For emerging infectious diseases, reliable controls support QC efforts

Feb. 20, 2023

The spate of recent public health crises, beginning with COVID-19 and including the mpox outbreak that began last year, underscored the importance of quality control measures in clinical laboratory testing. In large outbreaks or pandemics, lab results have to be more than just accurate; they must facilitate useful comparisons across labs, states, and even countries.

Of all the factors that go into quality control and quality assurance in clinical laboratories, the most important might also be the most humble: control material. Reliable, high-quality controls make it possible to ensure accurate results, proper workflow procedures, and instrument performance. Without such controls, there can be little confidence in the outcome of any lab procedure.

Unfortunately, COVID-19 and mpox both illustrated the tremendous challenges in establishing access to high-quality controls for emerging infectious diseases or even new outbreaks of known diseases. In these situations, many clinical labs look to secure residual positive samples from other facilities to help in the development and validation of their own tests. But with so much simultaneous demand for these samples, they are notoriously difficult to acquire and typically cannot be relied upon for a steady supply of control material. In addition, positive samples can be infectious and increase the risk to lab technicians.

In new outbreaks, a better approach could come from synthetic molecular controls. These can be designed quickly and easily from the pathogen’s genome sequence, making it possible to start development as soon as the source of the outbreak is identified. Because they are synthetic, they can be manufactured in high volumes to provide a steady, reliable supply for testing.

The roles of controls

Before diving into the specific challenges seen with COVID-19 and mpox testing, it is worth a quick review of the various types of molecular controls and how they are used by clinical labs. In general, they can be broken down into three broad groups.

The first group, positive and negative controls, tends to be the most familiar. These controls are designed so they always deliver positive results (or always deliver negative results) in a correctly performed assay. Useful for a variety of QC checks throughout the testing process, these controls are essential in the analytical phase as test results are being generated.

The second and third groups of controls are intended to confirm processes more than results. Controls may be internal or external, exogenous or endogenous. These controls are often combined to give the best view of the entire testing workflow. For example, internal controls move with the sample for confirmation of how certain phases of the assay worked, while external controls are kept separate from the sample and are processed in parallel to reflect the performance of the entire workflow. Introducing controls very early — in some cases as soon as the initial sample is collected — can help increase confidence in all of the processes that contribute to each patient’s test results.

COVID-19 testing

By early 2020, the enormous challenges clinical laboratories would face in COVID-19 testing were already becoming clear. As cases spread around the world, labs in every country and state found themselves competing with each other for critical testing supplies, including control material. There were nowhere near enough residual positive samples to allow all labs to develop their own tests, and of course in the early days there were no commercially available alternatives.

As labs increasingly faced staffing shortages — due in part to sickness among workers and in part to social distancing requirements or lockdowns — the risk of using infectious positive samples as controls was pronounced. Few labs could afford to lose staff members even temporarily to COVID-19 infections as they raced to meet the demand for test results.

Beyond testing clinical samples, some labs were also testing wastewater samples to help with community surveillance efforts. Wastewater surveillance has been quite helpful in predicting new surges in cases, often indicating regional spikes in the SARS-CoV-2 virus days or weeks before test positivity rates begin to rise. But testing wastewater comes with its own challenges. The sample goes through so many processing steps to capture the tiny fraction of viral RNA in vast quantities of water, and many process controls are not robust enough to function properly from sample collection all the way through to analysis.

The release of synthetic molecular controls addressed challenges for testing both clinical samples and wastewater samples. “Armored” versions of these controls have a protective casing that allows them to be put through harsh processing steps without any loss of performance. Manufacturing of commercially available controls at scale helped ease the supply chain constraints experienced by so many laboratories early in the pandemic. Having synthetic alternatives to controls based on positive samples also made the workflow safer for technicians and helped to reduce the risk of on-the-job infection.

Mpox testing

Much like the early days of COVID-19, the start of the mpox outbreak last year revealed the testing limitations of clinical laboratories for an emerging disease. The first major outbreak outside of Africa, mpox came to continents and countries where labs had never needed to test for it.

Unlike COVID-19, though, the constraints for mpox testing lasted for months. New York City quickly became an epicenter of the outbreak in the United States. In a city filled with hospitals and clinical lab facilities, only 10 people could be tested per day well into the third month of the outbreak.1 Much of that testing bottleneck was created by the lack of reference materials and other critical assay components.

Testing capacity has improved significantly, for a number of reasons. Last summer, the U.S. Centers for Disease Control and Prevention teamed up with several commercial laboratories, a move that increased the number of tests that could be run each week across the country by ten-fold.2 Later, the U.S. Food & Drug Administration was permitted to issue emergency use authorizations, streamlining the process for commercially developed tests to reach clinical labs. Finally, companies began releasing synthetic molecular controls that could be used for mpox tests, which addressed supply constraints many labs had faced.

Rapid control development

Sadly, COVID-19 and mpox are not flukes. Public health experts have spent years warning about the rising incidence of infectious diseases, particularly those brought into the human population from animals. Changes in climate and habitat, among others, are bringing humans and wild animals into contact more than ever. Spillover pathogens are an inevitable consequence.

Whether it’s a new infectious disease like COVID-19, or an existing one that spreads to a new area like mpox, one thing is clear: clinical laboratories need every advantage to ramp up testing in the earliest stages of an outbreak. General surveillance and screening programs could help, as would faster adoption of emergency use authorization protocols in regulatory agencies.

Synthetic molecular controls have a contribution to make too. They can be designed as soon as a pathogen’s genome sequence is known, and they offer a safer and more accessible alternative to other molecular controls. They can be used as positive or negative controls as well as process controls to give laboratory teams increased confidence in their workflows and test results. Collectively, all of these measures could help labs respond more quickly to new infectious disease threats — and do so with reliable results thanks to careful quality control.


1. Otterman S. Monkeypox vaccine rollout is marred by glitches in New York. The New York Times. Published July 7, 2022. Accessed January 19, 2023.

2. ASPR Press Office. HHS orders additional vaccine, increases testing capacity to respond to monkeypox outbreak. US Department of Health and Human Services. Published July 15, 2022. Accessed January 19, 2023.