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COVID Testing: Ambulatory Clinic testing - updates from Christopher Chao, MD

Posted: Aug 20, 2020
Comments: 0
Author: UCA Admin

Excerpt originated from Urgent Caring Vol 04, Issue 8 (e-Newsletter of the College of Urgent Care Medicine, offering free monthly CME) - Last updated 8/19/2020

Author: Christopher Chao, MD; with contributions from Joe Toscano, MD

 

Please note: This is a rapidly evolving and developing situation, so please refer to the Centers for Disease Control and Prevention (CDC), World Health Organization (WHO), and your local health department for the most up to date information

 

COVID-19 is the disease caused by a novel coronavirus, SARS-CoV-2 that was first identified in Wuhan, China in late 2019. Since then, COVID-19 has been declared a pandemic, and as of August 9, 2020 there were over 5 million confirmed cases in the United States. Unfortunately, COVID-19 is a highly contagious disease transmitted through respiratory droplets, has a long incubation period of 2 to 14 days and infected individuals may be contagious when asymptomatic or before symptoms develop. Thus, testing is an important tool to identify patients who may be contagious so that they may be isolated and for the purpose of contact tracing.

Unfortunately, there is no “easy button” when it comes to COVID-19 testing. COVID-19 testing is detecting viral RNA or viral antigen; thus, sampling requires swabbing areas where the virus is present. Appropriate PPE is needed by the health care worker (HCW) performing the swab and shortages of PPE have impeded the testing process. Initially, nasopharyngeal (NP) swabs were recommended, though more recently, mid-turbinate swabs are acceptable. Mid-turbinate swabs may cause less patient discomfort and are generally preferred by patients.

Once collected, tests are sent to either a reference lab or processed using a point of care testing system. Examples of reference labs include government laboratories such as the CDC, state labs, or private laboratories such as LabCorp or Quest Diagnostics. At reference labs, samples can be processed in batches up to several hundred samples on the same machine cycle. During surges, the sheer number of tests outnumbered the testing capacity resulting in delays of days to even weeks. Shortages of supplies such as pipettes and reagents can further contribute to the backlog of testing. Providers working in a large medical group or hospital system may have access to an in-house lab with a facility point of care test. The advantage of an in-house lab is decreased transport time, which may save 1-2 days off the overall processing time.

Reference labs use molecular tests or RT-PCR (reverse transcriptase-polymerase chain reaction), and the sensitivity of these tests is generally above 90%, with high specificity. Since there are over 100+ high complexity COVID-19 tests that have an EUA, it is advised to contact your laboratory provider for specific performance data.

There are currently 6 CLIA-waived point of care tests that have received an EUA from the FDA. These portable testing platforms are well suited for the ambulatory clinic and deliver real time results. Of the 6 tests, 4 detect SARS-CoV-2 nucleic acid and 2 detect SARS-CoV-2 surface antigen proteins. Initial data suggested that antigen tests are not as sensitive as nucleic acid tests, but recent studies have demonstrated comparable sensitivity to PCR if the test is performed within 5 days after the onset of patient symptoms.   

Clinicians are cautioned not to choose testing solely based on test sensitivity and specificity data. Sensitivity and specificity help a clinician decide which test to use for any particular disease, but these test characteristics are particular to the test and depend on the engineering behind how the test result is obtained. For COVID-19 tests, the sensitivity and specificity are based on small numbers of test samples and manufacturer’s data not independently confirmed by the FDA. There are publications in the literature that report widely different sensitivity values, with some claiming that the sensitivity of an individual test is grossly overestimated.
 

Diagnostic Test

Detection Method

EUA date

Sensitivity

Specificity

Cepheid Xpress

NAAT RT-PCR

3/20/2020

97.8% (95% CI 88.4-99.6)[1]

95.6% (95% CI 85.2-99.8)1

Mesa Accula

NAAT

3/23/2020

68% (95% CI 53.3-80.5)[2]

100% (95% CI 94.2-100)2

Abbott ID NOW

NAAT LAMP

3/27/2020

91.3% to ≥94.7%[3]

≥98.6%3

Cue Health

NAAT

6/10/2020

N/A

N/A

Quidel SOFIA

Antigen

5/08/2020

80% Original PI

96.7% (95% CI 83.3-99.4) if tested within 5 days of symptoms[4]

100%

BD Veritor

Antigen

7/02/2020

84% (95% CI 67-93)[5]

100% (95% CI 98-100)

Table 1: CLIA waived point of care (POC) tests for detection of SARS-CoV-2

 

Other factors that can impact test results include improper collection technique, use of incorrect swabs to collect the sample, improper storage of reagents and inappropriate transport techniques to the lab. Even if a test has 100% sensitivity, a false negative may occur if the nasal swab does not sample the correct tissue and viral particles are not captured by the swab. It is unclear if the discrepancy of sensitivity values reported in publications is due to intrinsic or extrinsic factors. Always familiarize yourself and your staff with the manufacturer’s instructions to minimize user error.

While sensitivity and specificity help a clinician decide which test to use to rule-in or rule-out for a particular disease, it is the positive predictive value (PPV) and negative predictive value (NPV) that help a clinician interpret a test result. The PPV and NPV is influenced by the patient’s pre-test risk, including likelihood of alternative diagnosis and prevalence of the disease in the community. Before testing, consider the purpose of your testing – are you confirming the diagnosis of COVID-19 or are you screening for COVID-19?

If the disease prevalence is low (e.g., < 5%), the ambulatory COVID-19 tests may be sufficient to rule out a patient with minimal symptoms. However, as disease prevalence rises, the negative predictive value will decrease. Patients want and expect laboratory testing to give an absolute answer – either positive or negative. As clinicians, we know it is not that simple and counseling patients on test results will prevent potential patient misinterpretation of a specific result.

One final note. Testing is not an unlimited resource and good stewardship is needed to ensure that we preserve resources for everyone.

 

[2] Catherine A. Hogan, Natasha Garamani, Andrew S. Lee, Jack K. Tung, Malaya K. Sahoo, ChunHong Huang, Bryan Stevens, James Zehnder, Benjamin A. Pinsky. 2020. Comparison of the Accula SARS-CoV-2 Test with a Laboratory-Developed Assay for Detection of SARS-CoV-2 RNA in Clinical Nasopharyngeal Specimens. Journal of Clinical Microbiology Jul 2020, 58 (8) e01072-20; DOI: 10.1128/JCM.01072-20

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