Novel Coronavirus Disease 2019 (COVID-19) - Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

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, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes novel coronavirus disease 2019 (COVID-19), can lead to more severe illness.

As of spring 2020, SARS-CoV-2 is widespread in the United States and many other countries. It is believed that the virus originated in a market in China through animal-to-human transmission. Subsequent 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. 

Reverse transcriptase polymerase chain reaction (RT-PCR) testing is currently the only recommended method for SARS-CoV-2 diagnosis. Testing decisions should be based on local epidemiology, clinical signs and symptoms, and the course of illness. The environment surrounding COVID-19 testing is evolving rapidly. Clinicians are advised to consult the CDC for the most current clinical criteria. 

Quick Answers for Clinicians

What are the clinical features of COVID-19?

Clinical presentation ranges from asymptomatic infection to mild, acute upper respiratory symptoms to more severe flulike illness and pneumonia. Frequently reported symptoms of patients admitted to the hospital include fever, cough, and shortness of breath.  The course of fever in patients with COVID-19 is not fully understood; it may be prolonged or intermittent.  Limited information is available about the spectrum of clinical illness related to COVID-19 in children, although they do appear to present with more mild signs and symptoms than adults. 

Who should be tested for COVID-19?

As of March 24, 2020, testing to determine possible severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection should be prioritized for hospitalized patients and symptomatic healthcare facility workers. Refer to Indications for Testing for other prioritized populations. For the most up-to-date national criteria, visit the CDC’s Evaluating and Testing Persons for Coronavirus Disease 2019 (COVID-19) site.  

Local and regional health authorities may provide additional guidance for prioritizing patients for COVID-19 testing. Clinicians are also encouraged to consider testing for other causes of respiratory illness, including influenza.

What are the risk factors for severe COVID-19 disease?

Data are still limited, but older patients and those with chronic medical conditions appear to be at higher risk for severe illness if infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). 

Do existing respiratory virus panels detect SARS-CoV-2?

No. Multipathogen molecular assays can detect other coronaviruses, but not severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).  New assays are under development from multiple organizations, however, so this information may change.

Which laboratory tests are available to diagnose COVID-19?

Reverse transcriptase polymerase chain reaction (RT-PCR) testing is currently used to diagnose COVID-19. Rapid point-of-care tests based on isothermal amplification have recently become available. At this time, there are limited data available to compare the sensitivity and specificity of these assays against RT-PCR.

The CDC is working to develop a serology test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).  Currently, this testing is not available in the United States, and, consequently, there is no means of testing for previous exposure to SARS-CoV-2.

Which specimens are acceptable for SARS-CoV-2 testing? Which collection media is preferred?

Nasopharyngeal (NP) swabs are the preferred specimens for SARS-CoV-2 qualitative polymerase chain reaction (PCR) testing. Alternatively, both NP and oropharyngeal (OP) swabs together are acceptable. Specimens should be collected with NP ultrafine or equivalent swabs. Dacron, polyester-tipped, or any other flocked swabs are acceptable alternatives. Cotton-tipped, calcium alginate, and wooden-handled swabs are NOT acceptable due to test interference. Viral transport media and universal transport media (VTM/UTM) are the preferred collection systems. 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 qualitative reverse transcriptase (RT)-PCR testing.

Some laboratories may accept alternative specimen types; clinicians are advised to check with their performing laboratory for specific specimen requirements. There are limited data on how alternative specimen types affect test sensitivity, but evidence thus far suggests that specimens such as nasal swabs are less sensitive than NP swabs. 

Indications for Testing

The CDC’s clinical criteria for persons who should be evaluated for COVID-19  are rapidly evolving as more is learned about the disease. Clinicians should use their judgment to determine if a patient has signs and symptoms compatible with COVID-19 and whether the patient should be tested.  The CDC recommends the following categories of prioritization for testing patients with suspected COVID-19 infection.

Priorities for Testing Patients with Suspected COVID-19 Infection

Priority 1

  • Ensure optimal care options for all hospitalized patients
  • Lessen the risk of healthcare-associated infections
  • Maintain the integrity of the healthcare system

Test

  • Hospitalized patients
  • Healthcare workers with symptoms

Priority 2

  • Ensure those at highest risk of infection complications are rapidly identified and appropriately triaged

Test

  • Patients in long-term care facilities with symptoms
  • Patients older than 65 yrs with symptoms
  • Patients with underlying conditions with symptoms
  • First responders with symptoms

Priority 3

  • As resources allow, test individuals to decrease community spread
  • Ensure health of essential workers

Test

  • Critical infrastructure workers with symptoms
  • Individuals who do not meet any of the above categories with symptoms
  • Healthcare facility workers and first responders
  • Individuals with mild symptoms in communities experiencing high numbers of COVID-19 hospitalizations

Nonpriority

Test

  • Individuals without symptoms
Source: CDC, Criteria to Guide Evaluation and Laboratory Testing for COVID-19 

Local and regional health authorities may provide additional guidance for prioritizing patients for COVID-19 testing. Prioritization of patients is important because 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.

Laboratory Testing

Diagnosis

RT-PCR testing is used to detect SARS-CoV-2 in respiratory specimens of patients meeting the CDC’s clinical criteria for COVID-19. SARS-CoV-2 RNA is generally detectable in nasopharyngeal (NP) and oropharyngeal (OP) swabs during the acute phase of infection. 

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 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 swabs, may reduce test sensitivity. 

Testing for Previous Exposure

The CDC is working to develop a serology test for SARS-CoV-2.  However, at this time, serology testing is not widely available for SARS-CoV-2, and, consequently, there is no means of testing for previous exposure to SARS-CoV-2.

ARUP Lab Tests

ARUP continues to perform SARS-CoV-2 testing for the state of Utah. At this time, ARUP is unable to accept testing from national clients. The environment surrounding COVID-19 testing is evolving rapidly. Please refer to ARUP’s Response to Coronavirus Disease 2019 (COVID-19) page for our most up-to-date testing information.

Medical Experts

Contributor

Couturier

Marc Roger Couturier, PhD, D(ABMM)
Associate Professor of Clinical Pathology, University of Utah
Medical Director, Parasitology/Fecal Testing, Infectious Disease Antigen Testing, Bacteriology, and Molecular Amplified Detection, ARUP Laboratories
Contributor

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