July 23, 2020 / Bharat Chandramouli

RT-qPCR for Definitive COVID-19 Cleanliness Testing

Sponsored by SGS Galson.

The ongoing COVID-19 pandemic presents an unprecedented industrial hygiene challenge. With workplaces facing operational challenges after extended shutdowns, ensuring that reopened facilities can be disinfected effectively is critical. This blog post addresses the science and uncertainty around the presence of the SARS-CoV-2 virus on surfaces and describes the benefits of Reverse Transcriptase-quantitative Polymerase Chain Reaction (RT-qPCR) testing for ensuring post-disinfection safety.


RT-qPCR is a well-established technique to detect and quantitate RNA. It has been used widely for virus detection based on a virus’s characteristic RNA and is the basis of clinical testing for SARS-CoV-2 infection. RT-qPCR testing is typically based on the protocol and primers provided by the CDC for clinical testing. This ensures that all testing done by PCR, when done correctly and with the appropriate quality controls, can provide definitive answers on the presence of the virus, whether on surfaces, in sewage, or in air samples.

Testing for COVID-19 on Surfaces

The science on the prevalence and risk from COVID-19 on surfaces is still emerging. The CDC, in guidance updated June 16, 2020, states, “It may be possible that a person can get COVID-19 by touching a surface or object that has the virus on it and then touching their own mouth, nose, or possibly their eyes. This is not thought to be the main way the virus spreads, but we are still learning more about how this virus spreads.”

A recent study showed that viruses can spread easily from the point of infection across a building. Hence, cleaning and disinfection (especially of high-touch surfaces on an ongoing basis) and verification (especially after a known contact or source of infection) are critical parts of a risk-reduction protocol. While there are indirect measures of cleaning efficacy such as fluorescent markers, or ATP testing, the use of RT-qPCR in this type of testing is the most definitive statement on the effectiveness of COVID-19 disinfection. Testing of cleaning efficacy cannot certify a space as COVID-free, and it is best used as part of a comprehensive risk mitigation plan.

RT-qPCR Surface Testing

Figure 1: Schematic of a qPCR Surface Test

A typical qPCR test on surfaces is shown in Figure 1. Facility swabbing is performed after disinfection, based on a risk assessment of potential for transmission from a surface, and with adequate replicates to ensure coverage of cleaning. The swabs are inactivated and preserved in a viral transport medium and transported to a laboratory for testing. At the end of the process, the testing facility provides a positive or negative result on the presence of the virus.

qPCR samples have typically been transported back to a lab for analysis, with results available 2-3 days after testing. Field-based qPCR testing, such as the options available from SGS Galson, can shorten the response time between test and result to two hours, realizing the “real time” promise of PCR. Because these tests are based on the same parameters as laboratory tests, there are no compromises in quality from a well-designed field test.

Quality Considerations

Lab customers should be aware of the following considerations regarding RT-qPCR testing:

  • Reporting limit: Laboratories report to 5-10 genome units per reaction, which translates to 50-200 genome units per swab. A lower reporting limit means a greater chance of detection. However, it’s important to note that the minimum viral load for infection is unknown at the moment.
  • Stability: Lab-based tests can run into hold-time (sometimes 72 hours or less), especially as viral loads on surfaces are low and prone to degradation. Field tests, with immediate results, overcome this barrier.
  • False negatives: RT-qPCR reactions can be compromised by multiple interferences including humic acids, iron, and more. Therefore, testing is always done after cleaning and disinfection. The use of synthetic RNA as an internal control ensures that qPCR quality issues can be detected on the instrument, thereby avoiding false negatives.

To conclude, testing is only one part of risk reduction best practices, which include well-defined risk assessment and reduction plans, social distancing, use of barriers, frequent cleaning and disinfection, screening for symptoms, and more.

For further information on SGS Galson’s services, visit the company website.

Bharat Chandramouli

Bharat Chandramouli is a senior scientist with more than 20 years of experience in the occurrence, fate, and transport of persistent organic pollutants and contaminants of emerging concern.


Presence = Infection Potential?

I am curious to know if the mere presence of viral matter translates into the infection potential. Depending on the surface material, the viability of the virus will vary. So a positive test may not necessarily mean the virus will cause infection, correct?

By Lawrence Sloan on July 23, 2020 4:09pm

Add a Comment