Diagnostics for Coronavirus Disease 2019 (COVID-19) Patients 

Updated: Jun 16, 2020
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What is the incubation period for coronavirus disease 2019 (COVID-19)?

The incubation period for coronavirus disease 2019 (COVID-19) is believed to extend to 14 days, with a median time of 4-5 days from exposure to symptomatic onset. [1]  In one study, 97.5% of symptomatic patients developed symptoms within 11.5 days of becoming infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). [1]

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What is the range of illness severity of patients with coronavirus disease 2019 (COVID-19)?

Patients with coronavirus disease 2019 (COVID-19) can be grouped into the following illness categories [2] :

  • Asymptomatic or presymptomatic infection: Individuals who test positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) but have no symptoms

  • Mild illness: Individuals with any of various signs and symptoms (eg, fever, cough, sore throat, malaise, headache, muscle pain) without shortness of breath, dyspnea, or abnormal imaging

  • Moderate illness: Individuals with evidence of lower respiratory disease by clinical assessment or imaging and an oxygen saturation (SaO2) over 93% on room air at sea level

  • Severe illness: Individuals with a respiratory frequency of over 30 breaths per minute, SaO2 up to 93% on room air at sea level, ratio of arterial partial pressure of oxygen to fraction of inspired oxygen (PaO2/FiO2) below 300, or more than 50% lung infiltrates

  • Critical illness: Individuals with respiratory failure, septic shock, and/or multiple organ dysfunction.

In general, the prevalence of the range of illness severity is as follows [1] :

  • Mild to moderate (mild symptoms up to mild pneumonia): 81%

  • Severe (dyspnea, hypoxia, or >50% lung involvement on imaging): 14%

  • Critical (respiratory failure, shock, or multiorgan system dysfunction): 5%

Discussion

In a Chinese study of over 44,000 patients, all deaths occurred among patients with critical illness, with a 2.3% overall case fatality rate but a 49% case fatality rate among patients with critical disease. [1]  In the Chinese pediatric population, there was a lower illness severity, with 94% having asymptomatic, mild or moderate disease; 5% having severe disease, and less than 1% having critical disease.

Among US COVID-19 cases with known disposition, 19% were hospitalized and 6% were admitted to the intensive care unit (ICU).

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What are the signs and symptoms of patients with coronavirus disease 2019 (COVID-19)?

Patients with coronavirus disease 2019 (COVID-19) have varying signs and symptoms at the onset of illness. However, most patients will experience the following [1] :

  • Fever (83-99%)

  • Cough (59-82%)

  • Fatigue (44-70%)

  • Anorexia (40-84%)

  • Shortness of breath (31-40%)

  • Sputum production (28-33%)

  • Myalgias (11-35%)

Discussion

Atypical presentations have been described, and older adults and persons with medical comorbidities may have delayed presentation of fever and respiratory symptoms. [1] Fever has been present in 44% of patients at hospital admission and later developed in 89% during hospitalization.

Less common symptoms (< 10%) include headache, confusion, rhinorrhea, sore throat, hemoptysis, vomiting, and diarrhea. [1] Some patients have experienced gastrointestinal symptoms such as diarrhea and nausea prior to developing fever and lower respiratory tract signs and symptoms. Anecdotally, anosmia or ageusia may preceed the onset of respiratory symptoms, but more information is needed to understand its role in identifying COVID-19.

Signs/symptoms in pediatric patients are similar to those of adults but are usually milder, with most children presenting with symptoms of upper respiratory infection. [1] However, severe outcomes have been reported in children including COVID-19 associated deaths. Data suggest that infants (age < 12 months) may be at higher risk for severe illness from COVID-19 compared to older children. Centers for Disease Control and Prevention (CDC) and partners are also investigating reports of multisystem inflammatory syndrome in children (MIS-C) associated with COVID-19.

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What is known about asymptomatic and presymptomatic infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)?

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has been documented in patients who never develop symptoms (asymptomatic) and in those who are not yet symptomatic (presymptomatic). [1] Because routine testing is not performed in asymptomatic persons, the prevalence of asymptomatic infection and detection of presymptomatic infection remains unclear.

In one study, as many as 13% of pediatric SARS-CoV-2 infections confirmed by reverse transcription polymerase chain reaction (RT-PCR) were asymptomatic. [1] In a separate study of skilled nursing facility residents infected with SARS-CoV-2 from a healthcare worker, half were asymptomatic or presymptomatic at the time of contact tracing evaluation and testing.

Chest imaging anomalies may be present before symptomatic onset. [1] Some data suggest a tendency for detection of presymptomatic infection in younger individuals as well as a lesser likelihood of being associated with viral pneumonia.

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What is known about asymptomatic and presymptomatic transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)?

Epidemiologic studies have documented severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission during the presymptomatic incubation period, and asymptomatic transmission has been suggested in other reports. [1]

Virologic studies using reverse transcription polymerase chain reaction (RT-PCR) have also detected SARS-CoV-2 with low cycle thresholds, indicating larger quantities of viral RNA. Viable virus has also been cultured among persons with asymptomatic and presymptomatic SARS-CoV-2 infection. [1]

It is not yet known what exact degree of SARS-CoV-2 viral RNA shedding confers risk of transmission, but the greatest transmission risk is thought to be when patients are symptomatic, because viral shedding is greatest at the time of symptom onset and falls over the course of several days to weeks. [1] However, the proportion of SARS-CoV-2 transmission in the population due to asymptomatic or presymptomatic infection compared to symptomatic infection is unclear.

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What is the clinical progression of patients with coronavirus disease 2019 (COVID-19)?

Among patients who developed severe disease, note the following clinical progression [1] :

  • Medium time to dyspnea: Range of 5 to 8 days

  • Median time to acute respiratory distress syndrome (ARDS): Range of 8 to 12 days

  • Median time to admission to the intenstive care unit (ICU): Range of 10 to 12 days

Note:  Some patients can rapidly deteriorate 1 week after illness onset. Among all hospitalized patients, 26% to 32% of patients were admitted to the ICU. [1]  Moreover, among all patients, 3% to 17% developed ARDS, compared to 20% to 42% for hospitalized patients and 67% to 85% for those admitted to the ICU. Mortality among COVID-19 ICU patients ranged from 39% to 72%. The median length of hospitalization among survivors was 10 to 13 days.

Critically ill patients admitted to an intensive care unit (ICU) generally require the following [2] :

  • High-flow oxygen therapy (11-64%)

  • Mechanical ventilation (47-71%)

  • Respiratory support with extracorporeal membrane oxygenation (ECMO) (3-12%)

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What are risk factors for severe illness in patients with coronavirus disease 2019 (COVID-19)?

Critically ill patients with coronavirus disease 2019 (COVID-19) are usually older (median age 66 years vs 51 years) and have underlying comorbid conditions (72% vs 37%). [2]

Age

Age is a strong risk factor for severe illnes, complications, and death. In a Chinese study comprising more than 44,000 patients with confirmed COVID-19, mortality data included the following [1] :

  • Age ≥80 years: 14.8%

  • Age 70-79 years: 8.0%

  • Age 60-69 years: 3.6%

  • Age 50-59 years: 1.3%

  • Age 40-49 years: 0.4%

  • Age < 40 years: 0.2%.

Similarly, early US epidemiologic data indicate the following case fatalities [1] :

  • Age ≥85 years: 10-27%

  • Age 65-84 years: 3-11%

  • Age 55-64%: 1-3%

  • Age 0-54 years: < 1%

Comorbidities

In the same Chinese study mentioned above, patients without an underlying condition had an overall case fatality rate of 0.9%. [1] Patients with the following comorbidities had high case fatality rates, as follows:

  • Cardiovascular disease: 10.5%

  • Diabetes: 7.3%

  • Chronic respiratory disease: About 6%

  • Hypertension: About 6%

  • Cancer: About 6%

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What data are available about reinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)?

There are no data concerning the possibility of reinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) after recovery from coronavirus disease 2019 (COVID-19). [1] Thus, previous infection with SARS-CoV-2 has not been proven to confer immunity. [2]

Viral RNA shedding falls as symptoms resolve and may continue for days to weeks. [1] However, RNA detection during recovery does not necessarily indicate the presence of viable infectious virus. Clinical recovery has been correlated with the detection of immunoglobulin (Ig)M and IgG antibodies, which signal the development of immunity. [1]

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What are complications of patients with coronavirus disease 2019 (COVID-19)?

Complications of patients with coronavirus disease 2019 (COVID-19) include the following [1, 2] :

  • Pneumonia

  • Hypoxemic respiratory failure/acute respiratory distress syndrome (ARDS)

  • Diffuse alveolar damage

  • Secondary bacterial infections

  • Sepsis and septic shock

  • Cardiac injury

  • Cardiomyopathy

  • Arrhythmia

  • Sudden cardiac death

  • Acute kidney injury

  • Liver dysfunction

  • Multiorgan failure

  • Thromboembolism

  • Gastrointestinal bleeding

  • Critical illness polyneuropathy/myopathy

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Are patients with coronavirus disease 2019 (COVID-19) at risk for hypercoagulability?

Some patients with coronavirus 2019 (COVID-19) may develop signs of a hypercoagulable state and be at increased risk for venous and arterial thrombosis of large and small vessels. [1] The pathogenesis for COVID-19-associated hypercoagulability remains unknown. However, hypoxia and systemic inflammation secondary to COVID-19 may lead to high levels of inflammatory cytokines and activation of the coagulation pathway.

Common laboratory abnormalities associated with COVID-19 coagulopathy among hospitalized patients include the following [1] :

  • Mild thrombocytopenia

  • Elevated D-dimer levels, which have been strongly associated with greater risk of death

  • Increased fibrin degradation products

  • Prolonged prothrombin time

The most frequently reported thrombotic complications in hospitalized patients are deep venous thrombosis and pulmonary embolism. [1] Others include the following:

  • Microvascular thrombosis of the toes

  • Clotting of catheters

  • Myocardial injury with ST-segment elevation

  • Large vessel strokes

Limited data are available to inform clinical management around prophylaxis or treatment of venous thromboembolism in COVID-19 patients.

Several national professional associations provide resources for up-to-date information concerning COVID-19-associated hypercoagulability, including management of anticoagulation. This is a rapidly evolving topic, with new information released often.

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What are common laboratory findings in patients with coronavirus disease 2019 (COVID-19)?

Lymphopenia (83%) is the most common laboratory finding in hospitalized patients with coronavirus disease 2019 (COVID-19). [1]

Findings that may be associated with more illness severity include the following [1] :

  • Lymphopenia

  • Neutrophilia

  • Elevated levels of serum alanine aminotransferase and aspartate aminotransferase

  • Elevated lactate dehydrogenase level

  • High C-reactive protein (CRP) level

  • High ferritin levels

Elevated D-dimer and lymphopenia have been associated with mortality.

Although procalcitonin is typically normal on admission, levels may increase among those admitted to the intensive care unit (ICU).

Critically ill patients generally have high plasma levels of inflammatory makers, suggesting potential immune dysregulation.

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What are common radiologic findings in patients with coronavirus disease 2019 (COVID-19)?

Chest radiographs of patients with COVID-19 typically demonstrate bilateral air-space consolidation, although plain films may be unremarkable early in the disease. [1]

Chest computed tomography (CT) scans from patients with COVID-19 typically demonstrate bilateral, peripheral ground-glass opacities, a nonspecific finding that also overlaps with other infections. [1] Thus, the diagnostic value of chest CT imaging for COVID-19 may be low and dependent upon radiographic interpretation. Findings from one study found that 56% of patients who presented within 2 days of diagnosis had a normal CT scan, whereas other studies identified chest CT abnormalities in patients before SARS-CoV-2 RNA was detected. [1]

Because of these and other variabilities in chest imaging findings, chest radiography or CT scanning alone is not recommended for the diagnosis of COVID-19. The American College of Radiology also does not recommend CT scanning for screening or as a first-line test for diagnosis of COVID-19. [1]

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What diagnostic test is used to detect coronavirus disease 2019 (COVID-19)?

Authorized assays for viral testing include those that detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid or antigen. [1] Viral (nucleic acid or antigen) tests check samples from the respiratory system (such as nasal swabs) and identify if an infection with SARS-CoV-2 is present. Viral tests are recommended to diagnose acute infection. Some tests are point-of-care tests, meaning results may be available at the testing site in less than an hour. Other tests must be sent to a laboratory to analyze, a process that may take 1-2 days once received by the laboratory. Testing the same individual more than once in a 24-hour period is not recommended. [1]

Diagnosis of coronavirus disease 2019 (COVID-19) requires detection of SARS-CoV-2 RNA by reverse transcription polymerase chain reaction (RT-PCR), which is better using nasopharynx samples compared to throat samples. [1] Lower respiratory samples may have better yield than upper respiratory samples.

SARS-CoV-2 RNA has also been detected in stool and blood. [1] The presence of SARS-CoV-2 RNA in blood may be a marker of severe illness. Older patients and those with severe illness requiring hospitalization may shed viral RNA over longer periods (median range of viral shedding among hospitalized patients: 12-20 days).

There have been reports of concurrent infection with SARS-CoV-2 and other respiratory viruses. [1] Detection of another respiratory pathogen does not rule out COVID-19.

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Is antibody testing recommended for diagnosing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection?

The Centers for Disease Control and Prevention (CDC) does not currently recommend using only antibody testing for diagnosing acute severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, and the US Food and Drug Administrations has not authorized antibody tests for such diagnostic purposes. [3] In certain situations, serologic assays may be used to support clinical assessment of persons who present late in their illnesses when used in conjunction with viral detection tests. In addition, serologic assays may be used if it is suspected that a postinfectious syndrome (eg, Multisystem Inflammatory Syndrome in Children (MIS-C) is caused by SARS-CoV-2 infection.

The relative broad availability of serologic assays for SARS-CoV-2 can play an important role in understanding the transmission dynamic of the virus in the general population and in identifying groups at higher risk for infection. [3] Unlike viral direct detection methods, such as nucleic acid amplification or antigen detection tests that can detect acutely infected persons, antibody tests help determine whether the individual being tested was previously infected—even if that person never showed symptoms.

It is currently not clear whether a positive serologic test indicates immunity against SARS-CoV-2; at this time, serologic tests should not be used to determine if an individual is immune. [3] As additional data are collected to understand the significance of the presence or level of antibodies and their correlation with immunity, serologic tests may have utility in infection control decisions, but for now this evidence is not available.

Antibody tests can help determine the proportion of a population previously infected with SARS-CoV-2. [3] Thus, demographic and geographic patterns of serologic test results can help determine which communities may have experienced a higher infection rate.

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What are the patient categories for viral testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)?

There are five categories of individuals for viral testing (ie, nucleic acid or antigen tests) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as follows [3] :

  • Individuals with signs or symptoms consistent with coronavirus disease 2019 (COVID-19)

  • Asymptomatic individuals with recent known or suspected exposure to SARS-CoV-2 to control transmission

  • Asymptomatic individuals without known or suspected exposure to SARS-CoV-2 for early identification in special settings

  • Determining resolution of infection (ie, test-based strategy for discontinuation of transmission-based precautions, healthcare personnel (HCP) return to work, and discontinuation of home isolation)

  • Public health surveillance for SARS-CoV-2

Discussion

Viral testing for SARS-CoV-2 is generally considered to be diagnostic when conducted among individuals with symptoms consistent with COVID-19 or among asymptomatic individuals with known or suspected recent exposure to SARS-CoV-2 to control transmission, or to determine resolution of infection. [3]

Testing is considered to be surveillance when conducted among asymptomatic individuals without known or suspected exposure to SARS-CoV-2 for early identification, or to detect transmission hot spots or characterize disease trends. [3]

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What testing is recommended for persons with signs or symptoms consistent with coronavirus disease 2019 (COVID-19)?

To test individuals with symptoms when there is a concern of potential coronavirus disease 2019 (COVID-19), the Centers for Disease Control and Prevention (CDC) recommends using authorized nucleic acid or antigen detection assays that have received a US Food and Drug Administration (FDA) Emergency Use Authorization (EUA). [3] Tests should be used in accordance with the authorized labeling; providers should be familiar with the tests’ performance characteristics and limitations.

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. [3]  Most patients with confirmed COVID-19 have developed fever and/or symptoms of acute respiratory illness (eg, cough), but some infected patients may also present with other symptoms.

Clinicians are encouraged to test for other causes of respiratory illness (eg, influenza) in addition to testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), depending on patient age, season, or clinical setting; detection of one respiratory pathogen (eg, influenza) does not exclude the potential for coinfection with SARS-CoV-2. [3]  These tests should not delay testing for SARS-CoV-2.

Symptoms and presentations may be different in the pediatric population; therefore, consider referencing the CDC guidelines for COVID in neonates and for multisystem inflammatory syndrome in children (MIS-C). [3]

The severity of symptomatic illness due to infection with SARS-CoV-2 may vary. [3, 4] Among persons with extensive and close contact to vulnerable populations (eg, healthcare personnel [HCP]), even mild signs and symptoms (eg, sore throat) of possible COVID-19 should prompt consideration for testing. [3] Additional information is available in CDC’s Interim U.S. Guidance for Risk Assessment and Work Restrictions for Healthcare Personnel with Potential Exposure to COVID-19.

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What testing is recommended for asymptomatic individuals with known or suspected exposure to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to control transmission?

Testing is recommended for all close contacts of individuals with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, especially initial testing during an outbreak or pandemic due to the high likelihood of exposure. [3] Rapid identification and testing of contacts of individuals with SARS-CoV-2 infection is important because of the potential for asymptomatic and presymptomatic transmission.

Settings in which broader testing beyond close contacts is recommended as part of a strategy to control SARS-CoV-2 transmission includes high-risk locations that have the potential for rapid and widespread SARS-CoV-2 dissemination (eg, meat processing plant) or in which populations at risk for severe disease (eg, long-term care facilities, including nursing homes, intermediate care facilities for individuals with intellectual disabilities, and psychiatric residential treatment facilities) could become exposed. [3] Expanded testing might include testing of all contacts in proximity to someone with SARS-CoV-2 infection, or even testing all individuals within a shared setting (eg, facility-wide testing).

The CDC currently recommends expanded contact testing in the following guidance documents [3] :

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What testing is recommended for asymptomatic individuals without known or suspected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exposure for early identification in special settings?

Approaches for early identification of asymptomatic individuals include [3] :

  • Initial testing of everyone residing and/or working in the setting,

  • Regular (eg, weekly) testing of everyone residing and/or working in the setting, and

  • Testing of new entrants into the setting and/or those reentering after a prolonged absence (eg, ≥1 day)

These approaches could be considered in settings such as the following [3] :

  • Long-term care facilities

  • Correctional and detention facilities

  • Homeless shelters

  • Other congregate work or living settings including mass care, temporary shelters, assisted living facilities, and group homes for individuals with intellectual disabilities and developmental disabilities

  • High-density critical infrastructure workplaces where continuity of operations is a high priority

Discussion

SARS-CoV-2 may spread quickly in certain settings and cause substantial adverse effects, particularly in settings that house vulnerable populations in close quarters for extended periods (eg, long-term care facilities, correctional and detention facilities) and/or settings where critical infrastructure workers (eg, healthcare personnel, first responders) may be disproportionately affected. [3]

A strategy aimed at reducing introduction of SARS-CoV-2 into the setting through early identification could reduce the risk of widespread transmission in these situations. [3]

Facilities are encouraged to work with local, territorial, and state health departments to help inform decision making about broad-based testing. Before testing large numbers of asymptomatic individuals without known or suspected exposure, the facility should have a plan in place for how it will modify operations based on test results. [3]

The CDC offers guidance to address such testing. Preadmission or preprocedure testing may be considered as part of the patient evaluation to inform decisions about deferring elective care (eg, certain dental procedures) or procedures and the use of personal protective equipment. The CDC also provides testing guidance for nursing homes.

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What testing is recommended to determine resolution of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)?

A test-based strategy, which requires serial tests, can be used as an alternative to a symptom-based or time-based strategy, to determine when a person with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection no longer requires isolation or work exclusion. This strategy could be considered in three situations, as follows [3] :

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What does public health surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) involve?

Viral tests are used in community, outpatient, and hospital-based surveillance systems to identify cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. [3] These data help identify areas of ongoing circulation (hot spots), determine trends in disease by location, provide insight into the impact of the disease over time and by location, and inform disease forecasts.

Antibody tests are increasingly used to monitor disease burden by location and over time. [3] Use of serologic assays in populations can help determine the proportion of a population previously infected with SARS-CoV-2. Thus, demographic and geographic patterns of serologic test results provide data that can be used in forecasts of disease spread that can support resource allocation decisions and planning by local, territorial and state officials.

Discussion

Testing is a fundamental part of the United States SARS-CoV-2 Surveillance Plan, which uses multiple surveillance systems and epidemiology networks, in collaboration with state, local, and academic partners, to monitor the progression and impact of SARS-CoV-2) spread in the country. [3]

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What is the testing procedure for coronavirus disease 2019 (COVID-19)?

Conduct all testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in consultation with a healthcare provider. [4, 5] Specimens should be collected as soon as possible once a decision has been made to pursue coronavirus disease 2019 (COVID-19) testing, regardless of the time of symptom onset.

Specimen types

Upper respiratory specimens

For initial diagnostic testing for SARS-CoV-2, collecting and testing an upper respiratory specimen is recommended. Acceptable specimens include the following [4] :

  • A nasopharyngeal (NP) or oropharyngeal (OP) specimen collected by a healthcare provider; or

  • A nasal midturbinate (NMT) swab collected by a healthcare provider or by a supervised onsite self-collection (using a flocked tapered swab); or

  • An anterior nares (nasal swab) (NS) specimen collected by a healthcare provider or by onsite or home self-collection (using a flocked or spun polyester swab); or

  • NP wash/aspirate or nasal wash/aspirate (NW/NA) specimen collected by a healthcare provider

Immediately place swabs into a sterile transport tube containing 2-3 mL of either viral transport medium (VTM), Amies transport medium, or sterile saline, unless using a test designed to analyze a specimen directly (ie, without placement in VTM), such as some point-of-care tests. [4] If VTM is not available, see the standard operating procedure for public health labs to create viral transport medium in accordance with Centers for Disease Control and Prevention's (CDC’s) protocol.

Immediately place the NW specimen and nonbacteriostatic saline use to collect the specimen into a sterile transport tube. [4]

Lower respiratory specimens

Another option is to test lower respiratory tract specimens. [4] For patients who develop a productive cough, sputum should be collected and tested for SARS-CoV-2. The induction of sputum is not recommended.

When it is clinically indicated (eg, those receiving invasive mechanical ventilation), a lower respiratory tract aspirate or bronchoalveolar lavage sample should be collected and tested as a lower respiratory tract specimen. [4]

Safely collecting and handling specimens

Maintain proper infection control when collecting specimens. [4] See Biosafety FAQs for handling and processing specimens from suspected case patients.

  • When collecting specimens or when within 6 feet of those suspected to be infected with SARS-CoV-2, maintain proper infection control, and use recommended personal protective equipment (PPE), which includes an N95 or higher-level respirator (or a facemask if a respirator is not available), eye protection, gloves, and a gown.

  • For providers who are handling specimens but are not directly involved in specimen collection (eg, self-collection) and not working within 6 feet of the patient, follow standard precautions; gloves are recommended. While in the healthcare facility, at all times, healthcare personnel are recommended to wear a form of source control (facemask or cloth face covering).

Properly handling bulk-packaged sterile swabs for upper respiratory sample collection

Sterile swabs for upper respiratory specimen collection may be packaged in one of two ways [4] :

  • Individually wrapped (preferred when possible)

  • Bulk packaged

Bulk-packaged swabs may be used for sample collection; however, exercise care to avoid SARS-CoV-2 contamination of any of the swabs in the bulk-packaged container. [4]

  • Before engaging with patients and while wearing a clean set of protective gloves, distribute individual swabs from the bulk container into individual disposable plastic bags.

  • If bulk-packaged swabs cannot be individually packaged, use only fresh, clean gloves to retrieve a single new swab from the bulk container; close the bulk swab container after each swab is removed, and leave it closed when not in use to avoid inadvertent contamination; store opened packages in a closed, airtight container to minimize contamination; keep all used swabs away from the bulk swab container to avoid contamination.

  • For all swabs, only grasp the swab by the distal end of the handle, using gloved hands only.

  • When patients are self-collecting their swabs under clinical supervision, hand a swab to the patient only while wearing a clean set of protective gloves; the patient can then self-swab and place the swab in transport media or sterile transport device and seal; if the patient needs assistance, help the patient place the swab into transport media or a transport device and seal it.

Discussion

Clinicians should work with local and state health departments to coordinate testing for individuals with possible COVID-19 through public health laboratories, or work with commercial or clinical laboratories using viral tests granted an Emergency Use Authorization (EUA) by the US Food and Drug Administration (FDA). [3, 4, 5]

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. [3]  Most patients with confirmed COVID-19 have developed fever and/or symptoms of acute respiratory illness (eg, cough), but some infected patients may also present with other symptoms.

Clinicians are encouraged to test for other causes of respiratory illness (eg, influenza) in addition to testing for SARS-CoV-2, depending on patient age, season, or clinical setting; detection of one respiratory pathogen (eg, influenza) does not exclude the potential for coinfection with SARS-CoV-2. [3]  These tests should not delay testing for SARS-CoV-2.

Symptoms and presentations may be different in the pediatric population; therefore, consider referencing the Centers for Disease Control and Prevention (CDC) guidelines for COVID in neonates and for multisystem inflammatory syndrome in children (MIS-C). [3]

Other considerations that may guide testing are epidemiologic factors such as the occurrence of local community transmission of COVID-19 infections in a jurisdiction. [3]  

Healthcare providers should report positive results for SARS-CoV-2 to their local/state health department. [3, 4, 5]  Clinical laboratories should NOT attempt viral isolation from specimens collected from people suspected to have COVID-19 unless this is performed in a biosafety level 3 (BSL-3) laboratory.

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What are general guidelines for specimens of patients with coronavirus disease 2019 (COVID-19)?

Respiratory specimens

Upper respiratory tract [4]

For nasopharyngeal (NP) swabs/oropharyngeal (OP) swabs, use only synthetic fiber swabs with plastic or wire shafts. Do not use calcium alginate swabs or swabs with wooden shafts, as they may contain substances that inactivate some viruses and inhibit polymerase chain reaction (PCR) testing. The Centers for Disease Control and Prevention (CDC) now recommends collecting only the NP swab, although OP swabs remain an acceptable specimen type. If both swabs are used, NP and OP specimens should be combined into a single tube to maximize test sensitivity and limit use of testing resources.

  • NP swab: Insert a minitip swab with a flexible shaft (wire or plastic) through the nostril parallel to the palate (not upward) until resistance is encountered or the distance is equivalent to that from the ear to the patient's nostril, indicating contact with the nasopharynx. The swab should reach a depth equal to the distance from the nostrils to the outer ear opening. Gently rub and roll the swab. Leave the swab in place for several seconds to absorb secretions. Slowly remove the swab while rotating it. Specimens can be collected from both sides using the same swab, but it is not necessary to collect specimens from both sides if the minitip is saturated with fluid from the first collection. If a deviated septum or blockage creates difficulty in obtaining the specimen from one nostril, use the same swab to obtain the specimen from the other nostril.

  • OP swab: Insert the swab into the posterior pharynx and tonsillar areas. Rub the swab over both tonsillar pillars and the posterior oropharynx; avoid touching the tongue, teeth, and gums.

For NP washes/aspirates or nasal washes/aspirates (NW/NA), attach a catheter to the suction apparatus. With the patient seated and head tilted slightly backward, instill 1 to 1.5 mL of nonbacteriostatic saline (pH 7.0) into one nostril. Insert the tubing into the nostril parallel to the palate (not upward). The catheter should reach a depth equal to the distance from the nostrils to the outer ear opening. Use gentle suction/aspiration and remove the catheter while rotating it gently. Collect the specimen in a sterile viral transport media tube.

For nasal midturbinate (NMT) swabs (also called deep nasal swabs), use a flocked tapered swab. Tilt patient’s head back 70º. While gently rotating the swab, insert the swab less than 1 inch (about 2 cm) into the nostril (until resistance is met at the turbinates). Rotate the swab several times against the nasal wall, and repeat this process in the other nostril using the same swab.

For anterior nares (NS) specimens, use a flocked or spun polyester swab. Insert the swab at least 0.5 inch (1 cm) inside the nostril and firmly sample the nasal membrane by rotating the swab and leaving it in place for 10 to 15 seconds. Sample both nostrils with the same swab.

Lower respiratory tract [4]

  • For bronchoalveolar lavage, tracheal aspirate, pleural fluid, or lung biopsy specimens, collect 2-3 mL into a sterile, leak-proof, screw-cap sputum collection cup or sterile dry container. Because increased technical skill and equipment is needed, collection of specimens other than sputum from the lower respiratory tract may be limited to patients who present with more severe disease, including those admitted to the hospital and/or fatal cases.

  • For sputum specimens, educate the patient about the difference between sputum and oral secretions (saliva). Have the patient rinse their mouth with water and then expectorate deep cough sputum directly into a sterile, leak-proof, screw-cap sputum collection cup or sterile dry container.

Storage and shipping

Store specimens at 2-8°C for up to 72 hours after collection. If a delay in testing or shipping is expected, store specimens at -70°C or below. [4]

Specimens must be packaged, shipped, and transported according to the current edition of the International Air Transport Association (IATA) Dangerous Goods Regulations. [4]

  • If specimens will ship to the CDC without delay, store specimens at 2-8°C, and ship overnight on an ice pack.

  • If a delay in shipping will result in the CDC receiving the specimen longer than 72 hours after collection, store specimens at -70°C or below and ship overnight to the CDC on dry ice.

  • Samples may be shipped to the CDC if repeated testing results remain inconclusive or if other unusual results are obtained. Contact the CDC at respvirus@cdc.gov prior to submitting samples.

  • Label each specimen container with the patient’s identification (ID) number (eg, medical record number), unique CDC or state-generated nCoV (novel coronavirus) specimen ID (eg, laboratory requisition number), specimen type (eg, serum), and the date the sample was collected.

  • Complete a CDC Form 50.34 for each specimen submitted. In the upper left box of the form, (1) for test requested; select “Respiratory virus molecular detection (non-influenza) CDC-10401” and (2) for At CDC, bring to the attention of enter “Unit 84 (Non-flu Resp Virus).”

  • Additional useful and detailed information on packing, shipping, and transporting specimens can be found at Interim Laboratory Biosafety Guidelines for Handling and Processing Specimens Associated with Coronavirus Disease 2019 (COVID-19)

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Questions & Answers

Overview

What is the incubation period for coronavirus disease 2019 (COVID-19)?

What is the range of illness severity of patients with coronavirus disease 2019 (COVID-19)?

What is known about asymptomatic and presymptomatic infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)?

What is known about asymptomatic and presymptomatic transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)?

What is the clinical progression of patients with coronavirus disease 2019 (COVID-19)?

What are risk factors for severe illness in patients with coronavirus disease 2019 (COVID-19)?

What data are available about reinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)?

What are complications of patients with coronavirus disease 2019 (COVID-19)?

Are patients with coronavirus disease 2019 (COVID-19) at risk for hypercoagulability?

What are common laboratory findings in patients with coronavirus disease 2019 (COVID-19)?

What are common radiologic findings in patients with coronavirus disease 2019 (COVID-19)?

What diagnostic test is used to detect coronavirus disease 2019 (COVID-19)?

Is antibody testing recommended for diagnosing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection?

What testing is recommended for persons with signs or symptoms consistent with coronavirus disease 2019 (COVID-19)?

What testing is recommended for asymptomatic individuals with known or suspected exposure to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to control transmission?

What testing is recommended for asymptomatic individuals without known or suspected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exposure for early identification in special settings?

What testing is recommended to determine resolution of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)?

What does public health surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) involve?

What is the testing procedure for coronavirus disease 2019 (COVID-19)?

What are general guidelines for specimens of patients with coronavirus disease 2019 (COVID-19)?

What are the signs and symptoms of patients with coronavirus disease 2019 (COVID-19)?

What are characteristics of critically ill patients with coronavirus disease 2019 (COVID-19)?

What are the patient categories for viral testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)?

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