INTRODUCTION — At the end of 2019, a novel coronavirus now known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as the cause of a cluster of pneumonia cases in Wuhan, a city in the Hubei Province of China. It rapidly spread, resulting in a global pandemic. In February 2020, the World Health Organization (WHO) named the disease COVID-19, which stands for coronavirus disease 2019 [1].
Guidance has been issued by public health and other expert organizations throughout the world, including the WHO and the United States Centers for Disease Control and Prevention (CDC) [2,3]. Links to these and other related society guidelines are found elsewhere. (See 'Society guideline links' below.)
This topic will discuss the diagnosis of COVID-19. The clinical features, epidemiology, virology, and prevention of COVID-19 are discussed elsewhere. (See "COVID-19: Clinical features" and "COVID-19: Epidemiology, virology, and prevention".)
The management of COVID-19 is also discussed in detail elsewhere:
●(See "COVID-19: Evaluation of adults with acute illness in the outpatient setting" and "COVID-19: Management of adults with acute illness in the outpatient setting".)
●(See "COVID-19: Management in hospitalized adults".)
●(See "COVID-19: Infection prevention for persons with SARS-CoV-2 infection".)
In addition, please refer to our COVID-19 homepage to view the complete list of UpToDate COVID-19 topics.
DIAGNOSTIC APPROACH
Clinical suspicion — The possibility of COVID-19 should be considered in anyone with new-onset fever and/or respiratory symptoms. Although cough and dyspnea are considered the classic respiratory features of COVID-19, other respiratory symptoms such as sore throat, rhinorrhea, and nasal congestion are commonly reported and are frequently the sole presenting symptoms of COVID-19. Other common clinical manifestations include smell or taste disturbances, myalgias, and diarrhea (table 1). COVID-19 should also be considered in patients with severe lower respiratory tract illness without another clear cause. (See "COVID-19: Clinical features", section on 'Initial presentation'.)
As SARS-CoV-2 is prevalent worldwide, clinicians should have a low threshold for suspicion of COVID-19. The threshold for suspicion should be particularly low if the individual resides in or has traveled to locations with high rates of community transmission, has had potential exposure to SARS-CoV-2 in an outbreak setting or as a close contact of someone with confirmed or suspected infection, or resides in a congregate setting.
There are no specific clinical features that can reliably distinguish COVID-19 from other viral respiratory infections [4]. Nevertheless, some features may warrant a higher level of clinical suspicion [5-7]. Several studies have suggested that loss of taste and loss of smell are the symptoms most strongly associated with a positive SARS-CoV-2 test [6,8,9]. Development of dyspnea several days after the onset of initial symptoms is also suggestive of COVID-19 [5]. However, none of these findings definitively establish the diagnosis of COVID-19 without microbiologic testing.
COVID-19 should also be a diagnostic consideration in patients who present with extrapulmonary complications that have been associated with SARS-CoV-2 infection, including cardiac injury, ischemic stroke and other thromboembolic events, and inflammatory complications (eg, the multisystem inflammatory syndrome in children). (See "COVID-19: Clinical features", section on 'Acute course and complications'.)
Whom to test
Symptomatic patients — If possible, all symptomatic patients with suspected infection (see 'Clinical suspicion' above) should undergo testing; the diagnosis cannot be definitively made without microbiologic testing.
However, in some resource-limited settings, limited capacity may preclude testing all patients with suspected COVID-19. Local health departments may have specific criteria for testing. The Infectious Diseases Society of America (IDSA) has suggested priorities for testing when testing capacity is limited (table 2); high-priority individuals include hospitalized patients (especially critically ill patients with unexplained respiratory illness) and symptomatic individuals who are health care workers or first responders, work or reside in congregate living settings, or have risk factors for severe disease [10].
The European Centre for Disease Prevention and Control has also suggested testing strategies when testing resources are limited.
Testing criteria suggested by the World Health Organization (WHO) can be found in its technical guidance online.
Selected asymptomatic individuals — Testing certain asymptomatic individuals may also be important for public health or infection control purposes, particularly when community transmission rates are high.
●The primary reason to test an asymptomatic individual:
•Following close contact with an individual with COVID-19 (this includes neonates born to mothers with COVID-19). The time to detectable ribonucleic acid (RNA) following exposure is unknown, so the optimal time to test for COVID-19 following exposure is uncertain. The Centers for Disease Control and Prevention (CDC) recommends testing once five days have passed since the last exposure [11]; we typically test five to seven days post-exposure.
●Other potential reasons for screening for SARS-CoV-2 infection include:
•Early identification of infection in congregate living facilities that house individuals at risk for severe disease (eg, long-term care facilities, correctional and detention facilities, homeless shelters). This includes testing in response to identified COVID-19 cases within the facility as well as intermittent screening of employees and residents.
•Screening hospitalized patients, prior to surgical or aerosol-generating procedures, particularly at locations where prevalence is high (eg, ≥10 percent polymerase chain reaction [PCR] positivity in the community).
•Prior to receiving immunosuppressive therapy (including prior to transplantation) [12,13]. (See "COVID-19: Issues related to solid organ transplantation", section on 'Pretransplantation screening'.)
●When to avoid testing in asymptomatic individuals – In the United States, the CDC suggests not testing for new infection in asymptomatic individuals who were previously diagnosed with SARS-CoV-2 within the prior month. A nucleic acid amplification test (NAAT), specifically, should be avoided in individuals who have had SARS-CoV-2 infection within the prior three months because of the low likelihood that a repeat positive NAAT during this interval represents an active reinfection. (See 'Persistent or recurrent positive NAAT during convalescence' below.)
Testing selected individuals with a known diagnosis of SARS-CoV-2 infection to determine precautions is discussed elsewhere. (See "COVID-19: Infection prevention for persons with SARS-CoV-2 infection", section on 'Duration and subsequent precautions'.)
Choosing an initial diagnostic test — A viral test is necessary to make the diagnosis of SARS-CoV-2 infection: either an NAAT, most commonly a reverse-transcription polymerase chain reaction (RT-PCR) assay, or an antigen test (table 3).
In general, we suggest NAAT, if readily available with reasonable turnaround time (eg, within 24 to 48 hours), because of its superior sensitivity. NAATs are usually performed at a laboratory. Rapid RT-PCR tests that can be performed at the point-of-care are also available and appear to perform comparably to standard laboratory-based NAAT; rapid isothermal tests may be less sensitive than other rapid NAAT [12]. (See 'NAAT (including RT-PCR)' below.)
However, antigen tests are more accessible, more convenient, and less costly than NAAT and have a shorter turnaround time than laboratory-based NAAT. Thus, they are reasonably used more commonly than NAAT for testing at home and at point-of-care sites. Individuals who use antigen testing should be aware that the sensitivity is lower than that of NAATs and negative antigen tests performed for symptoms or recent exposure generally warrant confirmation with additional testing (algorithm 1). (See 'Antigen testing' below.)
Antigen tests are also preferable to NAAT for individuals who had recently (ie, in the prior three months) tested positive for SARS-CoV-2 and have indications for repeat testing (eg, new symptoms); in the few months following infection, a positive NAAT may be more likely to reflect prolonged viral RNA shedding than a new infection, but it cannot distinguish between the two. (See 'Persistent or recurrent positive NAAT during convalescence' below.)
Specimen collection — Upper respiratory samples are the primary specimens for SARS-CoV-2 viral tests.
●Specimens for NAAT – In the United States, the CDC recommends collection of one of the following specimens [14]:
•Nasopharyngeal swab specimen, collected by a health care professional
•Nasal swab specimen from both anterior nares, collected by a health care professional or by the patient on-site or at home (using a flocked or spun polyester swab)
•Nasal mid-turbinate swab, collected by a health care professional or by the patient supervised on-site (using a flocked taper swab)
•Nasal or nasopharyngeal wash/aspirate, collected by a health care professional
•Oropharyngeal swab specimen, collected by a health care professional
•Saliva specimen (1 to 5 mL) collected by the patient while supervised
There is uncertainty regarding the optimal upper respiratory tract specimen for NAAT. The IDSA suggests a nasopharyngeal swab, a mid-turbinate swab, an anterior nasal swab, saliva, or a combined anterior nasal/oropharyngeal swab rather than an oropharyngeal swab because of limited data suggesting lower sensitivity with oropharyngeal specimens [12]. Test sensitivity with different specimens is discussed elsewhere. (See 'Accuracy' below.)
●Specimens for antigen tests – Nasopharyngeal, nasal mid-turbinate, and nasal swabs are the only recommended specimens. Antigen tests are not validated for use with oral or salivary specimens.
Patients who collect their own specimens (of any type) should be given detailed instructions on correct technique.
Additional information on testing and handling of clinical specimens can be found at the CDC website.
Infection control practices during specimen collection are discussed elsewhere. (See "COVID-19: Infection prevention for persons with SARS-CoV-2 infection", section on 'Specimen collection for respiratory viral pathogens'.)
Although SARS-CoV-2 RNA can be detected in nonrespiratory specimens (eg, stool, ocular specimens, blood), testing of these specimens has a limited role in the diagnosis of COVID-19 [15-17].
Diagnosis of SARS-CoV-2 infection — The diagnosis of COVID-19 is made by direct detection of SARS-CoV-2 RNA using NAATs or by detection of viral protein using an antigen test. A positive NAAT or antigen test is generally indicative of infection and does not need to be repeated.
Interpretation and further evaluation following a negative test vary for NAAT versus antigen testing and are discussed elsewhere. (See 'NAAT interpretation' below and 'Antigen test interpretation' below.)
Identifying specific variants — In general, clinically available diagnostic tests cannot confirm the specific SARS-CoV-2 variant causing infection. Viral sequencing or dedicated multiplex PCR genotype testing is needed to do this, and these methods are not routinely available for clinical decision-making.
Certain variants result in an S gene target failure with some NAATs (ie, the S gene is not detected but the NAAT results are positive because the other target is detected). Such results can be a proxy for infection with those particular variants if other circulating variants do not result in S gene target failure. However, this is not a definitive method of variant identification. Because different NAATs detect different regions of the S gene, a particular viral variant may result in S gene target failure with one NAAT but not another. Furthermore, laboratories do not routinely provide information on S gene target failure. (See 'Impact of SARS-CoV-2 mutations/variants on test accuracy' below.)
Testing for other pathogens — If influenza and respiratory syncytial virus (RSV) are circulating in the community, it is reasonable to also test for these viruses when testing for SARS-CoV-2, as this could have management implications. Depending on the presentation (eg, symptoms consistent with pneumonia, pharyngitis), testing for other pathogens may also be warranted. These are discussed in detail elsewhere. (See "Overview of community-acquired pneumonia in adults", section on 'Microbiologic testing' and "Evaluation of acute pharyngitis in adults", section on 'Evaluation'.)
However, detection of another viral (or bacterial) pathogen does not necessarily rule out SARS-CoV-2 in locations where there is widespread transmission. Coinfection with SARS-CoV-2 and other respiratory pathogens, including influenza virus, has been described, but the reported frequency is variable [18-22].
NAAT (INCLUDING RT-PCR)
Types of NAATs — Nucleic acid amplification tests (NAATs) detect SARS-CoV-2 RNA; reverse-transcription polymerase chain reaction (RT-PCR) assays are the most common type of NAAT (table 3) [23,24]. Various RT-PCR assays are used around the world; different assays amplify and detect different regions of the SARS-CoV-2 genome. Some target two or more genes, including the nucleocapsid (N), envelope (E), and spike (S) genes, and regions in the first open reading frame, including the RNA-dependent RNA polymerase (RdRp) gene [25]. Other, less common types of NAAT include isothermal amplification, CRISPR-based assays, and next-generation sequencing [26-28].
In the United States, the Food and Drug Administration (FDA) has granted emergency use authorization (EUA) for many different NAAT assays [29]; testing is performed by the Centers for Disease Control and Prevention (CDC), local public health departments, hospital laboratories, and commercial laboratories. For some assays, the patient can collect the specimen at home and submit it to a laboratory [30,31]; point-of-care NAATs, some of which can be completed at home, have also been developed, although they may be less sensitive than laboratory-based tests [26,32-35].
Specific NAAT assays have different performance characteristics and times to results (ranging from 15 minutes to several hours) and are authorized for different specimen types. For laboratory-performed tests, the turnaround time for clinicians to receive a result also depends on how often the laboratory performs the test.
Pooled specimen testing with NAATs (ie, testing several specimens together and only retesting individual specimens if the pool tests positive) can improve laboratory testing capacity [36-39]. However, this approach would not save time and resources in high-prevalence settings, since frequent retesting for pools that test positive is cumbersome; thus, it is best reserved for populations with expected low prevalence, such as asymptomatic individuals without known exposure. Clinicians should be aware that pooling specimens reduces test sensitivity (to greater extents with larger pool sizes) and may prolong the time to an individual positive result.
NAAT interpretation
Positive NAAT result — A positive nucleic acid amplification test (NAAT; eg, RT-PCR) for SARS-CoV-2 generally confirms the diagnosis of COVID-19. No additional diagnostic testing is necessary. However, additional testing may be warranted for management in hospitalized patients. This is discussed elsewhere. (See "COVID-19: Management in hospitalized adults", section on 'Evaluation'.)
Patients with COVID-19 can have detectable SARS-CoV-2 RNA in upper respiratory tract specimens for weeks after the onset of symptoms [40]; however, prolonged viral RNA detection does not necessarily indicate ongoing infectiousness [41,42]. These data and the implications for discontinuing isolation precautions are discussed in detail elsewhere. (See "COVID-19: Epidemiology, virology, and prevention", section on 'Viral shedding and period of infectiousness' and "COVID-19: Infection prevention for persons with SARS-CoV-2 infection", section on 'Duration and subsequent precautions'.)
There have also been reports of patients with COVID-19 who have positive NAATs soon after documented viral RNA clearance. Thus far, there is no evidence that this finding represents relapsed or repeat infection [43].
Negative initial NAAT result — For many individuals, a single negative NAAT result is sufficient to exclude the diagnosis of COVID-19. However, false-negative NAATs (eg, RT-PCR) from upper respiratory specimens have been well documented (see 'Accuracy' below). If initial testing is negative but the suspicion for COVID-19 remains (eg, suggestive symptoms without evident alternative cause) and confirming the presence of infection is important for management or infection control, we suggest repeating the test. The optimal timing for repeat testing is not known; it is generally performed 24 to 48 hours after the initial test. Repeat testing within 24 hours is not recommended.
In patients with evidence of lower respiratory tract illness, lower respiratory tract specimens can be an option for NAAT [12,44]. We agree with IDSA and WHO recommendations to reserve lower respiratory tract specimen NAATs for hospitalized patients who have an initial negative test on an upper respiratory tract specimen but for whom suspicion for lower respiratory tract SARS-CoV-2 infection remains [12,45]. For lower respiratory tract specimens, expectorated sputum should be collected from patients with productive cough, and tracheal aspirate or bronchoalveolar lavage should be collected from patients who are intubated. Most NAATs have not received EUA for lower respiratory samples, so laboratories need to validate these specimen types, and this may not be possible for all laboratories. Induction of sputum is not recommended.
In hospitalized patients suspected of having COVID-19 who have a negative SARS-CoV-2 NAAT, characteristic laboratory or imaging findings can further support the clinical diagnosis of COVID-19 and be reasons to maintain infection control precautions (see "COVID-19: Clinical features", section on 'Laboratory findings' and "COVID-19: Clinical features", section on 'Imaging findings'). It is also important to consider other potential causes of symptoms in patients with negative SARS-CoV-2 NAATs.
For patients who present three to four weeks into the course of illness and have negative NAAT, checking a serologic test may be informative [46,47]. If serology is performed in this setting, we suggest an IgG test; a total antibody test is also likely useful, but data are limited for this situation. A reactive IgG would be suggestive of COVID-19, whereas a negative test could suggest a decreased likelihood. However, the reliability of the serologic test result depends on the specific assay and the duration of illness. (See 'Serology to identify prior/late infection' below.)
Infection control precautions for COVID-19 should continue while repeat evaluation is being performed. (See "COVID-19: Infection prevention for persons with SARS-CoV-2 infection".)
In many cases, because of the limited availability of testing and concern for false-negative results, the diagnosis of COVID-19 is made presumptively based on a compatible clinical presentation in the setting of an exposure risk (residence in or travel to an area with widespread community transmission or known contact) in the absence of other identifiable causes.
Indeterminate NAAT result — The interpretation of an inconclusive or indeterminate result depends on the specific nucleic acid amplification test (NAAT) performed; the clinician should confer with the performing laboratory about additional testing.
In some cases, an inconclusive or indeterminate result indicates that only one of the two or more genes that the NAAT targets was identified. These results can be considered presumptive positive results, given the high specificity of NAAT assays. If the patient is early in the disease course, repeat testing can be helpful to confirm.
Accuracy — The accuracy and predictive values of SARS-CoV-2 NAATs have not been systematically evaluated. They are highly specific tests [48,49]. Although NAATs have high analytic sensitivity in ideal settings (ie, they are able to accurately detect low levels of viral RNA in test samples known to contain viral RNA), clinical performance is more variable (table 3).
False-positive results are rare but have been reported with certain platforms [50].
Reported false-negative rates have ranged from less than 5 to 40 percent, although these estimates are limited, in part because there is no perfect reference standard for comparison [51,52]. As an example, in a study of 51 patients who were hospitalized in China with fever or acute respiratory symptoms and ultimately had a positive SARS-CoV-2 RT-PCR test (mainly on throat swabs), 15 patients (29 percent) had a negative initial test and only were diagnosed by serial testing [53]. In a similar study of 70 patients in Singapore, initial nasopharyngeal testing was negative in 8 patients (11 percent) [54]. In both studies, rare patients were repeatedly negative and only tested positive after four or more tests. However, lower false-negative rates have also been suggested. In one study of 626 patients who had a repeat nasopharyngeal RT-PCR test within seven days of an initial negative test at two large health centers in the United States, 3.5 percent of the repeat tests were positive [52].
Sensitivity of testing likely depends on the type and quality of the specimen obtained, the duration of illness at the time of testing, and the specific assay:
●Test performance by specimen type – Test sensitivity may vary by type of specimen.
Among upper respiratory tract specimens, nasopharyngeal, nasal, and saliva specimens have high sensitivity, whereas the sensitivity of oropharyngeal swab specimens is lower [12,55-58]. In a meta-analysis of 23 studies that included approximately 8000 participants, compared with PCR results on nasopharyngeal swab specimens, the pooled sensitivities were 86 percent for nasal swabs, 85 percent for saliva samples, and 68 percent for throat swabs [58]. The combination of nasal and throat swabs was 97 percent. However, there was substantial heterogeneity across studies (eg, in timing of testing, inclusion of asymptomatic patients, and method of collection for saliva specimens), and some of them were unpublished. Furthermore, only two studies contributed data on throat swabs, and these had relatively different findings (50 versus 82 percent sensitivity) [41,56]. Self-collected specimens can reduce the need for personal protective equipment since a health care provider is not directly collecting the specimens. Accuracy of NAAT appears to be relatively good when nasal swabs and saliva specimens are self-collected. The sensitivity of NAAT with self-collected nasal or nasal mid-turbinate specimens appears similar to that with nasopharyngeal specimens collected by a health care provider [59,60].
Lower respiratory tract specimens may have higher viral loads and be more likely to yield positive tests than upper respiratory tract specimens [55,61]. In a study of 205 patients with COVID-19 who were sampled at various sites, the highest rates of positive viral RNA tests were reported from bronchoalveolar lavage (95 percent, 14 of 15 specimens) and sputum (72 percent, 72 of 104 specimens), compared with oropharyngeal swab (32 percent, 126 of 398 specimens) [55].
The variable performance of NAAT by specimen type may depend on the viral variant, although further studies are needed. Limited evidence from small studies suggests that saliva may be more sensitive than nasal specimens for the Omicron variant [62,63]. (See 'Impact of SARS-CoV-2 mutations/variants on test accuracy' below.)
●Test performance by illness duration – The likelihood of detectable SARS-CoV-2 RNA may also vary by the duration of illness [64,65]. In an analysis of seven studies (including two unpublished reports) that evaluated RT-PCR performance by time since symptom onset or exposure, the estimated rates of false-negative results were 100 percent on the day of exposure, 38 percent on day 5 (estimated as the first day of symptoms), 20 percent at day 8, and 66 percent at day 21 [64]. Heterogeneity across studies and assumptions made in the analysis (eg, about incubation period and time of exposure) reduce confidence in these results. One of the studies included in the analysis used a combination of RT-PCR and an immunoglobulin M (IgM) serologic test to make the diagnosis of COVID-19 and suggested that RT-PCR negative rates were <10 percent on days 1 to 3 of illness, >20 percent at day 6, and >50 percent after day 14; however, these results should also be interpreted with caution, since the serologic test used was not validated for detection of acute infection and IgM tests are frequently falsely positive [65]. Other studies have also suggested that viral RNA levels are high prior to the development of symptoms (ie, in presymptomatic patients) [66]. Nevertheless, low viral RNA levels should not be interpreted as reflecting a late stage of infection, as they may be low at the outset as well [67]. (See "COVID-19: Epidemiology, virology, and prevention", section on 'Viral shedding and period of infectiousness'.)
Data on test performance and viral RNA levels in asymptomatic patients are limited [66]. It is unknown how soon viral RNA can be detectable following exposure and infection.
●Test performance by assay type – There are differences in the limit of detection among the major commercial NAAT assays, and retesting samples on different platforms may yield conflicting results [48,49]. Additionally, certain point-of-care or rapid NAAT assays may not be as sensitive as standard laboratory-based tests [12,33,35,68]. In a systematic review conducted by the IDSA, rapid RT-PCR tests had similar sensitivity as standard laboratory-based NAAT (98 percent for both) when compared with a composite reference standard (ie, the combined results of multiple tests), whereas the sensitivity of the Abbott ID NOW test (a rapid isothermal test), was lower than laboratory-based NAAT (81 versus 99 percent) [12]. All methods had specificity ≥97 percent.
Cycle threshold — The cycle threshold (Ct) refers to the number of cycles in an RT-PCR assay needed to amplify viral RNA to reach a detectable level. The Ct value can thus indicate the relative viral RNA level in a specimen (with lower Ct values reflective of higher viral levels). Resulting laboratories generally do not provide the Ct value with the qualitative NAAT result, although it can be obtained upon request for some testing platforms. However, the clinical application of the Ct is uncertain [69]. Ct values are not standardized across RT-PCR platforms, so results cannot be compared across different tests. Furthermore, no clinical studies have validated use of Ct to guide management.
ANTIGEN TESTING — Tests that detect SARS-CoV-2 antigen can be performed rapidly and at the point of care and thus are more accessible with a faster time to results than most nucleic acid amplification tests (NAATs); various home antigen tests, performed on nasal swabs, allow individuals to test themselves without presenting to medical care or a testing site. Antigen tests are typically less sensitive than NAATs (table 3) [35,70,71]. Nevertheless, they can be useful when NAATs are inconvenient or unavailable or when NAAT turnaround times are too long to be clinically useful, provided that clinicians (and individuals who self-test) are aware of the possibility of false negatives and the results are interpreted based on the pretest probability of COVID-19.
Antigen test interpretation
In symptomatic patients — Antigen tests can be useful alternatives to NAAT for diagnosis of SARS-CoV-2 in symptomatic individuals [72,73]. In such cases, the test should be performed within the first five to seven days of symptoms. Although antigen testing cannot detect virus at levels as low as NAAT can, its sensitivity is greatest in the first week of symptoms, when virus replication is at its highest.
●A positive antigen test in a symptomatic individual is indicative of SARS-CoV-2 infection (algorithm 1). The false-positive rate is very low.
●A negative antigen test in a symptomatic individual could represent a false negative, does not exclude the possibility of SARS-CoV-2 infection, and should be followed by additional testing. Individuals testing at home should repeat an antigen test at 48 hours; this is consistent with recommendations from the US Food and Drug Administration (FDA) [74]. For individuals who are willing to repeat testing with an NAAT (rather than antigen testing), we suggest this approach given the greater sensitivity of NAAT. If the repeat test (with either an antigen test or NAAT) is negative, the likelihood of COVID-19 is low, but testing can be repeated if concern for COVID-19 remains following two negative antigen tests.
Although the sensitivity of antigen testing is higher in symptomatic than in asymptomatic individuals, it remains lower than that of NAAT. Sensitivity is improved with repeating antigen testing. (See 'Accuracy' below.)
For post-exposure testing — Antigen tests can be useful to evaluate for SARS-CoV-2 following close contact with an individual with known or suspected SARS-CoV-2 infection. In order to identify new infections, the CDC recommends that individuals get tested once five days have passed since the last exposure [11]; we typically test five to seven days post-exposure.
●A positive antigen test in an asymptomatic individual following exposure is generally indicative of SARS-CoV-2 infection (algorithm 1). The false-positive rate is very low.
●A negative antigen test in an asymptomatic individual following exposure could represent a false negative and should generally be followed by additional testing. The FDA recommends that individuals testing at home repeat antigen testing two additional times, each 48 hours apart (for a total of three tests) [74]. It is also reasonable to confirm an initial negative antigen test with a follow-up NAAT instead. If all the repeat testing is negative, the likelihood of COVID-19 is low. Any positive test performed in this setting is indicative of infection.
The decision to repeat a negative antigen test should take into account the potential transmission impact of an individual with a false-negative test, which depends on other factors, including vaccination rates in the community, use of masks, and extent of exposure. Repeat testing may reasonably be deferred if the potential impact of a false-negative antigen test is low. Regardless of whether a negative test is confirmed, individuals with known exposure should self-monitor for symptoms of COVID-19 after exposure and get tested if they develop.
Among asymptomatic individuals, the sensitivity of antigen testing is lower than that among symptomatic individuals, and the predictive value of a negative antigen test may be limited [73]. Sensitivity is improved with repeating antigen testing, and three serial tests are more sensitive than two among asymptomatic individuals [75]. (See 'Accuracy' below.)
For other screening purposes
●Serial screening in congregate settings – Antigen tests may be useful in outbreak settings and for repeated screening of individuals in high-risk congregate settings to quickly identify individuals with SARS-CoV-2 and isolate them; modelling studies have suggested that if the frequency of testing is high enough, even antigen tests with lower sensitivity could be successfully used to reduce cumulative infection rates [76]. If used for serial testing in these settings, positive tests indicate infection and negative antigen tests do not need to be confirmed [77]. Studies evaluating transmission outcomes after serial testing are limited, and the optimal frequency and duration of serial antigen testing to sufficiently identify infections have not been established. (See "COVID-19: Epidemiology, virology, and prevention", section on 'Screening in selected high-risk settings'.)
If antigen tests are used in situations when the likelihood of SARS-CoV-2 is low (eg, testing of an asymptomatic individual who has had no household contact with a patient with COVID-19 and lives in a community with low infection rates), a negative antigen test can be interpreted at face value.
Positive antigen tests generally do not warrant confirmation, even in settings of low prevalence. However, it is reasonable to confirm a positive antigen test with an NAAT when the diagnosis is suspect and prevalence is very low (eg, <1 percent); in that case, a negative NAAT would indicate no infection.
To inform duration of precautions after infection — Use of antigen testing in individuals with known infection to inform the duration of isolation and precautions is discussed elsewhere. (See "COVID-19: Infection prevention for persons with SARS-CoV-2 infection", section on 'Duration and subsequent precautions'.)
Accuracy — Systematic reviews of studies evaluating antigen test performance indicate that antigen tests have very high specificity but are generally less sensitive than NAAT; they are most sensitive in symptomatic individuals during the first week of illness [73,78,79]. As an example, in a July 2022 systematic review of 152 studies, in which 49 commercially available antigen tests were evaluated on specimens with known SARS-CoV-2 NAAT results, sensitivity was highly variable, while overall specificity exceeded 99 percent [79]. Average sensitivity was higher among symptomatic compared with asymptomatic participants (73 versus 55 percent) and was higher during the first compared with second week after symptom onset (81 versus 54 percent). Other studies have suggested that antigen test sensitivity peaks approximately four days after symptom onset [80], although there are many variables that may affect this timing, including the viral variant.
Serial antigen testing appears to improve sensitivity. In an unpublished prospective study of over 5500 individuals who underwent serial antigen and NAAT testing every 48 hours for two weeks, antigen test sensitivity on the first day of NAAT positivity was 60 percent for symptomatic individuals and 12 percent for asymptomatic individuals [75]. Sensitivity with two or three serial tests increased to 92 and 94 percent for symptomatic individuals and to 51 and 75 percent for asymptomatic individuals.
Antigen test sensitivity also improves with increasing levels of viral RNA in upper respiratory specimens (ie, as reflected by lower Ct values on NAAT). In the systematic review detailed above, average sensitivity was 94 to 97 percent for Ct value ≤25, 69 percent for Ct value 25 to 30, and 19 percent for Ct value >30 [79].
Studies have also suggested that a positive antigen test is more likely than a positive RT-PCR test to indicate that infectious virus could be cultured from specimens [81-83]. As an example, in a study of 60 individuals with SARS-CoV-2 infection who underwent daily antigen and viral culture testing, antigen test was positive on 93 percent of specimens that were culture positive but only 28 percent of specimens that were culture negative [83]. However, since infectious virus can still be isolated from antigen-negative specimens, clinicians and patients should be aware that a negative antigen test cannot be used to indicate that a person is not infectious. In other studies, the rate of positive viral culture in specimens that were antigen negative ranged from 9 to 16 percent [71,80].
Performance also varies by the specific antigen test. Antigen tests that have been granted EUA in the United States can be found on the FDA website and the COVID-19 Testing Toolkit site, which also lists the manufacturer reported sensitivity and specificity [84,85]. Most of these can be performed at the point of care or in a laboratory. Antigen tests that can be performed by the patient at home are also available.
Impact of the Omicron variant on antigen test accuracy is discussed elsewhere. (See 'Impact of SARS-CoV-2 mutations/variants on test accuracy' below.)
OTHER DIAGNOSTIC TESTS
Serology to identify prior/late infection — Serologic tests detect antibodies to SARS-CoV-2 in the blood, and those that have been adequately validated can help identify patients who previously had SARS-CoV-2 infection as well as patients with current infection who have had symptoms for three to four weeks (table 3). Because serologic tests are less likely to be reactive in the first several days to weeks of infection, they have very limited utility for diagnosis in the acute setting [24,86,87]. Checking serology three to four weeks after the onset of symptoms optimizes the accuracy of testing, since test sensitivity beyond five weeks is uncertain [47]. Interpretation of serologic tests in individuals who have received a COVID-19 vaccine is discussed elsewhere. (See 'Testing following COVID-19 vaccination' below.)
We suggest using IgG antibody or total antibody tests rather than IgM antibody, IgA antibody, or IgM/IgG differentiation tests because of their greater accuracy; this is consistent with recommendations from the Infectious Diseases Society of America (IDSA) [47]. If a serologic test to identify prior infection is performed in an individual who has received a spike protein COVID-19 vaccine, a test that detects antibodies to antigens other than the spike protein should be used.
To maximize the predictive value of the serologic test, assays with high specificity (≥99.5 percent) should be used and testing should be reserved for individuals with a high pretest probability of prior infection; the United States Centers for Disease Control and Prevention (CDC) also suggests an alternative strategy of using a two-step testing algorithm, in which an initial positive test is confirmed by a second, different antibody assay [86]. In areas of low seroprevalence or low pretest probability of infection, individual results should be interpreted with caution, since in this setting even serologic tests that have high specificity still have a low positive predictive value (ie, the positive test has a high likelihood of reflecting a false positive) [88,89].
In the United States, several serologic tests have been granted emergency use authorization (EUA) by the United States Food and Drug Administration (FDA) [29]. These are binding antibody tests that detect SARS-CoV-2 antigens (nucleocapsid or spike protein) and include tests that can be performed at the point of care as well as tests that require specialized equipment and trained laboratory personnel; these also include a test that can be used on home-collected specimens and submitted to a laboratory for results. The FDA has also granted EUA for a test that detects neutralizing antibodies [90]; although such tests are helpful to study the response to infection or vaccination, they do not offer a major diagnostic advantage over binding antibody tests since correlates of protection have not yet been established. The sensitivity and specificity of serologic tests are variable [91]; a catalog of these tests can be found at centerforhealthsecurity.org. The FDA is also independently evaluating the accuracy of certain serologic tests for COVID-19 and posting results on its website.
Detectable antibodies generally take several days to weeks to develop, and the time to antibody detection varies by test [65,92-94]. In a systematic review of 38 studies that evaluated the sensitivity of serologic testing by time since symptom onset in patients with COVID-19, IgM was detected in 23 percent by one week, in 58 percent by two weeks, and in 75 percent by three weeks; the corresponding detection rates for IgG were 30, 66, and 88 percent [95]. Other studies have suggested that the rate of positive IgG approaches 100 percent by 16 to 20 days [46,96,97].
However, various serologic tests, including in-house laboratory-developed tests, were used in these studies, and their sensitivities within different time frames vary substantially. In particular, some lateral flow assays (which are used for point-of-care tests) are less sensitive than enzyme-linked immunosorbent assays or chemiluminescent immunoassays [98].
Specificity also varies by type of serologic assay. In contrast with IgG antibody and total antibody tests, IgM antibody, IgA antibody, and IgM/IgG differentiation tests generally have specificities below 99 percent [47]. Cross-reactivity with other coronaviruses and other viral pathogens is a potential concern [99].
Most studies suggest that most individuals have durable, detectable IgG levels up to eight months after infection [100-106]; however, some have reported a faster rate of antibody decline [107-110]. For example, in a study of 1107 individuals with positive SARS-CoV-2 molecular testing in Iceland, total Ig antibody tests were reactive in 90 percent, with titers increasing over the first two months after diagnosis and remaining steady for another two months [100]. In a smaller study, 36 of 40 patients (90 percent) had detectable IgG against spike protein at six to eight months after infection [104]. In contrast, in another study, IgG levels were noted to decline by a median of approximately 75 percent from the acute to early convalescent phase of illness, and at eight weeks following infection, 40 percent of asymptomatic patients and 13 percent of symptomatic patients did not have detectable IgG [107]. The duration that antibodies remain detectable likely depends on the height of the initial antibody response as well as the severity of the infection [111].
Large-scale serologic screening with validated tests may be able to provide a better measure of disease activity (by identifying people who were not diagnosed by RT-PCR or who may have had asymptomatic or subclinical infection) and also identify individuals who may have immunity to infection; serologic correlates of protective immunity, however, have not been defined. Until further data are available, the CDC recommends that results of antibody testing not be used to determine rooming arrangements in congregate settings such as dormitories or prisons, make decisions about return to work, or alter work and personal protective equipment requirements for health care workers and first responders [86]. (See "COVID-19: Epidemiology, virology, and prevention", section on 'Viral shedding and period of infectiousness' and "COVID-19: Epidemiology, virology, and prevention", section on 'Immune responses following infection'.)
Tests with limited utility or availability
●Breathalyzer – In the United States, the FDA authorized a breathalyzer that uses gas chromatography-mass spectrometry to detect exhaled volatile organic compounds specific to SARS-CoV-2 infection [112,113]. The contraption is the size of a small suitcase and returns results in approximately three minutes. According to the authorization documents, sensitivity and specificity were 91 and 99.3 percent among a group of asymptomatic and symptomatic individuals compared with PCR on nasopharyngeal swabs. More detailed performance data, as well as other information such as cost, are necessary to inform the optimal role of this device in COVID-19 diagnosis.
●Viral culture – For safety reasons, specimens from a patient with suspected or documented COVID-19 should not be submitted to clinical laboratories for viral culture. Viral culture is mainly reserved for research purposes. (See "COVID-19: Epidemiology, virology, and prevention", section on 'Viral shedding and period of infectiousness'.)
●Other tests of SARS-CoV-2 immunity – The clinical utility of tests that can detect cell-mediated immune responses to SARS-CoV-2, such as with an interferon-gamma release assay, is also being explored [114].
SPECIAL SITUATIONS
Persistent or recurrent positive NAAT during convalescence — Patients diagnosed with COVID-19 can have detectable SARS-CoV-2 RNA in upper respiratory tract specimens for weeks after the onset of symptoms [40]. Recurrently positive nucleic acid amplification tests (NAATs) following several negative tests have also been well documented in some patients with COVID-19.
However, prolonged or recurrent viral RNA detection does not necessarily indicate prolonged infectiousness. Isolation of infectious virus from upper respiratory specimens more than 10 days after illness onset has only rarely been documented in patients who recovered from nonsevere infection [42,115,116]. Additionally, viral RNA levels during convalescence, if detectable, are lower than those detected during acute illness, and studies have suggested that infectious virus cannot be detected below a certain viral threshold [115]. These data and the implications for discontinuing isolation precautions are discussed in detail elsewhere. (See "COVID-19: Epidemiology, virology, and prevention", section on 'Viral shedding and period of infectiousness' and "COVID-19: Infection prevention for persons with SARS-CoV-2 infection", section on 'Duration and subsequent precautions'.)
In the United States, the Centers for Disease Control and Prevention (CDC) suggests against retesting asymptomatic individuals who were previously diagnosed with SARS-CoV-2 within the prior three months with NAAT because of the low likelihood that a repeat positive NAAT during this interval represents an active infection [117].
Diagnosis of reinfection — The diagnosis of reinfection is straightforward (ie, with positive NAAT or antigen testing) when many months have elapsed between the two infections. (See 'Diagnosis of SARS-CoV-2 infection' above.)
However, establishing the diagnosis of reinfection can be challenging when it occurs within a few months of the prior infection. For individuals who warrant testing within three months of an earlier infection, antigen testing is preferred. Because of the possibility of prolonged respiratory shedding of viral RNA following acute infection, a repeat positive NAAT in this setting does not necessarily indicate a new infection. If an NAAT was performed and is positive within three months of an earlier infection, features that increase the likelihood of reinfection include new symptoms consistent with COVID-19, a longer interval since the first infection, and a high viral RNA level on repeat testing (eg, Ct value <33).
Interpretation of antigen testing in this setting is the same as for the general population. (See 'Antigen test interpretation' above.)
Impact of SARS-CoV-2 mutations/variants on test accuracy — Over the course of the pandemic, several SARS-CoV-2 variants that have mutations in the spike protein have become prevalent globally. (See "COVID-19: Epidemiology, virology, and prevention", section on 'Viral evolution and variants of concern'.)
●Impact on NAAT – Some variants have spike mutations (in particular, a deletion at amino acids 69-70) that impact the ability of SARS-CoV-2 NAAT to detect the S gene that encodes the spike protein. Most NAATs will still detect SARS-CoV-2 RNA even if they fail to detect the mutated S gene because they have been designed to detect more than one gene target [118]. S gene target failure can be used as a marker for variants that contain spike protein mutations for surveillance purposes.
Most NAATs still detect Omicron and its subvariants; some result in S gene target failure with certain Omicron subvariants. Rare NAATs that are expected to fail to detect specific variants completely are detailed on the US Food and Drug Administration (FDA) website [119,120].
●Impact on antigen tests – Most antigen tests target nucleocapsid protein, so mutations in the spike protein would not impact the accuracy of such antigen tests.
The Omicron variant has four mutations in the nucleocapsid protein, although most antigen tests are still expected to detect Omicron and its subvariants. Although there is some concern that antigen tests may have lower sensitivity for Omicron subvariants compared with other variants, available data do not clearly indicate that antigen tests should be employed differently when Omicron is prevalent. As with other variants, a negative antigen test does not necessarily indicate that a person is not infectious, and when the clinical suspicion for COVID-19 is high, a negative antigen test should be repeated or confirmed with NAAT. (See 'Antigen testing' above.)
According to the US FDA, certain antigen tests may have lower sensitivity for the Omicron variant, but the data supporting this were not detailed [119]. In contrast, most available evidence suggests that the sensitivity of antigen testing relative to NAAT in detecting the Omicron variant on nasal specimens is similar to that with other SARS-CoV-2 strains (ie, overall sensitivity is modest but sensitivity for high viral levels is high [121-123]). In one study of 731 individuals in California who were tested simultaneously with anterior nasal rapid antigen testing (BinaxNOW) and anterior nasal NAAT during the Omicron surge, of the 296 who tested positive by NAAT, 193 had a positive antigen test (overall sensitivity 65.2 percent) [124]. However, antigen test sensitivity was higher among those whose NAAT indicated higher viral RNA levels (95 percent with Ct <30 and 82 percent with Ct <35).
These findings contrast with another unpublished study of 30 vaccinated individuals identified as having early Omicron infection in the setting of near-daily testing. In this study, antigen testing of nasal swabs were almost always negative on the first day or two of diagnosis despite positive simultaneous results from a saliva NAAT, even at high viral RNA levels; the median time to positive antigen test was three days after NAAT positivity [62]. However, it is uncertain whether the discrepancy between antigen testing and NAAT was related to differences in viral levels in saliva versus nasal swab specimens. Among the five individuals who underwent both saliva and nasal NAAT, viral RNA levels appeared to peak in saliva tests one to two days before nasal tests. Performance of antigen testing on saliva or oral specimens has not been validated, and other data suggest that oral specimens do not substantially improve detection of Omicron. In the California study described above, among 49 individuals who had a high viral RNA level (Ct <30) on nasal NAAT and collected both nasal and throat specimens, the antigen test was positive in 86 percent of nasal swabs and 47 percent of throat swabs; either the throat or the nasal swab was positive in 90 percent [124].
Testing following COVID-19 vaccination
●Viral tests – Virals tests in individuals who have received a COVID-19 vaccine should be interpreted in the same way as in unvaccinated individuals. Vaccination does not influence the results of viral tests, so a positive viral test result in a vaccinated individual should not be attributed to the vaccine.
●Serology – COVID-19 vaccination elicits antibodies against the SARS-CoV-2 spike protein. Some serologic tests detect anti-spike antibodies, and these tests cannot distinguish between prior infection and prior vaccination (a reactive result could indicate prior infection, prior vaccination, or both). Some serologic tests only detect antibodies against nucleocapsid protein; vaccines authorized in the United States, Canada, and Europe do not elicit such antibodies, so a reactive result on a nucleocapsid protein-based serologic test in an individual who has received one of these vaccines would suggest a history of infection. However, some evidence suggests that vaccinated individuals are less likely to develop anti-nucleocapsid antibodies after infection than unvaccinated individuals [125].
Multisystem inflammatory syndrome in children — For children or adolescents with suspected multisystem inflammatory syndrome, testing for SARS-CoV-2 includes both NAAT and serology. Many children with this syndrome have had detectable antibodies to SARS-CoV-2 but a negative NAAT. The diagnosis and evaluation of multisystem inflammatory syndrome are discussed elsewhere. (See "COVID-19: Multisystem inflammatory syndrome in children (MIS-C) clinical features, evaluation, and diagnosis", section on 'Evaluation'.)
SOCIETY GUIDELINE LINKS — Links to society and government-sponsored guidelines from selected countries and regions around the world are provided separately. (See "Society guideline links: COVID-19 – Index of guideline topics".)
INFORMATION FOR PATIENTS — UpToDate offers two types of patient education materials, "The Basics" and "Beyond the Basics." The Basics patient education pieces are written in plain language, at the 5th to 6th grade reading level, and they answer the four or five key questions a patient might have about a given condition. These articles are best for patients who want a general overview and who prefer short, easy-to-read materials. Beyond the Basics patient education pieces are longer, more sophisticated, and more detailed. These articles are written at the 10th to 12th grade reading level and are best for patients who want in-depth information and are comfortable with some medical jargon.
Here are the patient education articles that are relevant to this topic. We encourage you to print or e-mail these topics to your patients. (You can also locate patient education articles on a variety of subjects by searching on "patient info" and the keyword(s) of interest.)
●Basics topics (see "Patient education: COVID-19 overview (The Basics)" and "Patient education: COVID-19 and pregnancy (The Basics)" and "Patient education: COVID-19 and children (The Basics)" and "Patient education: COVID-19 vaccines (The Basics)")
SUMMARY AND RECOMMENDATIONS
●Clinical suspicion – The possibility of COVID-19 should be considered in patients with compatible symptoms (table 1), in particular fever and/or respiratory tract symptoms, who reside in or have traveled to areas with community transmission or who have had potential exposure to SARS-CoV-2 through an outbreak setting or close contact with a confirmed or suspected case. Clinicians should also be aware of the possibility of COVID-19 in patients with severe respiratory illness when no other etiology can be identified. (See 'Clinical suspicion' above.)
●Whom to test – All symptomatic patients with suspected COVID-19 should undergo testing for SARS-CoV-2. The main indication for testing asymptomatic individuals is recent exposure to SARS-CoV-2; if this is done, we suggest post-exposure testing be performed five to seven days after exposure, although the optimal timing is uncertain. (See 'Whom to test' above.)
●Choice of test – A viral test is necessary to make the diagnosis of SARS-CoV-2 infection: either a nucleic acid amplification test (NAAT, most commonly a reverse-transcription polymerase chain reaction [RT-PCR] assay), or an antigen test. We suggest NAAT, if readily available with a reasonable turnaround time, because of its superior sensitivity; however, antigen tests are more accessible, more convenient, provide results faster than laboratory-based NAAT, and they are good alternatives as long as users appreciate the potential need for repeat testing to optimize sensitivity. (See 'Choosing an initial diagnostic test' above.)
•NAAT accuracy and interpretation – NAATs detect SARS-CoV-2 RNA in patient specimens and are highly specific (table 3); they are most commonly laboratory based, although point-of-care NAATs are also available. They can detect low levels of viral RNA; the precise sensitivity of these tests in the clinical setting likely depends on the type and quality of the specimen obtained, the duration of illness at the time of testing, and the specific assay. (See 'NAAT (including RT-PCR)' above.)
A positive NAAT for SARS-CoV-2 confirms the diagnosis of COVID-19. (See 'Positive NAAT result' above.)
For many symptomatic individuals, a single negative NAAT result is sufficient to exclude the diagnosis of COVID-19. However, if initial testing is negative, but the suspicion for COVID-19 remains high, and confirming the presence of infection is important for management or infection control, we suggest repeating the test. In certain situations, NAAT on lower respiratory tract specimens (for hospitalized patients with evidence of lower respiratory tract illness) or serology (for patients with symptoms for at least two weeks) may be a useful adjunctive diagnostic test. (See 'Negative initial NAAT result' above.)
•Antigen test accuracy and interpretation – Antigen tests can be performed rapidly at home or at the point of care. Positive tests can be interpreted as indicative of SARS-CoV-2 infection. Because they are less sensitive than NAAT, negative antigen tests performed for symptoms or recent exposure should generally be confirmed with repeat testing (algorithm 1). Antigen tests can also be useful for serial screening for infection in high-risk settings (eg, congregate settings). (See 'Antigen testing' above.)
●Limited role for serology – Tests that detect antibodies to SARS-CoV-2 can help identify patients who previously had COVID-19 (table 3). Detectable antibodies generally take several days to weeks to develop; thus, serologic tests have less utility for diagnosis in the acute setting. Serologic tests should be used with caution because of variable performance among available assays, potential for low positive predictive value in settings of low seroprevalence, and uncertain serologic correlates of immunity. (See 'Serology to identify prior/late infection' above.)
●Interpreting tests in vaccinated individuals – Vaccination status does not influence interpretation of viral test (ie, NAAT or antigen test) results. Most serologic tests target the nucleocapsid protein; only serologic tests that target the spike protein can detect antibody response to currently available vaccines, but they cannot distinguish a vaccine response from prior infection. (See 'Testing following COVID-19 vaccination' above.)
●Detecting infection with Omicron subvariants – The approach to diagnostic testing in the context of Omicron subvariants is the same as with other variants. Some Omicron subvariants have spike protein mutations that result in S gene target failure in some NAATs. Most NAATs still detect Omicron subvariants since they have more than one gene target. Antigen tests (which generally target the nucleoprotein) are also expected to detect Omicron subvariants. Routine diagnostic testing cannot confirm infection with a specific variant. (See 'Impact of SARS-CoV-2 mutations/variants on test accuracy' above.)
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