COVID-19 - SARS-CoV-2

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.

Viral Detection

Diagnosis

Diagnostic testing for SARS-CoV-2 identifies current infection in symptomatic individuals and asymptomatic individuals with or without consistent symptoms. 

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, regardless of vaccination status or previous infection.   NAAT is the gold standard for detection of SARS-Cov-2 virus. 

Diagnostic testing for asymptomatic individuals with known or suspected recent exposure to SARS-CoV-2 may also be advised. 

In the event of overwhelming demand and diminished capacity for testing, prioritizing testing for high-risk groups (eg, hospitalized patients, symptomatic healthcare workers, or first responders) may be necessary. 

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.

Screening

The goal of screening is to identify individuals who may be contagious so that further transmission can be prevented. Both NAAT and antigen testing can be used for this purpose.  

The CDC suggests that testing for SARS-CoV-2 virus may be most valuable in areas with substantial or high community-transmission levels, in areas with low vaccination coverage, and in certain settings (eg, schools, high-density work sites, congregate settings). 

The IDSA recommends screening asymptomatic individuals who :

• 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

Surveillance

Surveillance testing is used to gain information at a population level in order to inform public health planning. NAAT or antigen testing may be used for this purpose. 

Antibody Testing

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. 

Although antibody testing is not currently central to COVID-19 clinical management, it can be used to study the seroprevalence of the virus in the general 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 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. 

Laboratory Testing

Diagnosis

Viral Detection

Molecular Diagnostic Testing

Molecular diagnostic assays, such as NAATs, are used to detect SARS-CoV-2 in respiratory specimens of patients suspected of having COVID-19.  

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. 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.

Antigen Testing

Antigen testing, performed on nasal or throat swab specimens, can also be used to detect SARS-CoV-2 infection. Antigen testing is often performed at the point of care, allowing for quicker results. 

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

Serology testing, also known as antibody testing, is used to detect antibodies against SARS-CoV-2 in serum or plasma. 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, data suggests that protective immunity is not 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.   

The CDC recommends serologic assays with very high sensitivity and specificity due to their likelihood of exhibiting high expected predictive values. 

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 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 antibodies that bind to 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.

Other Testing

Cytokine Testing

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.

Hemostasis Testing

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.  

Hyperfibrinogenemia has been reported in individuals with COVID-19, which may lead to increased fibrin formation and polymerization, increased thrombotic risk, and elevated D-dimer. 

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.