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What the Latest Data—Including Presentations From CROI 2022—Teach Us About SARS-CoV-2 Testing

Megan Coffee, MD, PhD (DPhil)

Clinical Assistant Professor of Medicine
Division of Infectious Diseases and Immunology
New York University School of Medicine
Infectious Disease Doctor
Bellevue Hospital
New York, New York


Megan Coffee, MD, PhD, has no relevant conflicts of interest to report.


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Released: June 2, 2022

COVID-19 continues its spread, and as restrictions are easing, more respiratory viruses are spreading alongside SARS-CoV-2, emphasizing the need to differentiate COVID-19 from other viral infections. In addition, although home testing for SARS-CoV-2 has improved convenience, it has decreased our ability to track community spread. As new variants emerge, the disease forecast remains uncertain.

For these reasons, accurate community risk tracking is required, highlighting our need to understand the details of SARS-CoV-2 testing. In this commentary, I discuss the most recent data presented at the 2022 Conference on Retroviruses and Opportunistic Infections (CROI) and elsewhere and what it has taught us about SARS-CoV-2 testing.

Rapid Tests Can Be Negative in the First Few Days of Symptoms
Negative rapid COVID-19 tests during the first 2 days of symptoms can give a false sense of security, especially for pregathering testing. Meiners and colleagues showed a decrease in rapid antigen test sensitivity among symptomatic healthcare employees despite a rise in median viral SARS-CoV-2 RNA concentrations early in their infection course. The authors hypothesize that this was because of increasing immunity thanks to previous infections and vaccination and not because of the properties of the omicron variant.

Tests Can Remain Positive for Longer
Many cases, including post vaccine and post booster, will test positive for COVID-19 even beyond the CDC-recommended 5 days of isolation or beyond the 10-day precautionary period (which includes isolation for 5 days followed by masking for 5 days). The timing when positive results are seen varies but can be longer with omicron vs other variants.

Rapid antigen tests are increasingly used as a marker of infectiousness to guide isolation of individuals who continue to test positive; these rapid tests become negative as viral shedding drops, whereas reverse transcription polymerase chain reaction (PCR) tests can persist as positive even when viral shedding is low. 

Optimization of testing strategies remains a moving target, especially if new variants arise or changes in transmission rates alter testing priorities. Sy and colleagues presented data at CROI 2022 suggesting that there is often a trade-off between testing effectiveness and efficiency. In the modeling groups assessed in the study, a bigger impact (ie, prevention of infections) was made with increased test frequency, but efficiency, defined as the number of tests needed to prevent one infection, was linked with lower testing frequency.

Testing to Identify COVID-19 Rebound
More options are available to prevent severe COVID-19 disease, like nirmatrelvir plus ritonavir (RTV), an oral antiviral therapy for COVID-19. With increased nirmatrelvir plus RTV use, COVID-19 rebound has emerged and is more common than initially described, especially with omicron variants. In such cases, COVID-19 symptoms may return after completion of antiviral therapy, resolution of symptoms, and testing negative. SARS-CoV-2 transmission has also been reported after COVID-19 rebound. Fortunately, the development of viral resistance to nirmatrelvir plus RTV has not been found.

Home-based COVID-19 testing by patients has helped closely track COVID-19 rebound and has helped patients guide their self-isolation to protect their families, coworkers, and others. But how often and for how long patients should test after completing their course of nirmatrelvir plus RTV remains unanswered, as does the impact on SARS-CoV-2 transmission on a larger scale. Currently, the CDC recommends masking for 10 days after rebound symptoms start, but additional data are needed to answer these questions.

Ensuring Testing Equity
COVID-19 is a global disease, and its continued threat is an ongoing reminder of the consequence of communicable disease. Unfortunately, inequities have been observed in the response to COVID-19 management, including global vaccine roll out, the availability of treatment/prevention options, and testing resources. A lack of COVID-19 testing may result in the underreporting of the true impact of the disease in the general population and in high-risk groups (eg, pregnant women).

The quantification of real-world performance of rapid tests in resource-limited settings is critical to optimize patient care and epidemiologic planning. At CROI 2022, Goga and colleagues showed data comparing PCR-based testing with rapid point-of-care antigen tests performed on patients presenting with acute COVID-19 symptoms (N = 1696) at public health clinics in 3 provinces in South Africa. Although more practical, rapid antigen test sensitivities ranged from 35% to 68% and varied with days since symptom onset and the test used. Rapid test performance was best at a median of 3 days from symptom onset.

New Options in Sampling
Nasopharyngeal swab (NPS) testing has its limitations; it can be uncomfortable and difficult to use with children. Simple nasal, throat, and oral swabs may be alternative options to improve comfort. At CROI 2022, Moraleda and colleagues tested 1174 symptomatic children who presented at 10 hospitals in Spain. Three samples/patient were collected: 1) oral saliva swab for the PCR test, 2) NPS for PCR, and 3) NPS for rapid antigen test. The authors found that oral saliva samples could be effectively used for PCR testing in children, displaying more accurate results vs rapid antigen tests.

Exhaled breath tests may also simplify testing and better quantify the risk of contagiousness. One such test is a portable sampler for a PCR assay. It provides direct quantification of viral shedding by sampling people using a 1-minute breathing protocol. Earlier reporting of negative results vs other tests (eg, PCR and antigen tests) was observed and is hypothesized to mark the end of infectiousness.

Nontraditional testing is another area of research. Kantele and colleagues showed that scent dogs effectively detect COVID-19 in airports and stadiums but require continuing education to recognize new variants.

Your Thoughts?
In your practice, which new data about SARS-CoV-2 testing do you find most helpful when diagnosing patients with COVID-19? Answer the polling question and join the conversation by posting a comment.

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