SARS-CoV-2 Diagnostics FAQ

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SARS-CoV-2 Diagnostics FAQ

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Last reviewed: May 24, 2022

Featured FAQs

Q: Do rapid tests work as well against the Omicron variant?

A: Yes. Several studies have now shown that analytic sensitivity of most rapid antigen tests against the Omicron variant is stable when tests are used in an approved manner. Read more about Omicron subvariants' impact on diagnostic performance on our Variants page.


Q: What is a cycle threshold value and can it be used to assess for contagiousness?

A: SARS-CoV-2 RT-PCR tests amplify viral RNA in a cyclic fashion. When the amount of fluorescence generated by the reaction crosses a predetermined threshold, the instrument declares the test positive, and the number of cycles it takes to reach that threshold is called the cycle threshold value. The lower the value, the greater the amount of viral RNA present in the original sample and vice versa. This information has been helpful from an infection control standpoint as there is an indirect correlation between Ct values and viral culture positivity, which is a widespread indicator for contagiousness. A person whose test has a low Ct value suggests a high burden of virus in the sample and is more worrisome for contagiousness than a test with a high Ct value. However, there are a number of caveats to this. First, a Ct value gives you the least amount of virus possibly present in a sample. A person may have more than what was collected in the specimen due to poor sampling, inefficient amplification or because they are early in infection. Furthermore, there are no standardized values for what constitutes ‘low,’ ‘medium’ or ‘high’ Ct values; therefore, it is possible that the cutoffs used may lead to misclassification of noncontagious patients.

The clinical use of Ct values is not approved by the Infectious Diseases Society of America or the Association for Molecular Pathology because they are also subject to numerous sources of variation (IDSA & AMP, March 2021 [PDF]). These include systematic bias between PCR platforms and even within a single platform, variability across sampling sites such as the anterior nares versus the nasopharynx, and variability in the methods by which instruments set thresholds and detect changes in fluorescence. Thus, a Ct value of 23 obtained from a PCR platform in one lab is not comparable to Ct value of 23 obtained from instruments at another lab or even different instruments in the same lab. Consultation with a clinical microbiologist or infectious diseases physician is recommended prior to making clinical decisions using Ct values.


Interpreting Results

Q: What should clinicians know about the reliability of at-home COVID-19 tests and the possibility of false-positive or false-negative results?

A: Test interpretation is highly dependent on an individual’s pretest probability for infection. A negative test in someone with symptoms or a known exposure may represent a false negative, and a positive test in someone with no symptoms and no known exposures may represent a false positive. Tests should be repeated in each of these instances. Conversely, a single positive test in a person with high pretest probability for infection confirms infection and should trigger appropriate initiation of treatments and infection control measures.

Q: My patient is asymptomatic and has no known exposures, but he/she has a positive COVID-19 rapid antigen test. Could it be a false positive?

A: It is not possible to distinguish a false positive or false negative from a single COVID-19 test without additional information. For patients with low pretest probability of infection with a positive test, the best course of action is to repeat the test in 24 to 48 hours, ideally using RT-PCR, and if it is positive on both, then it likely represents true infection. If negative, the antigen test may be a false positive, but a second negative follow-up test 24 hours later may provide further assurance that the initial test was falsely positive. As the person is at low pretest probability for infection to begin with, they do not necessarily need to isolate while waiting for confirmatory test results to return.


Test Timing

Q: How soon after exposure should patients test? For how long does a positive test indicate active infection?

A: Clinical sensitivity is the likelihood that someone with active infection has a positive test; positive predictive value is the likelihood someone with a positive test has active infection. RT- PCR tests have the highest sensitivity for detecting SARS-CoV-2, but because detection does not always indicate active infection, their positive predictive value decreases the farther an individual is from the time they were infected. Active infection refers to the time period where the virus is replicating, and the person is potentially contagious to others, which typically occurs days 2 to 5 post infection.

Q: Does a negative antigen test rule out infection or mean a patient cannot be contagious?

A: If a person has symptoms or suspects they have infection, a negative antigen test does not rule out the possibility they could be infected and contagious. The test may have been taken at a point when not enough virus was present to reach the limit of detection or be due to sampling error. In general, antigen tests turn positive ~1 day later than PCR tests but turn negative faster after infection has resolved, reflecting the fact that it takes more virus present for a rapid test to turn positive. There is a positive correlation between a true positive antigen test and contagiousness, but the relationship is complex. The likelihood a person transmits to another person depends not only on the amount of live virus but also its inherent transmissibility, the amount of exposure time, ventilation, the use of masks and vaccination status.



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