The COVID-19 pandemic resulted in a significant expansion of infectious diseases testing technology.1  As of November 2021, the US Food and Drug Administration (FDA) has conferred emergency use authorization (EUA) to 269 commercial molecular assays, 27 laboratory-developed molecular tests, 40 antigen tests, and 90 tests for determining adaptive immune response. Despite this impressive number of tests, significant confusion remains regarding the performance and role of these tests among the public—confounding timely adoption and appropriate implementation.2,3  Antigen methods, for example, were largely panned early in the pandemic, prompting decreased demand.4,5  Since then, antigen testing has gained significant popularity to the point of exceeding supply chains as communities reopen and highly infectious SARS-CoV-2 variants spread across the world.6,7  This observation highlights the major COVID-19 pandemic problem of suboptimal deployment of testing resulting in inefficient use of resources and exacerbation of health care inequities.811  A significant driver of this problem has been the lack of well-thought-out education related to testing methods and best practices for employment.2,3  Not all testing is created the same, and there is a right time and place to use certain tests.

Molecular techniques serve as the mainstay for SARS-CoV-2 detection, with reverse transcription–polymerase chain reaction (RT-PCR) and its derivatives being the technique preferred by many clinical laboratories.12  These molecular approaches detect viral RNA and achieve sensitivity and specificity as high as >99% and 100%, respectively.13,14  Sequencing has also gained popularity with the emergence of the Delta variant (B.1.617.2) and related lineages (AY), as well as the new Omicron variant (B.1.529).15,16  However, it must be noted that not all molecular techniques achieve high sensitivity and specificity.17,18  Some early isothermal nucleic acid amplification methods exhibit decreased sensitivity, whereas institutions using alternative specimen types or specimen processing techniques may exhibit lower performance.1921  The ability to appropriately characterize assays has been further confounded by the lack of a true “gold standard” to define sensitivity and specificity.22  Other limitations for molecular approaches, especially high-throughput systems, include the need to perform testing in a laboratory setting where total turnaround times could range from 12 to 48 hours. Ultrafast point-of-care (POC) molecular methods exist; however, these rapid platforms often test only 1 sample at a time, are expensive, and reagents are severely constrained due to high demand.23 

Antigen-based detection of SARS-CoV-2 provides a unique alternative to molecular methods.24  Both POC and laboratory-based antigen testing platforms exist.25  Benefits for antigen testing include its inherent lower cost, rapid turnaround time, and accessibility compared with laboratory-based molecular methods. Antigen testing is often cheaper to manufacture at scale by using existing infrastructure to produce common commercially available immunoassays (eg, home pregnancy tests, Group A Strep testing).25,26  POC SARS-CoV-2 antigen testing solutions produce results within 15 to 20 minutes, providing an alternative to rapid molecular platforms. Most importantly, several antigen tests have received FDA EUA for over-the-counter use.1  This transformative authorization allows self-testing at home and improves accessibility to the community.27  Concerns remain with public health reporting and use for testing in high-risk settings, such as congregate settings, but these tests may serve as a convenient and cheaper alternative to screening testing in low-risk environments, such as schools.

Antigen testing performance varies by method and disease prevalence.28  For symptomatic patients, antigen testing achieves sensitivities ranging from 85% to 97%. Specificity approaches 100%.29  However, for asymptomatic testing, sensitivity decreases in most cases to about 74%.30  Because of this lower sensitivity, many POC antigen tests are only authorized for over-the-counter serial testing or single testing as part of a formal screening program.31  However, it is likely that detection is more accurate with higher viral loads, and thus may be a fairly good indicator of infectivity. This can provide some reassurance, especially in settings where other mitigation measures such as use of masking indoors are in place. At least 1 POC antigen test has received EUA for over-the-counter asymptomatic screening without requiring serial testing. This platform has a reported sensitivity of about 96% and specificity approaching 100%,32  but some kits have been recalled because of false positives.33  Interestingly, laboratory-based rapid antigen testing has also become available in recent months and provides the means to overcome the tradeoff between testing speed and throughput inherent with molecular platforms.34  Furthermore, home tests can also be performed in Clinical Laboratory Improvement Amendment–waived environments where there are shortages of professional kits, and they may help alleviate some concerns about public health reporting. Unfortunately, few laboratory-based antigen tests have received EUA despite showing performance that may be equal to or superior to POC methods.

In terms of best practices for SARS-CoV-2 testing, a fundamental element of laboratory medicine is to provide the right test at the right time. Reagent shortages and the desire to return to a prepandemic state resulted in a surge of innovative testing solutions.35  An “arms race” at academic institutions and corporations ensued to determine who would be the first to provide sustainable and cost-effective mass testing for the community.36  Most solutions focused on molecular approaches because these were an accepted standard but ignored alternatives because of these same assumptions. Thus, antigen testing use was very limited early in the pandemic, creating a missed opportunity in the United States.37  A second consideration was the federal government's initial distribution of rapid antigen tests to be used in high-risk settings, such as skilled nursing facilities and long-term care settings, which arguably was not the right setting given the high risk of spread to vulnerable patients and by health care workers. In some cases, suboptimal molecular approaches were implemented by sacrificing supply-constrained components to create a perception of providing testing capacity, but these PCR-based methods often performed no better than antigen approaches, or worse, in real-world practice.38,39 

As defined by the US Centers for Disease Control and Prevention, the use of antigen testing should factor in the pretest probability that a person is likely to have COVID-19 or not.24  Likewise, the serial testing method proposed by Mina et al40  should be embraced.37  Antigen testing is uniquely suited for this approach where asymptomatic individuals could be quickly screened once a day or every other day to great effect. Such programs have been implemented for schools in California.41  This serial testing approach contrasts with current “just in time” or once-a-week testing methods using slower molecular methods and allows a “test to stay” model that keeps students safe but with the understanding of the importance of keeping students in school. In the end, antigen testing provides a means to optimize the use of molecular testing but not replace high-performance molecular methods. There is a time and place for molecular and antigen testing, highlighting that a one-size-fits-all settings approach is a short-sighted one. By leveraging the strengths of each method, we can create a testing ecosystem that optimizes performance while ensuring testing remains accessible to all as we transition to living with COVID-19 in our society.

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Competing Interests

Tran and May are consultants for Roche Diagnostics and Roche Molecular Systems.