Background
This webpage is intended to provide healthcare providers with an overview of SARS-CoV-2 tests authorized to diagnose current infection and to provide guidance for the use and interpretation of these tests. The LAC DPH Testing Guidelines and Resources page hosts local testing and laboratory information as well as testing recommendations. Consumer driven testing such as over the counter (OTC) and direct to consumer (DTC) SARS-CoV-2 testing SARS-CoV-2 is beyond the scope of this guidance.
Understanding Emergency Use Authorizations (EUA) and SARS-CoV-2 Tests
Only SARS-COV-2 tests with emergency use authorizations (EUAs) from the FDA should be used for patient care. A wide variety of molecular tests (more commonly referred to as nucleic acid amplification tests (NAAT)), antigen tests, and serologic tests have EUAs. The FDA SARS-COV-2 diagnostics EUA website lists all individual tests by test technology:
- Molecular diagnostic tests
- Antigen diagnostic tests
- Serology and other adaptive immune response tests.
With each individual test EUA, the FDA approves conditions of the authorization. Each test is approved for specific setting(s) (H, M, W for high complexity, moderate complexity, and waived CLIA laboratory settings and/or home testing) and with certain conditions of authorization. The conditions of each test’s authorization are listed in the “Attributes” column. For example, tests authorized for the screening of asymptomatic individuals without known exposure are listed with "screening" in the attribute column; pooling, multi-analyte, saliva, home collection, and home testing are similarly listed. Tests available without a prescription include the attribute "DTC" (for direct-to-consumer home collection tests) or "OTC" (for over-the-counter at-home tests). Each authorized test has at least three authorization documents: the Instructions for Use (IFU)/EUA summary, Healthcare Provider (HCP) Fact Sheets and Patient Fact Sheets.
Note: Regardless of FDA authorization, for the duration of the public health emergency, CMS has indicated all SARS-CoV-2 diagnostic tests can be used on asymptomatic people.
Accuracy of SARS-CoV-2 Tests
No tests give a 100% accurate result. Tests need to be evaluated to determine their sensitivity and specificity, ideally by comparison with a gold standard. For COVID-19, there is no clear-cut gold-standard which has made the evaluation of test accuracy more challenging. Clinical performance data is not required for an EUA.
Test accuracy is dependent on many factors including the test technology, specimen collection and handling, pre-test probability of disease, the timing of test, and the specific characteristics of the assay.
Clinicians should review the EUA documents for any SARS-CoV-2 test(s) they are using to understand the specific performance characteristics, attributes, the instructions for use, and how to interpret results. To facilitate accurate test results, they should follow all sample collection, storage, and transport instructions. If they are conducting the tests in a waived setting (i.e., POC tests), they must train staff conducting testing in laboratory best practices in addition to carefully following the instructions for use. See POC tests below. Patients undergoing testing should be given the EUA-approved Patient Fact Sheet.
Point of Care Tests
Many NAATs and the majority of antigen tests have been approved by the FDA for CLIA-waived testing at the point-of-care setting. This means that the point of care (POC) laboratory test can be performed at or near the place where a specimen is collected. Rapid POC tests provide results within minutes (depending on the tests).
Regulatory Requirements: A CLIA certificate is required for any facility conducting SARS-CoV-2 laboratory tests. A CLIA certificate of waiver is appropriate for POC SARS-CoV-2 tests. The CDPH Laboratory Field Services Branch website hosts information on applying for CLIA waivers, guidance on the operation of COVID-19 testing, and site specific Information for Physician Offices and Urgent Care Clinics.
For facilities performing only waived SARS-CoV-2 antigen tests, a temporary allowance has been made during the California emergency. Under this allowance, facilities may begin waived SARS-CoV-2 antigen testing as soon as they have submitted an application for a California Clinical Laboratory Registration and received acknowledgment of receipt. See CDPH Temporary Allowance for Waived SARS-CoV-2 Testing for more information.
Accuracy: POC tests conducted in a waived setting can have inaccurate results if not performed correctly and well. Facilities conducting POC tests must:
- closely follow the manufacturer's instructions for use
- observe best practices for handling and performing tests on infectious disease specimens
- fully train all staff engaged in sampling and test operations including training in good laboratory practices.
See CDC’s Ready? Set? Test! POC training resources.
Reporting: All positive test results from POC devices must be reported to Public Health. It is recommended that all non-positive results be reported, but not mandatory.
For more detailed information on POC testing see CDC Guidance for SARS-CoV-2 POC Testing.
Overview of SARS-COV-2 Test Types and Uses
Viral tests detect SARS-CoV-2 virus—they are used to diagnose current acute infection. There are two types of viral tests:
- Nucleic acid amplification tests (NAATs), also referred to as molecular tests.
- Antigen tests
See summary grid and discussion below.
Serologic tests detect antibodies—are used to detect previous infection with SARS-CoV-2 and can aid in the diagnosis of MIS-C. CDC does not recommend using antibody testing to diagnose current infection. See CDC Guidelines for COVID-19 Antibody Testing for more information.
Viral tests for SARS-CoV-2 can be used for both diagnostic and screening purposes. When choosing the type of test to use and when interpreting test results, it is important to consider the purpose of the testing (diagnostic or screening), the test performance characteristics (sensitivity and specificity), and the pre-test probability of infection.
Pretest probability is the likelihood that the person being tested actually has the infection. This likelihood is based on both the proportion of people in the test population or group who have the infection at a given time (prevalence) and the clinical presentation (including symptoms and known exposure) of the person being tested.
See “How does pre-test probability affect the predictive value of a test?” in the FAQs.
Diagnostic Testing
Diagnostic testing is performed when infection is suspected, such as when the person:
- has signs or symptoms consistent with COVID-19 or
- is asymptomatic but has had a recent known or suspected exposure to SARS-CoV-2.
Diagnostic testing for COVID-19 is used to identify infection in persons suspected of infection (based on symptoms or exposure) to help guide clinical and infection control decisions.
NAATs or antigen tests can be used for diagnostic testing. Negative results from less sensitive tests (e.g., antigen tests, some NAATs), should be considered presumptive and confirmed with a more sensitive laboratory-based NAAT test (e.g., RT-PCR, TMA) if important for clinical management or infection control decisions.
Screening Testing
Screening testing is performed on asymptomatic persons with no known or suspected exposure to SARS-CoV-2.
The rationale for screening is to try to identify persons with pre-symptomatic or asymptomatic SARS-CoV-2 infection in order to prevent additional spread of the virus.
NAATs or antigen tests can be used for screening testing.
Screening, when done serially in settings with highly vulnerable residents such as SNFs has been a useful additional infection control strategy in settings with frequent COVID-19 outbreaks and high levels of community transmission. With the advent of effective vaccines, the utility of screening testing is less clear and with low transmission rates, may result in a high number of false positive tests.
While currently available viral tests perform well when there is a high pre-test probability of infection, this is not the case when used for screening low risk persons in low prevalence settings. The interpretation of a positive viral test in an asymptomatic person with no known or suspected exposure is unclear, and when performed in a low prevalence setting, the likelihood that it is a false positive test is high.
Despite this, until more of the population is fully vaccinated and more is known about the emerging more infectious variants, screening in some settings is warranted. Current screening testing recommendations are primarily for persons who are not fully vaccinated in certain high-risk setting. With some exceptions, screening is not recommended for fully vaccinated persons. Persons who have recovered from laboratory confirmed COVID-19 within the past 90 days should not be included in screening testing programs. See LAC DPH Testing Guidelines for full local screening recommendations.
Organizations conducting screening testing should have a mechanism to confirm positive results when testing people unlikely to be infected. See interpretation of NAAT and antigen test sections below for more information.
SARS-CoV-2 Viral Tests
Summary Grid
| VIRAL TESTS | ||
|
Method |
Molecular Tests Amplify specific fragments of viral RNA using nucleic acid amplification
|
Antigen Tests Immunoassays that detect viral surface proteins |
|
Intended Use |
To detect current infection Many EUAs are for only diagnostic testing (in persons suspected of having COVID-19); some EUAs include screening. All are permitted for screening |
To detect current infection Most EUAs are for diagnostic testing (in persons suspected of having COVID-19-- within a range of days after onset of symptoms); some EUAs include screening. All are permitted for screening |
|
Type of sample* |
Nasopharyngeal (NP), oropharyngeal, or nasal swab; saliva; lower respiratory tract specimens | NP or nasal swab. |
|
Authorized for use at point of care (POC) |
Most are not, but some are. | Most are some are not. |
|
Test turn-around time |
Standard laboratory-based RT-PCR: < 48 hours
Rapid POC tests range from 15-45 min |
Range from 15-30 min |
|
Sensitivity |
Varies by test type, specific assay, and course of infection. Laboratory-based tests (e.g., RT-PCR) are considered the most sensitive POC tests are moderate to high sensitivity |
Varies depending on the specific assay and course of infection. Less sensitive compared to most NAATs. Generally moderate-to high sensitivity at times of peak viral load. |
|
Specificity |
High |
High |
|
Advantages |
Standard laboratory based NAATs are the most sensitive and specific test method available (RT-PCR; TMA) Short turn-around time for POC tests Confirmation of diagnostic test results usually not needed. |
Comparable performance to NAATs when testing symptomatic persons early in course of infection. Short turn-around time. Relatively simple to perform; lower cost/test |
|
Disadvantages |
Most are highly complex tests performed at laboratories. Longer turnaround time for lab-based tests (<48 hours). A positive NAAT diagnostic test is not recommended to be repeated within 90 days, since people continue to have detectable RNA after risk of transmission has passed. |
Less sensitive compared to NAATs. More false negatives when used for diagnostic testing. May need confirmatory testing. See Antigen Tests: Confirmatory Testing Recommendations. |
Discussion of Viral Tests
Nucleic Acid Amplification Tests (NAATs)
NAATs (also known as molecular tests) are the most accurate tests presently available for diagnosing current COVID-19. NAATs detect one or more viral ribonucleic acid (RNA) genes unique to the genetic sequence of the SARS-CoV-2 virus. The NAAT procedure works by first amplifying - or making many copies of - the virus's genetic material, if any is present in a person's specimen. Amplifying those nucleic acids enables NAATs to detect very small amounts of SARS-CoV-2 RNA in a specimen, making these tests highly sensitive for diagnosing COVID-19.
NAATs can use many different methods to amplify nucleic acids and detect the virus, including reverse-transcription polymerase chain reaction (RT-PCR) and isothermal amplification (e.g., transcription mediated amplification (TMA) and loop-mediated isothermal amplification (LAMP)).
Standard laboratory-based (moderate- and high-complexity) NAATs, such as RT-PCR are considered the “gold standard” method for diagnosing current infection. In addition, there are many different NAATs authorized to be conducted in the point-of-care (POC) setting under a Clinical Laboratory Improvement Amendments (CLIA) Certificate of Waiver and some with authorization to be performed at home or in non-healthcare settings.
The accuracy and predictive values of SARS-CoV-2 NAATs have not been systematically evaluated. In general, NAATs are considered very sensitive and specific, but there are differences in the limit of detection among the available assays.
To help compare the relative performance (sensitivity) of different commercial assays, the FDA is publishing comparative performance data of molecular tests against a standard reference panel. A systematic review conducted by the Infectious Disease Society of America (IDSA) found that rapid RT-PCR tests had a similar sensitivity to standard laboratory-based NAATs, while rapid isothermal NAATs were less sensitive. For this reason, the IDSA diagnostic testing guidelines recommend rapid RT-PCR or standard laboratory-based NAATs over rapid isothermal NAATs when testing symptomatic patients (note: Abbot ID NOW was the only available rapid isothermal NAAT available at the time). The sensitivity of NAATs is also dependent on many other factors including the timing of testing, the sampling technique, and sample type. While NAATs tests are considered to be very specific, they are less than 100% in real-world settings. IDSA guidelines report NAAT specificities ranging from 97%-99%.
A positive NAAT is not always direct evidence for the presence of virus capable of replicating or of being transmitted to others. For instance, NAATs may remain persistently positive after a person has recovered from a SARS-CoV-2 infection due to detection of non-viable RNA for prolonged periods.
Laboratory turn-around time (TAT) for standard laboratory-based NAAT results should be less than 48 hours; however, results can be delayed if laboratories are experiencing high volumes. Currently available POC NAATs' results have a TAT ranging from 15-45 minutes.
See FDA list of EUAs for Molecular Tests for more information on the performance and use of specific authorized test.
Interpretation of NAAT results:
When used for diagnostic purposes:
- A new* positive NAAT result generally confirms a SARS-CoV-2 infection. The patient is infected with the virus and presumed to be contagious.
*A positive test in an asymptomatic person within 3 months of a prior lab-confirmed COVID-19 infection likely represents detection of non-viable virus. - Negative NAATs should be interpreted in the context of the exposure history and clinical presentation of the person who was tested. A negative result means that SARS-CoV-2 RNA was not present in the specimen above the limit of the test’s detection. False-negative tests have been well documented, especially early in the course of infection (see Variation in False-Negative Rate of RT-PCR–Based SARS-CoV-2 Tests by Time Since Exposure).
Note: When there is a high clinical suspicion for SARS-CoV-2 infection or a moderate to high prevalence (10-40%) in the population, it is recommended that a negative test result from lower sensitivity NAAT be considered presumptive and be confirmed with a more sensitive laboratory-based NAAT test if important for clinical care or infection control purposes. See “What if I am concerned about a false negative NAAT”.
When used for screening purposes:
- A negative NAAT result indicates the patient was likely not infected with SARS-CoV-2 at the time of specimen collection. A negative result in a patient with a low pre-test probability of infection (e.g., asymptomatic without known or suspected exposures in a low prevalence setting) is more likely to be a true negative.
- A positive NAAT result indicates that SARS-CoV-2 virus was detected. If the result is new (no history of a positive test in the past 90 days), then the patient should be considered infected and infectious.
However, when screening asymptomatic persons with a low
pretest probability of infection, the positive
predictive value of the result decreases and the
likelihood of false positive increases. For this reason,
confirmatory testing is recommended for positive NAAT results in asymptomatic persons who have no known or suspected exposure when performed in a low prevalence setting.
Note: Screening testing is not recommended for fully vaccinated persons (with some exceptions) or those who have recovered from laboratory-confirmed COVID-19 within the past 90 days as long as they are asymptomatic. See LAC DPH SARS-CoV-2 Testing Guidelines.
See FAQs: “What if I am concerned about a false positive NAAT (molecular) result” and “How does pre-test probability affect the predictive value of a test?” below.
Confirmatory testing
Laboratory-based NAATs and some rapid NAATs can be used to confirm the results of lower sensitivity tests such as antigen tests, some POC NAATs, and over-the-counter (OTC) NAATs. Tests with lower limits of detection (LoD) as shown on the FDA's SARS-CoV-2 Reference Panel Comparative Data are considered to be more sensitive. Per the CDC, NAATs whose FDA authorization states they generate presumptive results are not recommended for confirmatory testing.
Confirmatory testing with a sensitive laboratory- based NAAT is recommended for negative results when there is a high pre-test probability of infection, especially if important for clinical management or infection control. See What if I am concerned about a result being a false negative result. Similarly, when asymptomatic patients with a low likelihood of infection screen positive for SARS-CoV-2 infection, confirmatory testing with a sensitive NAAT (laboratory-based NAATs or rapid NAATs) is recommended to minimize the harms of unnecessary isolation of the individual and quarantine of their contacts. See Testing FAQs pertaining to false positive antigen and NAAT results.
To optimize sensitivity, CDC recommends collecting nasopharyngeal, nasal mid-turbinate or anterior nasal swab specimens. Oral specimens (i.e., saliva) and home collection kits are not recommended for confirmatory testing.
In cases of discordant test results from different types of tests, results from laboratory based NAATs should be prioritized over POC or self-administered tests.
See FAQs below for more on confirmatory testing.
Cycle threshold (Ct) values
RT-PCR tests generate a number known as a cycle threshold (Ct) value. The Ct value refers to the number of PCR cycles required to amplify an assay’s targeted viral nucleic acid to a detectable level. Currently authorized RT-PCR tests for SARS-CoV-2 are qualitative assays, such that each assay generates a binary result of “positive” or “negative” based on a fixed cycle threshold. Specimens with lower amounts of virus require more cycles (a higher Ct value) to amplify viral RNA to reach the detection threshold while specimens containing a larger amount of viral RNA need fewer amplification cycles (a lower Ct value) to detect a positive result.
While there is a relationship between Ct values and the amount of virus in a patient specimen, it is not recommended they be used to infer viral load or patient infectiousness. There are many clinical and analytic variables that impact Ct values other than amount of viral RNA in a patient specimen and the current qualitative tests are not designed to provide an indication of viral load or infectivity.
In some instances, Ct values may provide information that assists in prioritizing or informing public health actions. For instance, samples with low CT values generally contain sufficient genetic material for whole genome sequencing (WGS) which can be used to assist public health variant surveillance or when there is a high suspicion of re-infection.
For more information see:
- Ct Values: What They Are and How They Can Be Used (APHL)
- The use of SARS-CoV-2 PCR cycle threshold (Ct) values for clinical decision-making (IDSA/Association for Molecular Pathology)
Antigen
Antigen tests detect the presence of SARS-CoV-2 viral surface proteins.
The main advantages of antigen tests are that results are available within 15-30 minutes, they are relatively simple to perform, and they are less expensive than NAATs. Most currently available EUA authorized SARS-CoV-2 antigen tests are all approved as POC tests for settings with a CLIA waiver. The intended for use of antigen tests is to evaluate symptomatic persons within 5-12 days of symptom onset (the number of days varies by manufacturer). See FDA’s list of EUAs for Antigen Tests.
In practice, antigen tests are being used more widely for diagnostic testing and for screening purposes outside their intended use. It is important that providers are aware of the limitations of these tests and that they use and interpret antigen test results based on the probability the patient has COVID-19 (pre-test probability). A summary of when confirmatory testing of antigen results is recommended is included below.
Limitations of Antigen Tests
False negative results: recently published reports as well as local experience has found that antigen tests in symptomatic persons are less sensitive than initially reported to the FDA. In addition, these tests have a much lower sensitivity when used to screen asymptomatic persons (~35-40%).
False positives: while the specificity of antigen tests is generally high, false positive antigen tests are known to occur when the manufacturer’s instructions for use are not followed correctly or if there are inadequate quality assurance procedures. False positives are also more likely to occur when testing persons with a low pre-test probability of infection (e.g., screening asymptomatic persons without risk factors). The FDA has issued an alert to healthcare providers regarding the potential for false-positive antigen results and steps to mitigate this risk.
Visit FAQs below for more on false positive antigen results.
Antigen test considerations for use
When used correctly, rapid antigen tests can help quickly identify patients early in the course of SARS-CoV-2 infection when viral load is highest and who pose the greatest risk of SARS-CoV-2 transmission to others. They perform best when there is a high pre-test probability of infection (e.g., symptoms consistent with COVID-19, recent exposure to a known case, and living/working in a setting where a high proportion of persons are infected).
Diagnostic testing
Antigen tests are useful as part of the evaluation of individuals with symptoms consistent with COVID-19 and/or those with a recent exposure to SARS-CoV-2. Positive antigen results are generally considered diagnostic of infection. Negative results in symptomatic persons are presumptive.
Facilities using antigen tests for diagnostic testing should have the ability to collect same day specimens for confirmatory NAAT testing of negative antigen test results.
Screening
When used for screening purposes, confirmation with a sensitive NAAT is recommended for persons who have a positive antigen test result. Negative screening tests generally do not need to be confirmed. See Confirmatory testing below.
Providers or facilities using antigen tests for screening should refer to their setting-specific protocols and be aware of the performance characteristics of these tests.
Confirmatory testing
Results should be interpreted in the context of risk of exposure to SARS-CoV-2 and prevalence of COVID-19 in the setting. To account for reduced antigen test accuracy, confirmatory testing with a more sensitive test (e.g., RT-PCR) is recommended after negative antigen test results in symptomatic persons and after positive antigen test results in asymptomatic persons without exposure, see below. See Testing FAQs; What if I am concerned about an antigen result being a false positive and What if I am concerned about a result being a false negative for more detailed information.
Note: Skilled nursing facilities and other congregate settings using antigen tests should follow their setting specific guidelines.
Antigen Tests: Confirmatory Testing Recommendations
Person with symptoms consistent with COVID-19
- If Positive – Confirmatory testing is generally not recommended*. The patient must isolate and provide quarantine instructions to their close contacts.
*Consider confirmatory testing if low clinical suspicion or low community prevalence. - If Negative – Presumptive negative, confirm with a laboratory-based NAAT (e.g., RT-PCR). The patient must isolate while awaiting the confirmatory RT-PCR test result. Provide patient with Information for Patients with Symptoms Who Have a Negative Antigen Test.
Asymptomatic person with known exposure in the past 14 days (e.g., a close contact to a known case or someone living/working in an outbreak setting)
- If Positive – Confirmatory testing is generally not recommended*. The patient must isolate and provide quarantine instructions to their close contacts.
*Consider confirmatory testing if there is lower pre-test probability of infection (e.g., a fully vaccinated non-household exposure) and/or to minimize unnecessary quarantine of their close contacts. - If Negative – Presumptive negative. Confirmatory testing may be needed if clinical judgment deems it important for patient management or infection control. The patient must continue to quarantine as instructed. If confirmatory testing is performed, a negative test does not release them from the required quarantine.
Asymptomatic person with no recent known exposure (e.g. screening)
Antigen tests perform poorly in asymptomatic persons with low risk of infection. If antigen tests were used for screening:
- If Positive – Confirmatory testing is recommended. The patient must be treated as a case and instructed to isolate while awaiting the
confirmatory result.
Note: if confirmatory testing is not performed, then the result is considered diagnostic and the patient must isolate and provide quarantine instructions to their close contacts. - If Negative – Confirmatory testing is not needed. The patient should be advised to continue all physical distancing and mask requirements.
Related References
Interpreting Viral Test Results-Key Points
- Interpreting the result of a viral test for COVID-19 depends on two things: the accuracy of the test and the pre-test probability
- Factors that increase the pre-test probability of infection include:
- Symptoms consistent with COVID-19
- Recent exposure to a person with COVID-19
- Living or working in a setting where a high proportion of persons are infected
- Not immunized against COVID-19
- Increased prevalence of infection among the group being tested
- When there is a high pre-test probability of infection, a positive viral test result generally rules in infection with COVID-19 but a negative result is less good for ruling out COVID-19. This is because viral tests have a high specificity but lower sensitivity.
- To account for reduced antigen test accuracy, confirmatory NAAT testing is recommended after negative antigen test results in symptomatic persons and positive antigen test results in asymptomatic persons without known exposure.
- Negative viral diagnostic tests for COVID-19 should always be interpreted in the context of the exposure history and clinical presentation.
- A single negative viral test should not be used to rule-out infection when there is a high probability of infection nor can it be used to release a confirmed case from isolation.
- A close contact cannot be released early from quarantine on the basis of a negative viral test.
- The likelihood of false positive viral tests is high when used for screening in low-risk individuals (e.g., fully vaccinated persons, those with no risk factors) in low prevalence settings.
Definitions
- Pretest probability: Probability of a patient having an infection before the test result is known; based on the proportion of people in a community with the disease at a given time (prevalence) and the clinical presentation of the patient.
- Negative predictive value: Probability that a patient who has a negative test result truly does not have the infection.
- Positive predictive Value: Probability that a patient who has a positive test result truly does have the infection.
Frequently Asked Questions
Negative SARS-CoV-2 viral test results should always be interpreted in the context of the patient’s exposure history and the clinical presentation of person being tested.
A negative viral test result in a patient with a high pre-test probability of infection has an increased likelihood of being a false negative. If there is strong clinical suspicion for COVID-19 (compatible symptoms and/or exposure), and a patient has a negative viral test result, the patient should continue isolation and be managed as a presumed positive.
When using lower sensitivity assays (e.g. antigen tests and some NAATs), negative results are considered presumptive and confirmation with a sensitive laboratory-based NAAT (e.g., RT-PCR) is recommended, especially if important for clinical management or infection control. If the initial negative test was a RT-PCR, consider repeating the test to confirm infection.
- To optimize sensitivity, CDC recommends the use of specimens that are considered optimal for detection (e.g., nasopharyngeal, nasal mid-turbinate, and anterior nasal swab). Oral specimens (i.e., saliva) are not recommended for confirmatory testing.
Negative test results when there is a low pre-test probability of infection have a high negative predictive value and are likely to be true.
Reminder:
- A close contact cannot be released early from quarantine on the basis of negative viral test(s).
Any patient with a positive antigen test for COVID-19 should be treated as a case and isolated.
False positives antigen tests are known to occur when instructions for use are not followed correctly or if there are inadequate quality assurance procedures. False positives are also more likely to occur when testing persons with low probability of infection (e.g., screening low-risk persons).
Positive antigen tests when used as screening tests should be confirmed with a NAAT.
If a false positive antigen test result is suspected, then a confirmatory NAAT test is recommended. Note: confirmatory NAAT testing is not recommended in situations where there a high pre-test probability of infection (e.g., COVID-19 is clinically suspected, they are a household close contact, they live or work in a setting with an outbreak, especially if not fully vaccinated).
If confirmatory testing is pursued, the person must remain isolated until the result of the NAAT test is available. The following can be used to rule out current infection (provided the person does not develop symptoms consistent with COVID-19):
A single negative result from a sensitive NAAT* within ~48 hours of the initial collection.
*This includes laboratory-based NAATs (e.g., RT-PCR) or rapid PCR tests. For information on assay sensitivity, refer to FDA SARS-CoV-2 Reference Panel Comparative Data.
- If the confirmatory test is positive, then the person is confirmed positive, and they must stay in isolation for the full 10 days.
Any new* positive NAAT (molecular test) for COVID-19 should be considered true, treated as a case, and isolated per guidelines.
*A repeat positive NAAT within 3 months of recovery from a confirmed SARS-CoV-2 infection in the absence of symptoms likely represents persistent shedding of non-viable viral RNA. See Patients with a History of Recent Recovery from COVID-19.
False positive NAAT results can occur when instructions for use are not followed correctly or if there are inadequate quality assurance procedures. These are more likely to occur when done outside a laboratory such as POC tests and home test kits. Even with their very high specificity, false positive laboratory based NAATs are possible, particularly when testing persons with a low pre-test probability of infection (e.g., screening asymptomatic persons with no known exposure in low prevalence settings).
If there is a low pre-test probability of infection (e.g., the patient is asymptomatic with no known or suspected exposures to COVID-19 and is fully vaccinated or in a low prevalence setting) then confirmatory testing is recommended. In these situations, the person must remain isolated until the result of the confirmatory test is available. The following can be used to rule out current infection (provided the person does not develop symptoms consistent with COVID-19):
- A single result from a sensitive NAAT*
within ~48 hours of the initial collection.
*This includes laboratory-based NAATs (e.g., RT-PCR) or rapid PCR tests. For information on assay sensitivity, refer to FDA SARS-CoV-2 Reference Panel Comparative Data.
Note: skilled nursing facilities and high-risk congregate residential settings should follow their site-specific protocols regarding confirmatory testing and discontinuing isolation.
- If the confirmatory test is positive, then the person is confirmed positive and they must stay in isolation for the full 10 days.
When false-positive tests are suspected, CDC recommends that facilities should review and gather the following information:
- Review the FDA EUA and instructions for use of the point-of-care test to ensure correct use. For instance, the use of viral transport medium has been shown to produce false-positive results and should not be used for some antigen platforms (including BD Veritor and Quidel Sofia platforms).
- Review recent control results to ensure accuracy of the POC test machine. If able, perform procedural quality control tests to ensure correct operation of the machine.
- Compare the percent positivity of the samples that were run that day (or week) to their previous percent positivity (e.g., the rolling 7-day average percent positive). Identifying many positives in one day might indicate an issue with the test results (either due to operator error or test supplies).
- Consider the pre-test probability of disease. Testing in low-prevalence populations with antigen or NAAT tests might produce false positives.
A low pretest probability has a high negative predictive value but a lower positive predictive value. This means there is an increased likelihood of true negatives and false positives.
A high pretest probability has high positive predictive value and a low negative predictive value. This means there is an increased likelihood of true positives and false negatives.
For instance, if testing a population with a COVID-19 prevalence of <1% (e.g., screening asymptomatic persons who are not fully vaccinated) with a single test with 99% specificity, the positive predictive value (probability that a positive test is a true-positive) could be <40%. If the prevalence is >10% (e.g., testing asymptomatic persons who are not fully vaccinated as part of an outbreak response) with that same test with 99% specificity, the positive predictive value may be >90%.
See CDC interpreting test results.
