Determining actual COVID-19 incidence rates requires a sensitive screening procedure

It is axiomatic that decisions relating to opening up the economy and relaxation of mitigations in the current COVID-19 era and assessing the effectiveness of preventive measures should be based on real-time evaluation of the incidence rate of the infection. By definition, incidence is the number of new cases in a population identified within a specific time period.

Questions have arisen as to the sensitivity and specificity of some new rapid tests approved by the FDA under an emergency use authorization. Most kits rely on immuno-based technology to detect viral protein (antigens) produced by the RdRp and N-genes from SARS-CoV-2 virus responsible for COVID-19. However, these two genes are conserved in all coronaviruses and may detect viral proteins from coronaviruses, which can cause the common cold. In addition, the presence of these viral proteins may not indicate that the virus is still alive and, therefore, a positive test does not indicate the person is still spreading live virus.

The intended use of rapid antigen assays is to quickly screen large numbers of individuals in the community for the presence of virus. Effective suppression of COVID-19 requires that infected individuals should be quarantined, and contacts should be traced. Swabs for testing can be taken from nasal passages, nasopharynx and throat. These newer tests have the advantages of results in five to 15 minutes and compactness with respect to equipment and are deployable at any site, which obviates the need to submit specimens to a remote diagnostic laboratory. The high-throughput (RealTIME® rt-PCR assay) batch tests for the presence of viral genetic material. This testing platforming must be performed at a remote lab and can run hundreds of tests at a time, but it takes several hours and two days for the results to be sent back to the patient. In contrast, the newer test platforms use a bench-top instrument, which can be run at physician offices and urgent care clinics. The platform is typically used to run tests for other respiratory illnesses—such as the flu, strep and RSV—and similarly uses samples from throat and nasal swabs.

During the first few months of the COVID-19 outbreak, antigen tests were in short supply. Health care providers restricted their use to those presenting with symptoms consistent with the infection, especially in patients not demonstrating positive influenza assays. With the realization that asymptomatic carriers are responsible for dissemination of virus, possibly with an R0 (transmission rate of one person to others) of two or more, infections can spread quickly when susceptible individuals are in close proximity to either symptomatic or asymptomatic carriers. The “super spreader” situation is evidenced by cruise ships, mass gathering, nursing homes, prisons and, more recently, in meat packing plants where infection rates of 25 to 50 percent have been recorded. It is interesting to note that 80 percent of cruise passengers, which debarked from ships harboring passenger with clinical COVID19 disease, tested positive using these early tests even though they never showed any clinical signs of the disease. These results questioned the accuracy of the tests.

Any diagnostic test has two major characteristics that define whether it is suitable for a given application: sensitivity and specificity. Sensitivity is the ability to detect the pathogen of interest. Tests with low sensitivity provide false negative results. Tests with high sensitivity should detect most if not all infected individuals. Specificity is the ability of a test to distinguish between related pathogens. A test with low specificity may not be able to distinguish between the SARS-CoV-2 virus and an unrelated coronavirus. Assay procedures with low specificity will yield a high number of false positives. In contrast, high specificity presumes that the test can successfully identify the pathogen of interest to the exclusion of related or even unrelated disease-causing organisms.

In contrast to the data generated by some test manufacturing companies, studies of patients at hospitals determined that some of these new rapid antigen tests have demonstrated low sensitivity, generating an unacceptable level of false negative results. Some of these assays have been used extensively in screening programs despite the fact that respected health care organizations have abandon their deployment. Some pharmacies are using these rapid antigen tests for mass screening and, in some cases, hospitals are verifying negative results in patients with clinical symptoms using more specific secondary assays including the RealTIME® rt-PCR assay.

Patient literature provided with the newer rapid antigen tests notes “that in the event of a positive test result in a person with clinical symptoms it is very likely that you have COVID-19.” Their literature also states that “a negative test means that the SARS-CoV-2 virus proteins were not found in the sample.”  However, they acknowledge the possibility of false negatives in the statement, “This means that you could possibly still be infected with the SARS-CoV-2 virus even though the test is negative.” Persons presenting with COVID19 like symptoms or exposed to a person with COVID19 should check with their physician using telemedical conferences to determine the best type of testing for each patient. If the test is one of the newer antigen tests and it renders a negative result, they might want to consider a second test that uses a more accurate RealTIME® rt-PCR assay.

Extensive deployment of these new rapid antigen tests may be underestimating the true prevalence of COVID-19 in specific populations. Accurate RealTIME® rt-PCR assay results are important when making decisions as to whether businesses, recreation parks, schools, etc., should be closed and whether preventive procedures should be intensified. Accepting the low sensitivity of antigen tests may still play an important role in the rapid screening of confined populations such as in prisons, nursing homes and daily testing of professional athletes. Obviously, clinicians in hospitals must be guided by clinical presentation in patients and submit questionable results to their diagnostic laboratories for validation using more sensitive and specific RealTIME® rt-PCR assays to accurately determine a diagnosis to guide in the selection of treatment options.

About Joseph Giambrone:

Joseph Giambrone is a professor emeritus in Auburn University’s Department of Poultry Science with a joint appointment in the Department of Pathobiology in the College of Veterinary Medicine. During his graduate research career at the University of Delaware, he was part of a research group that developed the first vaccine against an antigenic variant of an avian coronavirus. During a sabbatical leave during his tenure at Auburn, he was part of a research group in Australia that sequenced the entire genome of antigenic variant of a coronavirus of chickens. During his 42-year research career as a molecular virologist, immunologist and epidemiologist, he has made critical advancements in understanding the ecology of viral pathogens, led efforts to improve detection and surveillance of viral diseases and developed new and effective vaccines and vaccine strategies to protect commercially reared chickens as well as pathogens, such as avian influenza viruses, which have spilled over into human populations. His research has had a profound impact on practices used today to reduce the incidence and severity of viral diseases of commercially reared poultry as well in human populations.