Template:COVID-19 Testing, Reporting, and Information Management in the Laboratory/Diagnostic testing of COVID-19 and other coronaviruses/Organizational and agency guidance on COVID-19 testing

2.3 Organizational and agency guidance on COVID-19 testing

NOTE: Information shown here may rapidly become outdated given how quickly response to pandemic testing can change. A full attempt to keep the content relevant will be made.

CDC 2019-nCoV Real-time RT-PCR Panel (Research Use Only)

Laboratory guidance for testing for SARS-CoV-2 has been relatively quick to evolve. The timely development and organized use of accurate assays and meaningful screening protocols, however, has been inconsistent worldwide, with some countries more urgently and agilely responding than others. With any novel virus, clinicians and public health experts are dealing with unknown factors. However, public health organizations and agencies have had a base to work from when creating laboratory testing guidance for a novel coronavirus, with more than 40 years of experience with coronavirus biology, pathogenesis, and diagnosis. And while there are fundamental differences between SARS-CoV-2 and its predecessor SARS-CoV, they still share approximately 70 to 80 percent of their genetic code. In fact, the WHO had draft guidance for laboratory testing out as early as January 10, 2020, before gene sequencing was even completed. This guidance and similar draft guidance from national public health organizations and agencies have received steady revisions since as understanding of the virus has grown.

Similar to its predecessors SARS-CoV and MERS-CoV, RT-PCR is being recommended in guidance for detecting SARS-CoV-2's RNA in specimens and thus laboratory confirmation of COVID-19 cases. Serology has its place in testing as well, though with similar lessons from SARS and MERS that it's best used to test for past infection (typically after 14 days of suspected contact with a carrier, or mild symptoms) and thus potential short-term immunity due to the presence of antibodies in blood. In its March 19 guidance, the WHO said: "In cases where NAAT assays are negative and there is a strong epidemiological link to COVID-19 infection, paired serum samples (in the acute and convalescent phase) could support diagnosis once validated serology tests are available." On April 3, the U.S. Food and Drug Administration (FDA) approved the countries first COVID-19 serology test created by Cellex, though Mayo Clinic was also on the verge of rolling out its own in-house serology test as well As of April 28, the U.S. FDA has granted emergency use authorizations (EUA) for eight serology tests. (Note: Johns Hopkins appears to be maintaining a page tracking approved serology tests around the world.)

The following sample collection and test procedures have evolved from the COVID-19 pandemic (note that this is only a summary; consult the cited literature directly for full details):

• Determine that the patient is indicating clinical and/or epidemiological evidence of COVID-19 (meets case definitions). Case definitions and testing criteria have initially been strict, but as the CDC notes, as test kit availability ramps up, it "will allow clinicians to consider COVID-19 testing for a wider group of symptomatic patients." However, clinicians are still encouraged to consider other causes for respiratory illness. The CDC provides a priority list, making hospitalized patients and symptomatic healthcare workers the top priority, followed by "those who are at highest risk of complication of infection," then "individuals in the surrounding community of rapidly increasing hospital cases." In the future, as more serology options and other resources become available, serological surveys of people who have never been diagnosed (asymptomatic or otherwise) may begin.

• Collect at a minimum upper respiratory tract specimens and, whenever possible, lower respiratory tract specimens. Although too early to say with certainty, it appears lower respiratory tract specimens such as sputum and bronchoalveolar lavage fluid are typically the most reliable specimen type for RT-PCR applications, as they have been shown to contain the highest viral load, in comparison to upper respiratory tract specimens. As Wang et al. point out, "testing of specimens from multiple sites may improve the sensitivity and reduce false-negative test results," which is largely reflected in WHO, CDC, Public Health England (PHE), and Public Health Laboratory Network (PHLN; Australia) testing guidance.

Slight differences in upper respiratory tract specimen collection procedures can be found between the WHO/CDC and PHE/PHLN. Both the WHO and CDC offer nasopharyngeal and oropharyngeal swabs as options. The WHO doesn't appear to give a preference, whereas the CDC has a preference for nasopharyngeal swabs but maintains oropharyngeal as still remaining "an acceptable specimen type." In comparison, the latest PHE and PHLN guidance prefer the approach of collecting from both pharynx locations—even with the same swab—"to optimize the chances of virus detection." Nasopharyngeal aspiration is also an acceptable sample collection method for the upper respiratory tract according to all mentioned entities, though the PHLN specifies that it is a substitution for only the nasopharyngeal (they now refer to it as "deep nasal") specimen.

Regarding serum specimens, statements differ slightly. The WHO notes serology to be useful for retrospective case definition, using paired specimens from the acute and convalescent phases of the disease. The CDC doesn't make reference to serum or serology in their clinical specimen guidance. The PHE suggests hospital patients have "a sample for acute serology" taken but say little else. The PHLN gives similar advice as the WHO, while emphasizing a need "to facilitate retrospective testing, if this is relevant, once serology tests become available."

Finally, and more recently, potential evidence of saliva having diagnostic value for detecting SARS-CoV-2 has arisen. As Xu et al. note in their mid-April paper, the "diagnostic value of saliva specimens for ... nucleic acid examination remains limited but promising." Another paper awaiting peer review by researchers at Yale School of Public Health provides similiar thoughts, though is generally more optimistic than the paper published by Xu et al., suggesting salive from the opening of the mouth (in contrast to Xu et al. and their finding of better results from salive in the throat) may be viable specimen. In fact, an April EUA by the FDA has been made for the first saliva-based COVID-19 test, produced by Vault Health, Inc. As these and similar studies get peer reviewed and methods validated, preferred sample types (and the guidance recommending them) may change. Stay aware of the evolving science.

• Conduct testing. NAAT methods like rRT-PCR have been the primary tools for diagnosing SARS-CoV-2 infection due to their high sensitivity. The PHLN provides the most background about PCR in their guidance, noting that laboratories in its network are confirming positive infections "either with RT-PCR assays detecting a different target gene, or broadly reactive PCR tests with sequencing of amplicons." The latter option is less common due to long turnaround time. They also note that other zoonotic viruses such as SARS-CoV are capable of being detected from PCR assays, though endemic coronaviruses like -229E won't be. The WHO, CDC, and PHLN underscore the idea that viral cultures for routine diagnoses are not practical and, if attempted, should only be performed in Biosafety Level 3 (BSL-3) laboratories. As of April 5, no specific methods have been suggested for serological antibody detection, though the current set of approved serology tests from around the world appear to use lateral flow immunoassay, ELISA, or neutralization methods.

• Confirm the results. The strongest public guidance for considering a potential case as being laboratory-confirmed for SARS-CoV-2 infection comes from the WHO. In their guidance, they differentiate between cases by NAAT "in areas with no known COVID-19 virus circulation" and "in areas with established COVID-19 virus circulation." In the first case, one of these conditions must apply: either a validated NAAT test providing a positive result for at least two different genomic targets, or a validated NAAT test providing a positive result for the presences of betacoronavirus along with sequencing confirmation of a separate genomic target, "as long as the sequence target is larger or different from the amplicon probed in the NAAT assay used." In the latter case of established virus circulation, the WHO notes that "a simpler algorithm might be adopted in which, for example, screening by rRT-PCR of a single discriminatory target is considered sufficient." However, if testing produces one or more negative results, that doesn't necessarily rule out SARS-CoV-2 infection. If suspicion of infection remains high, particularly if only upper respiratory tract specimens were collected, additional specimens from the lower respiratory tract should be collected and analyzed. They also emphasize that both external and internal controls should be applied to NAAT runs.

• Report using state and, if applicable, national reporting requirements. (See the next chapter for more on reporting.) Regardless of result, the final positive or negative laboratory confirmation should also be reported to state and national authorities. In the U.S., for example, this means reporting to the local or state health department using the CDC's PUI and Case Report Form. In Canada, reports are sent to the Public Health Agency of Canada (PHAC) via their Coronavirus Diseases (COVID-19) Case Report Form.

2.3.1 Regulatory considerations

CLIA

The Clinical Laboratory Improvement Amendments (CLIA) are a set of U.S. federal regulatory requirements applied to all non-research-based clinical laboratory testing performed on humans. These requirements are intended to further ensure a higher standard of quality in clinical laboratory testing, focusing in on improving the accuracy, reliability and timeliness of tests. (The implications of these requirements on U.S. clinical labs and their ability to test for COVID-19 are discussed later, in the next section.)

CLIA uses seven different criteria to gauge and assign one of three complexity levels to laboratory devices and assays: high, moderate, and waived. Additionally, CLIA mandates clinical laboratories handling specimens originating from the U.S. and its territories to apply for a CLIA certificate that is appropriate for the type of testing it performs. Labs using complex devices and assays would have to apply for a high complexity certificate, and so on. Waived tests are recognized as simple to perform with a low risk of erroneous results and include among others urinalysis for pregnancy and drugs of abuse, blood glucose and cholesterol tests, and fertility analysis.

Anything but waived testing requires meeting "the CLIA quality system standards, such as those for proficiency testing, quality control and assessment, and personnel requirements. The standards for moderate and high complexity testing differ only in the personnel requirements." As the Centers for Medicare and Medicaid Services (CMS) points out in a frequently asked questions (FAQ) document—and as can be verifed on the FDA's EUA page—a huge majority of COVID-19 tests are only authorized for moderate or high complexity testing, and thus labs certified to do that sort of testing. As of May 18, only four of 75 FDA EUAed tests are approved to be performed in a CLIA-waived laboratory setting.

CMS' FAQ, as well as their March 2020 guidance document, provides additional insight in regards CLIA and COVID-19:

• CLIA regulations remain in effect during the U.S.-declared public health emergency; a Section 1135 waiver, under the Social Security Act, that modifies or suspends CLIA requirements is not within the authorizing jurisdiction of the CLIA program.

HIPAA