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Testing for SARS-CoV-2 Infection

Last Updated: December 17, 2020

Testing for SARS-CoV-2 Infection
Summary Recommendations
  • The COVID-19 Treatment Guidelines Panel (the Panel) recommends using a nucleic acid amplification test (NAAT) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on a sample collected from the upper respiratory tract (i.e., nasopharyngeal, nasal, or oropharyngeal specimen) to diagnose acute infection (AIII).
  • For intubated and mechanically ventilated adults who are suspected to have COVID-19 but who do not have a confirmed diagnosis:
    • The Panel recommends obtaining lower respiratory tract samples to establish a diagnosis of COVID-19 if an initial upper respiratory sample is negative (BII).
    • The Panel recommends obtaining endotracheal aspirates rather than bronchial wash or bronchoalveolar lavage samples when obtaining lower respiratory samples to establish a diagnosis of COVID-19 (BII).
  • The Panel recommends against the use of serologic testing as the sole basis for diagnosis of acute SARS-CoV-2 infection (AIII).
  • The Panel recommends against the use of serologic testing to determine whether a person is immune to SARS-CoV-2 infection (AIII).
Rating of Recommendations: A = Strong; B = Moderate; C = Optional
Rating of Evidence: I = One or more randomized trials with clinical outcomes and/or validated laboratory endpoints; II = One or more well-designed, nonrandomized trials or observational cohort studies; III = Expert opinion

Diagnostic Testing for SARS-CoV-2 Infection

Testing to diagnose severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (i.e., using a nucleic acid amplification test [NAAT] or an antigen test to detect SARS-CoV-2) should be done for all persons who have symptoms that are consistent with COVID-19 and for people who are known to have high-risk exposures to SARS-CoV-2. Ideally, diagnostic testing should also be performed for people who are likely to be at repeated risk of exposure, such as health care workers and first responders. Testing should be considered for individuals who spend time in environments with high population densities (e.g., those who work at or attend a school in person, those who work in the food industry) and for persons after they travel. Testing requirements may vary by state, local, and employer policies. For individuals who are planning to travel, documentation of a recent negative test result may be required to enter some states or countries; in some cases, the documentation may be an acceptable alternative to a period of quarantine upon arrival.

The Food and Drug Administration (FDA) has issued emergency use authorizations (EUAs) for a number of SARS-CoV-2 diagnostic tests (e.g., NAATs, antigen tests),1 but currently there are no FDA-approved diagnostic tests.

Although nasopharyngeal specimens remain the current standard for SARS-CoV-2 diagnostic testing, nasal (anterior nares or mid-turbinate) or oropharyngeal swabs are acceptable alternatives.2 Lower respiratory tract samples have a higher yield than upper tract samples; however, they are often not obtained because of concerns about aerosolization of the virus during sample collection procedures. Some tests that have received EUAs can also be performed on saliva specimens. Other sample types, including stool samples, are currently being studied.

Some tests that have received EUAs allow for self-collection of specimens at home, but these specimens must be sent to a laboratory for processing. In addition, some tests allow for collection and testing of specimens by trained personnel in nonclinical settings, such as in the home or in nursing or assisted living facilities. This allows real-time antigen results to be obtained on site.

Nucleic Acid Amplification Testing for SARS-CoV-2 Infection

Reverse transcriptase polymerase chain reaction (RT-PCR)-based diagnostic tests (which detect viral nucleic acids) are considered the gold standard for detecting current SARS-CoV-2 infection. More recently, NAATs have included a variety of additional platforms (e.g., real-time loop mediated isothermal amplification). Clinically, there may be a window period of up to 5 days after exposure before viral nucleic acids can be detected. However, false negative NAAT results can also occur outside of this 5-day window. Therefore, a single negative test result does not completely exclude SARS-CoV-2 infection in people with a high likelihood of infection based on their exposure history and/or their clinical presentation, and repeat testing using a NAAT should be considered.3

SARS-CoV-2 poses several diagnostic challenges, including potentially discordant shedding of virus from the upper versus the lower respiratory tract. Due to the high specificity of NAAT, there is no need to obtain a lower respiratory tract sample to diagnose COVID-19 when a patient with recent onset of COVID-19-compatible symptoms has a positive NAAT on an upper respiratory sample. Because the viral load is higher in the lower respiratory tract than in the upper respiratory tract of patients with COVID-19, severe acute respiratory syndrome (SARS), and Middle East respiratory syndrome (MERS), more positive results are reported for lower respiratory tract specimens.4-10 In intubated or mechanically ventilated patients who have clinical signs and symptoms consistent with COVID-19 pneumonia and an initial negative result on an upper respiratory tract sample, a NAAT of a lower respiratory tract sample is recommended (BII). The COVID-19 Treatment Guidelines Panel (the Panel) recommends obtaining endotracheal aspirates rather than bronchial wash or bronchoalveolar lavage (BAL) samples when collecting lower respiratory samples to establish a diagnosis of COVID-19 (BII).

BAL and sputum induction are aerosol-generating procedures that should be performed only with careful consideration of the risk of aerosol generation to staff. Endotracheal aspiration appears to carry a lower risk of aerosolization than BAL, and in the view of some experts, the sensitivity and specificity of endotracheal aspirates and BAL specimens are comparable.

Antigen Testing for SARS-CoV-2 Infection

When compared with RT-PCR-based tests, antigen-based diagnostic tests (which detect viral antigens) are less sensitive but have a similarly high specificity. Antigen tests perform best early in the course of symptomatic SARS-CoV-2 infection, when the viral load is thought to be highest. When a person who is strongly suspected of having SARS-CoV-2 infection receives a negative result on an initial antigen test, repeat testing using a NAAT should be considered. Advantages of antigen-based tests are their low cost and rapid turnaround. The availability of immediate results makes antigen-based tests an attractive option for point-of-care testing in high-risk congregate settings where preventing transmission is critical. Antigen-based tests also allow for repeat testing to quickly identify persons with SARS-CoV-2 infection. Currently, there are limited data to guide the use of rapid antigen tests to detect or exclude SARS-CoV-2 infection in asymptomatic persons or to determine whether a person who was previously confirmed to have SARS-CoV-2 infection is still infectious.11

Serologic or Antibody Testing for Diagnosis of SARS-CoV-2 Infection

Unlike NAATs and antigen tests for SARS-CoV-2 that detect the presence of the virus, serologic or antibody tests are intended to identify persons with recent or prior SARS-CoV-2 infection. Because it may take 21 days or longer after symptom onset for seroconversion or detection of immunoglobulin (Ig) M and/or IgG antibodies to SARS-CoV-2,12-17 the Panel does not recommend the use of serologic testing as the sole basis for diagnosing acute SARS-CoV-2 infection (AIII). Given that NAATs and antigen tests for SARS-CoV-2 occasionally yield false negative results, serologic tests have been used in some settings as an additional diagnostic test for patients who are strongly suspected to have SARS-CoV-2 infection. Using serology in combination with a NAAT to detect IgG or total antibodies 3 to 4 weeks after symptom onset maximizes the sensitivity and specificity to detect past infection.

No serologic tests for SARS-CoV-2 are approved by the FDA; some, but not all, commercially available serologic tests for SARS-CoV-2 have received EUAs issued by the FDA.1 Several professional societies and federal agencies, including the Infectious Diseases Society of America, the Centers for Disease Control and Prevention, and the FDA, provide guidance for clinicians regarding the use of serologic testing for SARS-CoV-2.

Several factors should be considered when using these tests, including:

  • Important performance characteristics, including the sensitivity and specificity (i.e., the rates of true positive and true negative results) of many of the commercially available serologic tests, have not been fully characterized. Serologic assays that have FDA EUAs should be used for public health and clinical use. Formal comparisons of serologic tests are in progress.
  • Serologic assays may detect IgM, IgG, IgA, and/or total antibodies, or a combination of IgM and IgG antibodies. Serologic assays that detect IgG and total antibodies have higher specificity to detect past infection than assays that detect IgM and/or IgA antibodies or a combination of IgM and IgG antibodies.
  • False positive test results may occur due to cross-reactivity from pre-existing antibodies to other coronaviruses.

Serologic Testing and Immunity to SARS-CoV-2 Infection

The Panel recommends against the use of serologic testing to determine whether a person is immune to SARS-CoV-2 infection (AIII). If serologic tests are performed and antibodies are detected, the results should be interpreted with caution for the following reasons:

  • It is currently unclear how long antibodies persist following infection; and
  • It is currently unclear whether the presence of antibodies confers protective immunity against future infection.

In communities where the prevalence of SARS-CoV-2 infection is low, the proportion of false positives among all positive test results may be quite high. In these situations, confirmatory testing using another antibody assay, ideally one that uses a different antigenic target (e.g., the nucleocapsid phosphoprotein if the first assay targeted the spike glycoprotein), can substantially improve the probability that persons with positive test results are antibody positive.

Assuming that the test is reliable, serologic tests that identify recent or prior SARS-CoV-2 infection may be used to:

  • Determine who may be eligible to donate convalescent plasma;
  • Measure the immune response in SARS-CoV-2 vaccine studies; and
  • Estimate the proportion of the population exposed to SARS-CoV-2.

Serologic tests should not be used to:

  • Determine how to separate persons in congregate settings (e.g., schools, dormitories, correctional facilities) based on SARS-CoV-2 status; or
  • Determine whether persons should return to the workplace.

  1. Food and Drug Administration. Coronavirus disease 2019 (COVID-19) emergency use authorizations for medical devices. 2020. Available at: https://www.fda.gov/medical-devices/emergency-situations-medical-devices/emergency-use-authorizations. Accessed December 10, 2020.
  2. Centers for Disease Control and Prevention. Interim guidelines for collecting, handling, and testing clinical specimens from persons for coronavirus disease 2019 (COVID-19). 2020. Available at: https://www.cdc.gov/coronavirus/2019-ncov/lab/guidelines-clinical-specimens.html. Accessed December 10, 2020.
  3. Kucirka LM, Lauer SA, Laeyendecker O, Boon D, Lessler J. Variation in false-negative rate of reverse transcriptase polymerase chain reaction-based SARS-CoV-2 tests by time since exposure. Ann Intern Med. 2020;173(4):262-267. Available at: https://www.ncbi.nlm.nih.gov/pubmed/32422057.
  4. Chan PK, To WK, Ng KC, et al. Laboratory diagnosis of SARS. Emerg Infect Dis. 2004;10(5):825-831. Available at: https://www.ncbi.nlm.nih.gov/pubmed/15200815.
  5. Tang P, Louie M, Richardson SE, et al. Interpretation of diagnostic laboratory tests for severe acute respiratory syndrome: the Toronto experience. CMAJ. 2004;170(1):47-54. Available at: https://www.ncbi.nlm.nih.gov/pubmed/14707219.
  6. Memish ZA, Al-Tawfiq JA, Makhdoom HQ, et al. Respiratory tract samples, viral load, and genome fraction yield in patients with Middle East respiratory syndrome. J Infect Dis. 2014;210(10):1590-1594. Available at: https://www.ncbi.nlm.nih.gov/pubmed/24837403.
  7. Centers for Disease Control and Prevention. Evaluating and testing persons for coronavirus disease 2019 (COVID-19). 2020. Available at: https://www.cdc.gov/coronavirus/2019-nCoV/hcp/clinical-criteria.html. Accessed December 10, 2020.
  8. Centers for Disease Control and Prevention. Interim guidelines for collecting, handling, and testing clinical specimens from persons under investigation (PUIs) for Middle East Respiratory Syndrome Coronavirus (MERS-CoV)—Version 2.1. 2020. Available at: https://www.cdc.gov/coronavirus/mers/guidelines-clinical-specimens.html. Accessed December 10, 2020.
  9. Hase R, Kurita T, Muranaka E, Sasazawa H, Mito H, Yano Y. A case of imported COVID-19 diagnosed by PCR-positive lower respiratory specimen but with PCR-negative throat swabs. Infect Dis (Lond). 2020. Available at: https://www.ncbi.nlm.nih.gov/pubmed/32238024.
  10. Wang W, Xu Y, Gao R, et al. Detection of SARS-CoV-2 in different types of clinical specimens. JAMA. 2020. Available at: https://www.ncbi.nlm.nih.gov/pubmed/32159775.
  11. Centers for Disease Control and Prevention. Coronavirus Disease 2019 (COVID-19): interim guidance for rapid antigen testing for SARS-CoV-2. 2020. Available at: https://www.cdc.gov/coronavirus/2019-ncov/lab/resources/antigen-tests-guidelines.html. Accessed December 10, 2020.
  12. Guo L, Ren L, Yang S, et al. Profiling early humoral response to diagnose novel coronavirus disease (COVID-19). Clin Infect Dis. 2020. Available at: https://www.ncbi.nlm.nih.gov/pubmed/32198501.
  13. Haveri A, Smura T, Kuivanen S, et al. Serological and molecular findings during SARS-CoV-2 infection: the first case study in Finland, January to February 2020. Euro Surveill. 2020;25(11). Available at: https://www.ncbi.nlm.nih.gov/pubmed/32209163.
  14. Long QX, Liu BZ, Deng HJ, et al. Antibody responses to SARS-CoV-2 in patients with COVID-19. Nat Med. 2020. Available at: https://www.ncbi.nlm.nih.gov/pubmed/32350462.
  15. Okba NMA, Muller MA, Li W, et al. Severe acute respiratory syndrome coronavirus 2-specific antibody responses in coronavirus disease patients. Emerg Infect Dis. 2020;26(7):1478-1488. Available at: https://www.ncbi.nlm.nih.gov/pubmed/32267220.
  16. Xiang F, Wang X, He X, et al. Antibody detection and dynamic characteristics in patients with COVID-19. Clin Infect Dis. 2020. Available at: https://www.ncbi.nlm.nih.gov/pubmed/32306047.
  17. Zhao J, Yuan Q, Wang H, et al. Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019. Clin Infect Dis. 2020. Available at: https://www.ncbi.nlm.nih.gov/pubmed/32221519.