Coronaviruses are a large family of respiratory viruses. Common coronaviruses usually cause mild illness. Rarer coronaviruses, including severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the recently discovered coronavirus, SARS-CoV-2, which causes COVID-19, can lead to more severe illness.
SARS-CoV-2 is widespread in the United States and many other countries. Spread of infection has been person-to-person through the respiratory route of transmission, similar to other respiratory viruses. Identification of patients with SARS-CoV-2 can help to isolate cases and prevent further person-to-person transmission, thus limiting the number of cases, slowing the spread of infection, and mitigating the impact on healthcare resources.
Viral detection is recommended for COVID-19 diagnosis. The gold standard is molecular (nucleic acid amplification) testing. Testing decisions should be based on local epidemiology, clinical signs and symptoms, and the course of illness. Serology (antibody) testing is recommended for evaluating exposure to SARS-CoV-2; it is not recommended for the diagnosis of acute illness.
The environment surrounding COVID-19 testing is evolving rapidly. Clinicians are advised to consult the CDC's Overview of Testing for SARS-CoV-2 and ARUP’s COVID-19 resource site for the most up-to-date testing information.
Quick Answers for Clinicians
Viral detection of SARS-CoV-2 by nucleic acid amplification or antigen testing is used to diagnose infection. Nucleic acid amplification testing (NAAT), which includes polymerase chain reaction (PCR), is performed on a nasopharyngeal (NP) swab, oropharyngeal (OP) swab, nasal swab, or saliva specimen that is sent to a laboratory for analysis. NAAT is the gold standard for SARS-CoV-2 detection.
Serology (also known as antibody) testing is used to evaluate exposure to the virus that causes COVID-19. Although antibody testing should not be used as an initial diagnostic test, there are circumstances in which this testing might be useful for diagnosing later-stage disease. For example, antibody testing can be used to evaluate individuals presenting with COVID-19-like disease but late in the course of the illness (when the sensitivity of molecular diagnostic testing is decreased) and individuals with late complications of suspected COVID-19 disease (eg, multisystem inflammatory syndrome in children [MIS-C]). Currently, no professional society, including the American Association for Clinical Chemistry (AACC) or CDC, recommends the use of serology to assess COVID-19 vaccination response.
Two types of serology tests are available—laboratory-based immunoassays and rapid lateral flow immunoassays that can be used near the point of care. Some tests detect total antibodies, whereas others detect specific isotypes (immunoglobulin G [IgG], IgM, IgA).
To reduce the likelihood of a false-positive result and to maximize the positive predictive value (PPV) of a test, the CDC Interim Guidelines for COVID-19 Antibody Testing suggest testing individuals with a high pretest probability or choosing a test with a high specificity. In low-prevalence settings, an orthogonal testing algorithm may be useful.
Nasopharyngeal (NP) specimens are the gold standard for COVID-19 viral detection. Some laboratories may accept alternative specimen types such as saliva, oropharyngeal (OP) swab, mid turbinate swab, or anterior nares swab specimens. Clinicians are advised to check with their performing laboratories for specific specimen requirements.
Recent studies, including one performed by researchers at ARUP and University of Utah Health, found that self-collected saliva and NP swabs collected by healthcare providers are equally effective for detecting SARS-CoV-2. Both saliva and NP swabs are superior to anterior nasal swabs. The study, published in the Journal of Clinical Microbiology, represents one of the largest COVID-19 specimen-type comparisons to date.
Detection rates in specimen types vary from patient to patient and may change over the course of the illness. For example, because of potentially discordant shedding of virus in the upper versus the lower respiratory tract, patients with pneumonia may have negative nasal or OP samples but positive lower airway samples.
Swab specimens should be collected with nasopharyngeal (NP) ultrafine or equivalent swabs. Dacron, polyester-tipped, or any other flocked swabs are acceptable alternatives. Calcium alginate swabs or swabs with wooden shafts are NOT acceptable due to test interference. Viral transport media and universal transport media (VTM/UTM) are the preferred collection systems for swabs. Media types that are equivalent to VTM/UTM are also acceptable. For alternative transport media, refer to the FDA’s guidance on specimen collection for SARS-CoV-2 molecular diagnostic testing.
Yes, some multipathogen molecular assays can detect SARS-CoV-2. For example, ARUP offers a multipathogen assay that detects and differentiates COVID-19, influenza A/B, and respiratory syncytial virus (RSV). Clinicians are advised to confirm which respiratory viruses are detected by an assay before ordering. The U.S. Food and Drug Administration (FDA) maintains a list of COVID-19 assays with Emergency Use Authorization (EUA).
Variants, including the United Kingdom variant, also known as the Alpha variant, and South African variant, also known as the Beta variant, may impact the results of molecular tests that utilize genetic targets that include the site of mutation. However, most assays include multiple genetic targets, which allows for redundancy so that natural viral variation is less likely to impact test performance.
ARUP is currently using four nucleic acid amplification assays performed on three different platforms (Thermo Fisher, Roche, and Hologic) to test for SARS-CoV-2. Of these, only the Thermo Fisher assay uses the spike protein (S gene) as a target for SARS-CoV-2 identification. Therefore, only the Thermo Fisher assay is at risk of failing to detect the virus in samples with strains such as the Alpha or Beta variants that contain mutations in the S gene. However, the Thermo Fisher assay utilizes multiple targets, so it still detects variants with S gene mutations. The Roche and Hologic assays do not use the S gene as an amplification target, and their performance is unaffected by S gene mutations.
The Thermo Fisher assay utilizes three gene targets for the detection of SARS-CoV-2 (Orf1ab/O-methyltransferase, N gene, and S gene). For this assay to return a positive result, two of the three targets must be amplified. ARUP has observed a lack of S gene amplification in some variants, including the Alpha variant, but because of amplification in the other two targets, the assay still yielded a positive result. It is important to note that lack of S gene amplification does not necessarily indicate the presence of the Alpha or Beta variants. Genetic sequencing is required to fully characterize and identify a particular SARS-CoV-2 strain.
There is a possibility that these variants may result in low-positive samples that are positive for only Orf1ab/O-methyltransferase and N gene targets and yield an “inconclusive” result. It is also possible that different variants may result in amplification of the S gene but would be Orf1ab/O-methyltransferase and N gene negative, but these different variants are likely rare at this time.
Most diagnostic assays utilize techniques such as polymerase chain reaction (PCR) and transcription-mediated amplification (TMA) and do not identify specific strains of a virus. For a particular strain to be characterized, the virus must undergo genetic sequencing. Because of this, routine diagnostic testing does not distinguish between wild-type SARS-CoV-2 and its variants, and further analysis using genetic sequencing is required.
Strains such as the United Kingdom (UK) variant, also known as the Alpha variant, or South African (SA) variant, also known as the Beta variant, may cause dropout of a particular genetic target, meaning that the site of mutation inhibits amplification. In fact, dropout of S gene amplification in diagnostic testing led researchers to perform sequencing studies and later confirm the presence of the Alpha variant in the United States.
ARUP is currently sequencing variants that have exhibited S gene dropout in order to characterize potential mutations. S gene dropout does not necessarily indicate the presence of the Alpha or Beta variants because there are several circulating strains with mutations in this region.
Laboratory testing is the only way to distinguish between SARS-CoV-2 and the flu. Importantly, laboratory testing is also the only way to determine cases of viral coinfection. Infection with one respiratory virus does not exclude the possibility of infection with another because patients may be infected with more than one virus at the same time. When SARS-CoV-2, influenza, and respiratory syncytial virus (RSV) are cocirculating (eg, during flu season), the National Institute of Health (NIH) recommends cotesting to determine proper medical management.
Children of all ages are at risk for COVID-19 infection, but there are relatively fewer cases of COVID-19 among children compared with adults. Children appear to present with more mild signs and symptoms than adults. Although severe disease is uncommon, children are still at risk of developing severe illness and complications from COVID-19. Early case studies and reports suggest that infants may be at a higher risk for severe illness from COVID-19 when compared with older children.
It is unclear whether children are as susceptible to SARS-CoV-2 infection compared with adults. Recent evidence suggests that, compared with adults, children likely have similar viral loads in their nasopharynges and similar secondary infection and transmission rates. Additionally, children can spread the virus to others in households and camp settings.
Due to early community mitigation efforts and school closures, transmission of SARS-CoV-2 to and among children may have been reduced in the United States during the pandemic in the spring and early summer of 2020. It is possible that comparing trends in pediatric infections before and after the return to in-person school and other activities may provide additional understanding about infections in children.
Multisystem inflammatory syndrome in children (MIS-C) is a serious condition marked by inflammation that is related to resolved COVID-19 infection.
At this time, there is limited information available about risk factors, pathogenesis, and clinical course. The CDC has issued a health advisory instructing clinicians to watch for signs and symptoms, which may include a persistent fever, elevated inflammatory markers, and multiorgan (eg, cardiac, gastrointestinal, renal) involvement. Diagnosis of MIS-C must include a positive laboratory test result by reverse transcription polymerase chain reaction (RT-PCR), serology, or antigen testing. For more information, refer to the CDC’s case definition for MIS-C.
Indications for Testing
The CDC and the Infectious Diseases Society of America (IDSA) offer the following recommendations for viral detection of SARS-CoV-2 in symptomatic and asymptomatic groups.
The CDC and IDSA recommend that all symptomatic individuals with signs or symptoms consistent with COVID-19 be tested by nucleic acid amplification testing (NAAT) or antigen testing. NAAT is the gold standard for detection of SARS-Cov-2 virus.
- Hospitalized patients (especially critically ill patients with unexplained respiratory illness)
- Symptomatic individuals who are healthcare workers or first responders; who have risk factors for severe disease; or who work or reside in congregate living settings
A rapid increase in test demand could exceed the capacity of laboratories as well as the ability of manufacturers to supply test kits and reagents and lead to further guidance from local and regional health authorities on testing prioritization.
- Have had no known exposure to COVID-19 but are being hospitalized in areas with a high prevalence of COVID-19 in the community (eg, hotspots)
- Are immunocompromised and are being admitted to the hospital
- Are undergoing an immunosuppressive procedure, regardless of a known exposure to COVID-19
- Are undergoing major time-sensitive surgeries, but have no known exposure to COVID-19
- Are undergoing a time-sensitive aerosol-generating procedure (eg, bronchoscopy) when personal protective equipment (PPE) is limited and testing is available, but have no known exposure to COVID-19
Exposure to COVID-19 can be assessed by antibody (serology) testing. This testing is not recommended for diagnosis and should not be used for patients in the acute phase of infection. There are currently no recommendations for using antibody tests to assess response to vaccination.
Antibody testing is also useful for vetting candidates interested in donating convalescent plasma, evaluating individuals who present with COVID-19-like disease but late in the course of the illness (when the sensitivity of molecular diagnostic testing is decreased), and in individuals with late complications of suspected COVID-19 disease. For example, SARS-CoV-2 serologic testing is suggested for children who present with suspected MIS-C.
Molecular Diagnostic Testing
A negative result indicates that SARS-CoV-2 RNA was not present in the specimen above the limit of detection. However, a negative result does not exclude the possibility of COVID-19 and should not be used as the sole basis for treatment or patient management. The possibility of a false-negative result should be considered if the patient’s recent exposures or clinical presentation suggests that COVID-19 is likely. Retesting may be advisable in symptomatic individuals with an intermediate or high clinical suspicion of COVID-19, and should be considered based on clinical judgment in combination with the recommendation of public health authorities.
Overall test sensitivity may be reduced if optimal sample collection is not followed. Early data suggest that some specimens, including nasal swab specimens, may lead to reduced test sensitivity as compared with saliva and NP swab specimens.
In some situations, it may be advisable to obtain a lower respiratory tract specimen for diagnostic testing because these specimens are thought to carry a higher viral load than upper respiratory tract specimens. Due to the high specificity of NAAT, a positive result based on an upper respiratory tract specimen is generally adequate to establish a COVID-19 diagnosis. For this reason, the IDSA panel suggests initially obtaining an upper respiratory tract sample rather than a lower respiratory sample when testing hospitalized patients with suspected COVID-19 lower respiratory tract infections. However, if the initial upper respiratory sample result is negative and the suspicion for disease remains high, the panel suggests collecting a lower respiratory tract sample rather than collecting another upper respiratory sample.
In intubated and mechanically ventilated patients with unknown COVID-19 status, the National Institutes of Health (NIH) recommends carefully collecting a lower respiratory tract specimen for diagnostic testing.
In the early stage of infection (within the first 7 days symptoms are experienced), antigen testing can be used to detect SARS-CoV-2 infection when NAAT is not available. This testing can also be used to screen individuals with known exposure to confirmed COVID-19 cases and individuals in high-risk congregate settings.
Antigen testing is less sensitive than NAAT and is associated with an increased risk of false-negative results. Because antigen testing requires a higher viral load for detection of SARS-CoV-2, it is most useful early in the course of illness when viral load is higher.
Clinicians should consider the performance characteristics of antigen tests when interpreting results. Negative and positive test results should be considered in the context of clinical observations, patient history, and local epidemiologic information. Confirmation testing by NAAT may be advised in some situations.
However, it is not necessary to perform confirmatory testing in the event of a negative result for an individual who is asymptomatic without known exposure, or in patients with a negative result obtained during routine screening or surveillance.
Testing for Exposure
Serology testing, also known as antibody testing, is used to detect antibodies against SARS-CoV-2 in serum or plasma. Early studies suggest the majority of patients with COVID-19 seroconvert approximately 2 weeks after symptom onset; because of this natural delay, serology testing is not recommended for COVID-19 diagnosis. Furthermore, there are not enough data available to determine if protective immunity is consistently achieved in all patients after infection and if that immunity wanes and/or disappears over time.
Studies suggest that severity of disease may affect the magnitude of antibody response. Both IgM and IgG develop almost simultaneously, generally 7-14 days after symptom onset, in response to SARS-CoV-2 infection. IgM persists for only a few weeks, whereas IgG levels are more durable and can sometimes be detected for months after natural infection. It is recommended that serology testing be performed 2-4 weeks after symptom onset. IgG and total antibody assays are useful for evaluating patients who present later in the disease course.
Although antibody testing is not recommended to diagnose infection, to assess vaccination response, or to infer an individual’s immunity to the virus, it may aid in determining the rate of exposure in a given population. Antibody testing is also useful for vetting candidates interested in donating convalescent plasma, evaluating individuals who present with COVID-19-like disease but late in the course of the illness (when the sensitivity of molecular diagnostic testing is decreased), and individuals with late complications of suspected COVID-19 disease (eg, multisystem inflammatory syndrome in children [MIS-C]).
Vaccination results in the production of antibodies to specific viral protein targets. Current EUA-approved COVID-19 vaccines target the spike protein of SARS-CoV-2. Therefore, serology assays that use the spike protein as a target will detect antibodies that develop in response to vaccination or to natural infection. Serology assays that target different proteins, such as the nucleocapsid protein, should only detect antibodies from natural infection.
ARUP offers two tests for IgG antibodies that target different SARS-CoV-2 proteins. One test detects IgG against the nucleocapsid protein, and the other detects IgG against the receptor-binding domain (RBD) of the spike protein. Test selection and interpretation should take into account the vaccination status of the patient.
Early data suggest that in some patients, COVID-19 may trigger cytokine storm syndrome, a phenomena marked by hyperinduction of proinflammatory cytokine production.
Cytokine testing is used primarily for research and to support attempts to understand the pathogenesis of immune, infectious, allergic, or inflammatory disorders. There are currently no well-defined guidelines on how the results should be interpreted and/or used to guide treatment decisions in COVID-19.
Increased venous thromboembolism (VTE) and arterial thrombotic events (eg, myocardial infarction, stroke) have been described in patients with severe COVID-19. However, the exact contributing factors to the observed increase in thrombotic risk are not yet fully understood. The most likely mechanism behind most of the thrombotic risk and coagulation test abnormalities appears to be endothelial damage within the lungs, which triggers inflammatory and coagulation cascades.
Disseminated intravascular coagulation (DIC) is another thrombotic mechanism that affects some patients, particularly those who are critically ill. Elevated D-dimer has been described in patients with COVID-19 infection who require intensive care unit (ICU) admission, but the elevation is not always to the very high level expected with DIC. In one single-center study from Wuhan, China, approximately 70% of patients who died as a result of COVID-19 met current diagnostic criteria for DIC as set forth by the International Society of Thrombosis and Haemostasis (ISTH). Prothrombin time (PT) may be mildly prolonged at admission in patients with COVID-19. Thrombocytopenia has been reported in some but not all patients with COVID-19.
Lupus anticoagulant and antiphospholipid antibodies have been reported in patients with COVID-19, but the significance of this finding is uncertain, given that transient antiphospholipid antibodies (present for <12 weeks) are described with other acute infections and do not necessarily represent a thrombotic risk factor.
Bleeding complications have not been widely reported in those with COVID-19. Platelet counts are variable in patients with COVID-19. One meta-analysis indicated that thrombocytopenia was more prominent in patients with more severe COVID-19. Low platelet counts have not been observed in all case series of patients with COVID-19.
The therapeutic implications and prognostic relevance of the abnormal hemostasis laboratory findings in COVID-19 are as yet unclear, and additional studies are needed. Prophylactic anticoagulation has been used in hospitalized patients with COVID-19, and recommendations around this are currently evolving. A 2021 American Society of Hematology (ASH) guideline on thromboprophylaxis in patients with COVID-19 recommends prophylactic intensity anticoagulation in patients with critical or acute COVID-19-related illness but without clinically suspected or confirmed venous thromboembolism (VTE).
Vaccine-Induced Immune Thrombotic Thrombocytopenia
A rare syndrome of unusual thrombotic events with thrombocytopenia has been reported in a small number of patients following receipt of two SARS-CoV-2 vaccines (ChAdOx1 nCov-19 [AstraZeneca] and Ad26.COV2.S [Johnson and Johnson/Janssen], both of which use recombinant adenovirus vectors). This syndrome, referred to as vaccine-induced immune thrombotic thrombocytopenia (VITT), appears to involve platelet-activating antibodies directed against PF4, but as a syndrome, it is clinically distinct from heparin-induced thrombocytopenia (HIT). The underlying pathogenesis of VITT requires further investigation to fully elucidate. Additionally, VITT appears to be rare based on current case reports (risk of less than one in 1,000,000 based on cases reported and vaccine doses given in the U.S.).
Patients with VITT presented 5-24 days postvaccination with thrombocytopenia and thromboses, which were located in unusual anatomic sites in some cases (eg, in cases of cerebral venous sinus thrombosis [CVST]). None of the patients had heparin exposure before development of thrombosis; however, anti-PF4 ELISA assays (typically used for diagnosis of HIT) were positive. At least three commercially available anti-PF4 ELISA assays have been described to detect the pathologic antibodies in these patients. Commercially available ELISAs use plates coated with heparin-PF4 or polyanion-PF4, and these may have different performance characteristics. Latex immunoassays and chemiluminescent immunoassays for anti-PF4 antibodies may be negative in patients with VITT. Functional platelet assays for heparin-induced thrombocytopenia (HIT), such as the serotonin release assay (SRA), showed more variable performance, and although some patients had positive results, others may show indeterminate or even negative results based on the preliminary data available. Samples for antibody testing in patients with suspected VITT should be collected before initiation of intravenous immunoglobulin (IVIG) therapy. Investigation into VITT, including identification of optimal laboratory testing, is ongoing; please refer to emerging guidelines updated on an ongoing basis, such as the ISTH Interim Guidance for the Diagnosis and Treatment on Vaccine-Induced Immune Thrombotic Thrombocytopenia and Science Briefs of the Ontario COVID-19 Science Advisory Table.
Mental Health Testing
Mental health issues that have been exacerbated by the pandemic include stress, depression, and anxiety. Drugs used to treat mental health conditions such as major depressive disorder are some of the most widely prescribed drugs in the U.S. However, these medications are highly variable in terms of patient response and are associated with undesirable side effects. Pharmacogenetic testing and/or therapeutic drug monitoring may assist in the mental health care and management of patients with COVID-19.
Pharmacogenetic testing assesses genetic variations associated with drug response or drug disposition that may predispose a patient to be at risk for drug-related toxicity, nonstandard dose requirements, or lack of therapeutic benefit. Refer to the ARUP Consult Pharmacogenetics topic for examples of antidepressant testing.
Therapeutic drug monitoring is the clinical practice of measuring specific drugs or their metabolites at designated intervals to maintain a therapeutic concentration in a patient’s bloodstream and optimize individual dosage regimens. Refer to the ARUP Consult Therapeutic Drug Monitoring topic for examples of antidepressant and antipsychotic tests.
ARUP Laboratory Tests
Detects the 2019 novel coronavirus (SARS-CoV-2)
Specimen types include NP swab, saliva (self-collected while observed by a health care provider), OP swab, and/or nasal swab; for more information, refer to ARUP’s COVID-19 Specimen Collection Guide
ARUP is accepting new COVID-19 molecular test orders; for more information, visit our COVID-19 Test Information for Hospitals and Labs page
Use for the qualitative detection of IgG antibodies against the nucleocapsid protein of SARS-CoV-2 (COVID-19) that develop in response to natural infection with SARS-CoV-2; these antibodies do not develop as a result of a COVID-19 vaccination; there are no current recommendations for assessing COVID-19 vaccine response
Results are reported as “negative” or “positive”
Not recommended for COVID-19 diagnosis
This Abbott assay is available under the FDA’s Emergency Use Authorization (EUA)
Use for the semiquantitative detection of IgG antibodies against the receptor-binding domain (RBD) region of the spike protein (S1) of SARS-CoV-2 (COVID-19) that develop in response to natural infection with SARS-CoV-2 or from a COVID-19 vaccination; there are no current recommendations for assessing COVID-19 vaccine response
Results are reported as “negative” or “positive” and include an index value
Not recommended for COVID-19 diagnosis
This Siemens assay has received Emergency Use Authorization (EUA) as a semiquantitative assay
Primarily used for research and to support attempts to understand the pathogenesis of immune, infectious, allergic, or inflammatory disorders
Recommended test for evaluating patients with thrombocytopenia and thrombosis who were recently vaccinated
Semi-Quantitative Enzyme-Linked Immunosorbent Assay
May be used to evaluate patients with thrombocytopenia and thrombosis who were recently vaccinated; includes recommended initial test, but the results of reflex SRA component may be variable
Semi-Quantitative Enzyme-Linked Immunosorbent Assay/Serotonin Release Assay
May be used as a follow-up test to evaluate positive ELISA results; not recommended as a first-line test because results may be variable
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