it's worth, the Food and Drug Administration first approved pooled testing for a COVID-19 test developed by Quest Diagnostics that would group four individuals at a time back on 19 July 2020. On Monday, 28 September 2020, the FDA granted an emergency use authorization to Hologic for a new COVID-19 test that would increase the number of individuals in a pooled test group to five.

That's the size of pooled COVID-19 saliva testing now being conducted at the University of Tennessee. Starting with 574 individual samples, divided into 115 pools for testing (114 pools made from 5 individual samples and 1 pool made from the remainder), university researchers found 21 pooled samples with positive results, with individual tests to be conducted on 105 to identify students actually testing positive. Adding 115 tests to the 105 tests to be conducted, pooled testing will have reduced the amount of needed testing to find students testing positve by over 61% from what would have been needed if each student had to have their samples tested individually.

Pooled testing for COVID-19 is looking to be super beneficial indeed.

References

Horemheb-Rubio, Gibran & Ramos-Cervantes, Pilar & Arroyo Figueroa, Hugo & Ávila-Ríos, Santiago & García Morales, Claudia & Reyes-Teran, Gustavo & Escobedo, Galileo & Estrada, Gloria & García-Iglesias, Trinidad & Muñoz-Saucedo, Claudia & Kershenobich, David & Ostrosky-Wegman, Patricia & Ruiz-Palacios, Guillermo. (2017). High HPgV replication is associated with improved surrogate markers of HIV progression. PLoS ONE. 12. e0184494. DOI: 10.1371/journal.pone.0184494.

Summer J Decker et al, 3D Printed Alternative to the Standard Synthetic Flocked Nasopharyngeal Swabs Used for COVID-19 testing, Clinical Infectious Diseases (2020). DOI: 10.1093/cid/ciaa1366.

Image Credit: Photo by Mufid Majnun on Unsplash

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