What is Pooled Surveillance Testing?

Bringing K-12 back to school: Expanded access to testing through source pooling (Information provided by Ginkgo Bioworks)

What is pooled testing?

Source pooling is a testing method for SARS-CoV-2 that enables widespread testing by multiplying the number of tests that can be run with the same testing infrastructure thus dramatically reducing cost per test. With source pooling a large number of samples are combined in the same tube at the source of collection and sent to the lab together instead of individual samples being sent one at a time. This collection process reduces bottlenecks at central lab sites and makes it possible to test twenty or more people using the reagents and cost of processing a single individual sample.

What is classroom pooling?

It’s a method that combines test samples from all individuals in one classroom/group/cohort into one tube that’s then tested. 

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Source pooling as a surveillance testing method for K-12 reopening

Thus far, few school districts have been able to afford any routine testing; with source pooling, an entire classroom can be tested together for about $100. Because individual test swabs are combined at the site of collection, an individual result cannot be given with source pooling, instead providing a population-level result. This information can be particularly useful to support public health decision making for in-person learning in K-12 schools; using the data returned in this process, leaders can better make decisions about when to switch to remote learning or when more individual diagnostic testing is required. Schools and other congregate settings are a particularly good fit for source pooling because classrooms, activity groups, and sports teams create natural pods. Especially in lower grades, there is minimal interaction between classrooms, and in many districts there are protocols already in place for quarantine and contact tracing in classrooms in the event of a positive case. Students and staff supporting each classroom would provide an anterior nares swab (a swab of the front of the nostril that can be self-administered by adults and older children, younger kids can be swabbed by a nurse) and all the swabs from a classroom could be combined together in a large tube and shipped for processing. In the event of a positive result, a classroom could be quarantined while the students and their families are retested using a confirmatory diagnostic test. These confirmatory tests could be a combination of traditional molecular tests and rapid, point-of-care antigen solutions that are now just becoming available. 

 

Scaling across America

There are about 50 million K-12 students in the US. We estimate that costs per person in a pool could be as low as $5. With pools of 20, it would take about 500,000 pooled tests per day in order to test all those students once per week at a cost of just $1B per month. Unlike laboratory pooling, where samples are diluted as they are added together, the number of swabs that can be tested together with source pooling is theoretically limited only by the size of the tube. As we scale vaccine distribution, it is inevitable that there will continue to be pockets of virus—source pooling offers an extremely cost effective method to gain the edge in monitoring future outbreaks. Ginkgo is currently validating this method of testing leveraging our next generation sequencing lab in Boston’s Seaport, with the target of being able to test hundreds of thousands of individuals per day by early 2021. However, this method of testing could also be used with any lab that can process SARS-CoV-2 tests, once the lab has validated the test to detect virus in pooled samples. Such samples can be transferred from the larger tube containing the swabs into a tube format preferred by any validated lab that has excess capacity, enabling a massive scaling of the country’s existing testing infrastructure. With logistics support to bring pooled samples to regional labs, schools across America could use pooled testing as part of their public health response to COVID-19.

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