An Interesting New Angle On Environmental Testing for SARS-CoV-2

Author’s note: Full disclosure. I work in research for one of the world’s largest testing laboratories. In addition to providing Coronavirus testing services, they develop and manufacture (clinical and environmental) diagnostic tests for Coronavirus. This article was not written at their behest and the opinions expressed in it are my own and not necessarily shared by my employer.

In a recent article extolling the untapped potential of environmental testing for slowing the spread of COVID19 I described three main environmental sample types: surfaces, wastewater, and masks. While myself, and a few others, continue to proselytize for the value of environmental testing, judging by continued lackluster sales of environmental SARS-CoV-2 tests, the majority of industry and the scientific community seem to have given up on the approach. Moreover, judging by the meager 16 views my original piece managed to garner, the general public is also not exactly enthusiastic about it either.

I can understand the hesitance. The problem is that environmental testing’s greatest strength, the inability to tie a particular result to a particular person is also its greatest weakness.

One can always ask the question about any environmental test result, so what? What am I going to do with the information?

With a clinical diagnostic result you can point to the person or persons and say don’t come in to work for two weeks, go quarantine yourself and your family, do contact tracing, and on and on goes the list of possible tangible actions. If a breakroom table comes back positive from an environmental test and 60 people share that table over the course of a day, what does that mean for the 60 people who sat at it? Do they all need to be quarantined? Should they be tested? etc. To a certain extent that objection can be countered with smart sampling plans, but their is still a vagueness to the result which is frustrating for many even if it is full of possibilities. Mask testing would seem to obviate this problem as only one person wears a given mask over the course of a given day (presumably). Unfortunately even in this case one can always argue that, for example, it was the outside of the mask that was contaminated by someone else and not the wearer. This is a weak argument, but a real possibility, and it is one of the main reasons that mask testing does not fall under FDA regulatory scope and is not classified as a diagnostic test. Once a particular test is classified as diagnostic, it brings with it a host of validation/certification requirements on both the test and the testing laboratory that add significant cost and rule out the ability of non clinical certified (CLIA certified) labs to run the method.

When the idea of mask testing was first proposed their was great concern that it would be considered a diagnostic test and so the idea of mask pooling was born (see my earlier article linked above for much more on pooling). Sample pooling, combined with destruction of any remaining unpooled individual samples, results in a total inability to tie a particular result to a particular person (in the industry this is referred to as reflexing the test. After a pooled sample tests positive the retesting of each individual sample in the pool to identify the one or more positive samples is called a reflex) and like magic an environmental test is born. If mask pooling is an environmental test, following the same logic, what other sample types could be a potentially useful as pooled environmental tests? This brings us finally to the idea of pooled saliva testing. To re-emphasize testing saliva is a clinical diagnostic test, but testing pooled saliva (with the proviso that the individual samples cannot be tested following the pooled sample test so no individual can ever be linked to a particular result, i.e. cannot be reflexed) is an environmental test, or at least it would seem to be. It also would seem to be a particularly very useful test that, for example, employers could use to screen carefully designed pools of their employees and get them out of the workplace as soon as feasible with minimal disruption to their operations. A pool can be as small as two individuals but how large might it be?

This is where the promise of pooled saliva testing bumps up against the realities of SARS-CoV-2 diagnostic methods, mostly still RT-qPCR based. Saliva is a difficult matrix to work with for a host of reasons and can be particularly difficult for PCR and qPCR methods to handle. Enzymes are present in saliva that can interfere with the PCR reaction and/or destroy the intended viral target before it can be detected. Various stabilizers are often used in saliva sample collection and the samples need to go through a laborious and time consuming RNA purification/extraction scheme that requires expensive capital equipment and can limit throughput. For clinical labs this is no big deal as they already have the equipment and expertise to handle these extra steps since they do it all the time. Moreover, they have the inflated budgets and profit margins to absorb the additional costs incurred. Most labs doing environmental testing do not have that luxury. There have been some promising advances in research in this area and recent papers have been published describing various “direct” detection approaches. I am heavily involved in work in this area currently and can’t say much other than attempting to reproduce the results seen in the literature has not gone exactly as planned. (author’s note: more recent testing and additional published work have shown the feasibility of direct testing of saliva for SARS-CoV-2 with detectable viral RNA present even out to two weeks when stored at ambient temperature) The problem of detection sensitivity reduction inherent in pooled sample testing remains and will always limit the sample pool size to a certain extent. Fortunately since this testing does not fall under FDA regulatory scope the restriction of sample pools to five is not applicable and how large a given pool might be is only limited by our tolerance for the concomitant reductions in test sensitivity. It remains to be seen if pooled saliva testing has legs, but interest from industry has been high, and if we can solve the sample preparation problems and agree on a pooled sample test method detection sensitivity all can live with, it may be the first environmental test to get any serious traction.