Difference between revisions of "User:Shawndouglas/sandbox/sublevel1"

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[[File:MERS-CoV Particles (8414774264).jpg|thumb|Colorized transmission electron micrograph showing particles of the Middle East respiratory syndrome coronavirus that emerged in 2012]]Unlike SARS, Middle East respiratory syndrome, or MERS, continues to appear in the human population. Since its appearance in 2012, several thousand laboratory-confirmed cases of MERS have been reported to the WHO.<ref name="Bernard-StoecklinCompar19">{{cite journal |title=Comparative Analysis of Eleven Healthcare-Associated Outbreaks of Middle East Respiratory Syndrome Coronavirus (Mers-Cov) from 2015 to 2017 |journal=Scientific Reports |author=Bernard-Stoecklin, S.; Nikolay, B.; Assiri, A. et al. |volume=9 |at=7385 |year=2019 |doi=10.1038/s41598-019-43586-9 |pmid=31089148 |pmc=PMC6517387}}</ref> The virus MERS-CoV is believed to have originated from bats, which at some unknown point spread to Dromedary camels. Approximately 55 percent of MERS-CoV infections have come from direct contact with such camels, though it's not entirely clear how the rest of known cases have been caused<ref name="BanerjeeBats19">{{cite journal |title=Bats and Coronaviruses |journal=Viruses |author=Banerjee, A.; Kulcsar, K.; Misra, V. et al. |volume=11 |issue=1 |at=E41 |year=2019 |doi=10.3390/v11010041 |pmid=30634396 |pmc=PMC6356540}}</ref> (Alshukairi ''et al.'' suggest asymptomatic or mildly symptomatic camel workers may serve as a possible transmission source<ref name="AlshukairiHigh18">{{cite journal |title=High Prevalence of MERS-CoV Infection in Camel Workers in Saudi Arabia |journal=mBio |author=Alshukairi, A.N.; Zheng, J.; Zhao, J. et al. |volume=9 |issue=5 |pages=e01985-18 |year=2018 |doi=10.1128/mBio.01985-18 |pmid=30377284 |pmc=PMC6212820}}</ref>). The following sample collection and test procedures have evolved from working with the MERS-CoV virus (note that this is only a summary; consult the cited literature directly for full details)<ref name="CDCLabTestMERS19">{{cite web |url=https://www.cdc.gov/coronavirus/mers/lab/lab-testing.html |title=CDC Laboratory Testing for Middle East Respiratory Syndrome Coronavirus (MERS-CoV) |author=Centers for Disease Control and Prevention |publisher=Centers for Disease Control and Prevention |date=02 August 2019 |accessdate=04 April 2020}}</ref><ref name="CDCInterimMERS19">{{cite web |url=https://www.cdc.gov/coronavirus/mers/guidelines-clinical-specimens.html |title=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 |author=Centers for Disease Control and Prevention |publisher=Centers for Disease Control and Prevention |date=02 August 2019 |accessdate=04 April 2020}}</ref><ref name="WHOLabMERS18">{{cite web |url=https://www.who.int/csr/disease/coronavirus_infections/mers-laboratory-testing/en/ |title=Laboratory testing for Middle East Respiratory Syndrome Coronavirus: Interim guidance |work=WHO/MERS/LAB/15.1/Rev1/2018 |author=World Health Organization |publisher=World Health Organization |date=January 2018 |accessdate=04 April 2020}}</ref><ref name="Al-AbdelyMiddle19">{{cite journal |title=Middle East Respiratory Syndrome Coronavirus Infection Dynamics and Antibody Responses among Clinically Diverse Patients, Saudi Arabia |journal=Emerging Infectious Diseases |author=Al-Abdely, H.M.; Midgley, C.M.; Alkhamis, A.M. et al. |volume=25 |issue=4 |pages=753-766 |year=2019 |doi=10.3201/eid2504.181595}}</ref><ref name="Kelly-CirinoAnUpdated19">{{cite journal |title=An updated roadmap for MERS-CoV research and product development: focus on diagnostics |journal=BMJ Global Health |author=Kelly-Cirino, C.; Mazzola, L.T.; Chua, A. et al. |volume=4 |issue=Suppl. 2 |at=e001105 |year=2019 |doi=10.1136/bmjgh-2018-001105 |pmid=30815285 |pmc=PMC6361340}}</ref>:
''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.''  


* Determine that the patient is indicating clinical and/or epidemiological evidence of MERS (meets case definitions). "Testing for other respiratory pathogens using routinely available laboratory procedures, as recommended in local management guidelines for community-acquired pneumonia, should also be performed but should not delay testing for MERS-CoV."<ref name="WHOLabMERS18" />
[[File:CDC COVID-19 test kit.jpg|right|thumb|430px|CDC 2019-nCoV Real-time RT-PCR Panel (Research Use Only)]]Early in the COVID-19 pandemic, laboratory guidance for testing for SARS-CoV-2 was relatively quick to evolve. The timely development and organized use of accurate assays and meaningful screening protocols, however, has been inconsistent but improving worldwide, with some countries more urgently and agilely responding than others.<ref name="SubbaramanCorona20">{{cite web |url=https://www.nature.com/articles/d41586-020-00827-6 |title=Coronavirus tests: Researchers chase new diagnostics to fight the pandemic |author=Subbaraman, N.; Callaway, E. |work=Nature - News Explainer |date=23 March 2020 |accessdate=05 April 2020 |doi=10.1038/d41586-020-00827-6}}</ref><ref name="ApuzzoCant20">{{cite web |url=https://www.nytimes.com/2020/03/20/world/europe/coronavirus-testing-world-countries-cities-states.html |title=Can’t Get Tested? Maybe You’re in the Wrong Country |author=Apuzzo, M.; Gebrekidan, S. |work=The New York Times |date=20 March 2020 |accessdate=05 April 2020}}</ref><ref name="HindsleyTheLost20">{{cite web |url=https://www.nytimes.com/2020/03/28/us/testing-coronavirus-pandemic.html |title=The Lost Month: How a Failure to Test Blinded the U.S. to COVID-19 |author=Hindsley, G. |work=The New York Times |date=28 March 2020 |accessdate=05 April 2020}}</ref> 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.<ref name="DenisonCorona04">{{cite book |chapter=Coronavirus Research: Keys to Diagnosis, Treatment, and Prevention of SARS |title=Learning from SARS: Preparing for the Next Disease Outbreak |author=Denison, M.R. |publisher=Institute of Medicine |pages=137–72 |year=2004 |isbn=9780309182157 |doi=10.17226/10915 |url=https://www.nap.edu/read/10915/chapter/5}}</ref> 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.<ref name=CeccarelliDiff20">{{cite journal |title=Differences and similarities between Severe Acute Respiratory Syndrome (SARS)-CoronaVirus (CoV) and SARS-CoV-2. Would a rose by another name smell as sweet? |journal=European Review for Medical and Pharmacological Sciences |author=Ceccarelli, M.; Berretta, M.; Venanzi Rullo, E. et al. |volume=24 |issue=5 |pages=2781-2783 |year=2020 |doi=10.26355/eurrev_202003_20551 |pmid=32196628}}</ref><ref name=Wilder=SmithCanWe20">{{cite journal |title=Can we contain the COVID-19 outbreak with the same measures as for SARS? |journal=The Lancet Infectious Diseases |author=Wilder-Smith, A.; Chiew, C.J.; Lee, V.J. |year=2020 |doi=10.1016/S1473-3099(20)30129-8 |pmid=32145768 |pmc=PMC7102636}}</ref> In fact, the WHO had draft guidance for laboratory testing out as early as January 10, 2020, before gene sequencing was even completed.<ref name="WHOLabJan20">{{cite web |url=https://apps.who.int/iris/bitstream/handle/10665/330374/WHO-2019-nCoV-laboratory-2020.1-eng.pdf |title=Laboratory testing of human suspected cases of novel coronavirus (nCoV) infection: Interim guidance 10 January 2020 |work=WHO/2019-nCoV/laboratory/2020.1 |author=World Health Organization |publisher=World Health Organization |date=10 January 2020 |accessdate=05 April 2020}}</ref> 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.


* Collect at a minimum both lower respiratory and upper respiratory tract samples. Lower respiratory tract specimens are typically the most revealing, as they have been shown to contain the highest viral load (due to the expression of the virus's cellular receptor DPP4 in the lower respiratory system). Bronchoalveolar lavage, tracheal aspiration, or a pleural tap can be used to collect specimens from the lower respiratory tract. (Sputum can also be collected.) Upper respiratory tract specimens (in this case, both a nasopharyngeal and an oropharyngeal swab are recommended) are also valuable in diagnosis, though extra care should be taken to ensure nasopharyngeal swabs gather secretions from the [[Pharynx#Nasopharynx|nasopharynx]] and not just the nostril. Nasopharyngeal aspiration is also an acceptable sample collection method for the upper respiratory tract.
Similar to its predecessors SARS-CoV and MERS-CoV, RT-PCR has largely been the predominant diagnostic method used in guidance for detecting SARS-CoV-2's RNA in specimens and thus laboratory confirmation of COVID-19 cases. Other diagnostic methods such as isothermal amplification (e.g., [[LAMP]]) and antigen testing have also emerged as the pandemic has progressed. 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. It also has other uses; in its September 2020 guidance, the WHO said: "If negative NAAT results are obtained from a patient in whom SARS-CoV-2 infection is strongly suspected, a paired serum specimen could be collected."<ref name="WHOLabMar20">{{cite web |url=https://apps.who.int/iris/handle/10665/334254 |title=Diagnostic testing for SARS-CoV-2 |work=WHO/2019-nCoV/laboratory/2020.6 |author=World Health Organization, et al. |publisher=World Health Organization |date=11 September 2020 |accessdate=18 November 2020}}</ref> On April 3, the U.S. Food and Drug Administration (FDA) approved the country's 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<ref name="TerryCellex20">{{cite web |url=https://www.biospace.com/article/fda-approves-1st-covid-19-antibody-test/ |title=Cellex and Mayo Clinic Launch Tests to Determine COVID-19 Immunity from Previous Exposure |author=Terry, M. |work=BioSpace |date=03 April 2020 |accessdate=05 April 2020}}</ref> As of September 2021, the U.S. FDA has granted emergency use authorizations (EUA) for 88 serology/antibody tests.<ref name="FDAEmerg20">{{cite web |url=https://www.fda.gov/medical-devices/coronavirus-disease-2019-covid-19-emergency-use-authorizations-medical-devices/vitro-diagnostics-euas#individual-serological |title=In Vitro Diagnostics EUAs |publisher=U.S. Food and Drug Administration |date=20 August 2020 |accessdate=23 August 2020}}</ref> (Note: Johns Hopkins also appears to be maintaining [https://www.centerforhealthsecurity.org/covid-19TestingToolkit/serology/Serology-based-tests-for-COVID-19.html a page] tracking approved serology tests around the world.)


:Regarding serum specimens, slight differences in guidance appear between WHO guidance and CDC guidance. The WHO appears to differentiate between symptomatic and asymptomatic patient testing, whereas the U.S. CDC seems to only indirectly differentiate the two. The WHO suggests if testing symptomatic patients, stick with lower and upper respiratory tract specimens, which will be tested using nucleic acid amplification (molecular) testing (NAAT). Serological testing of serum specimens should be used for symptomatic patients "only if NAAT is not available."<ref name="WHOLabMERS18" /> If this is the case, the WHO recommends paired samples, one collected within the first week of illness and the second about three to four weeks later. For asymptomatic patients in high-contact outbreak scenarios, the WHO recommends all three sample types (with respiratory samples taken preferably within 14 days of last documented contact).
'''Primary testing guidance'''


:The current CDC guidance differentiates between molecular testing for active infections and serology for previous infections. The CDC adds that "MERS-CoV serology tests are for surveillance or investigational purposes and not for diagnostic purposes."<ref name="CDCLabTestMERS19" /> Whether or not to collect a serum specimen in MERS diagnostics may depend on the assay used, however. For example, the CDC, in its Version 2.1 guidance, indicates that testing using the CDC MERS rRT-PCR assay requires collection of serum in addition to upper and lower respiratory tract specimens. For that specific assay, the CDC differentiates between patients who've had symptom onset less than 14 days prior and those who've had it 14 days or later: if prior, serology is for the rRT-PCR test, and if later, serology is for antibody testing. In either case, 200 µL of serum is required.
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)<ref name="WHOLabMar20" /><ref name="CDCEvalTest20">{{cite web |url=https://www.cdc.gov/coronavirus/2019-ncov/hcp/testing-overview.html |title=Overview of Testing for SARS-CoV-2 |author=Centers for Disease Control and Prevention |publisher=Centers for Disease Control and Prevention |date=02 August 2021 |accessdate=06 September 2021}}</ref><ref name="CDCInterimGuidC19_20">{{cite web |url=https://www.cdc.gov/coronavirus/2019-nCoV/lab/guidelines-clinical-specimens.html |title=Interim Guidelines for Collecting and Handling of Clinical Specimens for COVID-19 Testing |author=Centers for Disease Control and Prevention |publisher=Centers for Disease Control and Prevention |date=26 February 2021 |accessdate=06 September 2021}}</ref><ref name="UKGovCOVID20">{{cite web |url=https://www.gov.uk/government/publications/wuhan-novel-coronavirus-guidance-for-clinical-diagnostic-laboratories |title=COVID-19: Guidance for sampling and for diagnostic laboratories |author=Public Health England |publisher=U.K Government |date=29 March 2021 |accessdate=06 September 2021}}</ref><ref name="AusGovPHLN20">{{cite web |url=https://www.health.gov.au/resources/publications/phln-guidance-on-laboratory-testing-for-sars-cov-2-the-virus-that-causes-covid-19 |title=PHLN guidance on laboratory testing for SARS-CoV-2 (the virus that causes COVID-19) |author=Public Health Laboratory Network |publisher=Department of Health, Australian Government |date=22 June 2021 |accessdate=06 September 2021}}</ref>:


* Conduct testing. NAAT methods like real-time reverse-transcription polymerase chain reaction (rRT-PCR) assays have been the most common tool for diagnosing MERS-CoV infection due to their high sensitivity. According to late 2018 research by Kelly-Cirino ''et al.'', at least 11 commercial single assay and five commercial multiplex assay kits are available (see [https://gh.bmj.com/content/bmjgh/4/Suppl_2/e001105/DC1/embed/inline-supplementary-material-1.pdf Table S1], a PDF file, from their highly relevant paper), perhaps more as of April 2020. Serological antibody detection is performed using ELISA, [[Immunofluorescence#Secondary (indirect)|indirect immunofluorescence]] (IIF), and [[Neutralisation (immunology)|microneutralization]].
* Determine that the patient is indicating clinical and/or epidemiological evidence of COVID-19 (meets case definitions). Early on in the pandemic, case definitions and testing criteria were initially strict due to lack of test kits<ref name="CDCClinical20">{{cite web |url=https://www.cdc.gov/coronavirus/2019-ncov/hcp/clinical-criteria.html |archiveurl=https://web.archive.org/web/20200501002841/https://www.cdc.gov/coronavirus/2019-ncov/hcp/clinical-criteria.html |title=Evaluating and Testing Persons for Coronavirus Disease 2019 (COVID-19) |author=Centers for Disease Control and Prevention |publisher=Centers for Disease Control and Prevention |date=27 April 2020 |archivedate=01 May 2020 |accessdate=08 July 2020}}</ref><ref name="BranswellCDC20">{{cite web |url=https://www.statnews.com/2020/04/04/cdc-launches-studies-to-get-more-precise-count-of-undetected-covid-19-cases/ |title=CDC launches studies to get more precise count of undetected Covid-19 cases |author=Branswell, H. |work=STAT |date=04 April 2020 |accessdate=05 April 2020}}</ref><ref name="JHSerology20">{{cite web |url=https://www.centerforhealthsecurity.org/covid-19TestingToolkit/serology/Serology-based-tests-for-COVID-19.html |title=Serology tests for COVID-19 |author=Center for Health Security |publisher=Johns Hopkins University |date=26 August 2021 |accessdate=06 September 2021}}</ref>, but test kit availability has ramped up since, allowing for testing a wider group of symptomatic patients, as well as asymptomatic patients. However, clinicians are still encouraged to consider other causes for respiratory illness.<ref name="CDCEvalTest20" />


* Confirm the results. Laboratory confirmation of MERS-CoV infection is the same for both the WHO and the CDC: one of 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 a specific genomic target along with sequencing confirmation of a separate genomic target. Persons under investigation who receive one negative NAAT result on a recommended specimen are considered to be negative for active MERS-CoV infection. The laboratory should consider testing additional specimens after the first negative. The CDC considers known MERS patients to be negative for active MERS-CoV infection after two consecutive negative NAAT tests on all specimens. The WHO adds: "A patient with a positive NAAT result for a single specific target without further testing but with a history of potential exposure and consistent clinical signs is considered a probable case."<ref name="WHOLabMERS18" /> The WHO also has additional guidance on using serology for confirming MERS-CoV infection for purposes of reporting under the International Health Regulations.
* Collect at a minimum an upper respiratory tract (URT) specimen. Some guidance like that found in the U.K. also suggests collecting lower respiratory tract (LRT) specimens, whenever possible.<ref name="UKGovCOVID20" /> Broadly, it appears lower respiratory tract specimens such as sputum and bronchoalveolar lavage fluid are a more 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.<ref name="WangDetect20">{{cite journal |title=Detection of SARS-CoV-2 in Different Types of Clinical Specimens |journal=JAMA |author=Wang, W.; Xu, Y.; Gao, R. et al. |year=2020 |doi=10.1001/jama.2020.3786 |pmid=32159775 |pmc=PMC7066521}}</ref><ref name="YuQuant20">{{cite journal |title=Quantitative Detection and Viral Load Analysis of SARS-CoV-2 in Infected Patients |journal=Clinical Infectious Diseases |author=Yu, F.; Yan, L.; Wang, N. et al. |at=ciaa345 |year=2020 |doi=10.1093/cid/ciaa345 |pmid=32221523}}</ref> In most cases, a URT will be sufficient; however, an LRT is especially useful when a patient tests negative with a URT but is still high suspicious of having COVID-19. Yet, as Wang ''et al.'' point out, "testing of specimens from multiple sites may improve the sensitivity and reduce false-negative test results,"<ref name="WangDetect20" /> which is largely reflected in WHO, CDC, Public Health England (PHE), and Public Health Laboratory Network (PHLN; Australia) testing guidance.


* Report using national reporting requirements. More broadly, state or local health departments should receive details about received specimens to be tested for MERS-CoV, even before testing begins. Regardless of result, the final positive or negative laboratory confirmation should also be reported to national authorities. If the infection becomes widespread, updates for each new confirmed case or suspected positive should also be made.
: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."<ref name="CDCInterimGuidC19_20" /> 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."<ref name="AusGovPHLN20" /> Nasopharyngeal aspiration is also an acceptable sample collection method for the upper respiratory tract according to all mentioned entities except the PHLN, which appears to have removed mention of nasopharyngeal aspirate from its guidance sometime in 2021.<ref name="AusGovPHLN20" />


: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 used to suggest hospital patients have "a sample for acute serology" taken, but that appears to have been removed from 2021 guidance.<ref name="UKGovCOVID20" /> The PHLN initially provided similar advice as the WHO, but in late April they expanded their guidance to discuss the value of serology.<ref name="AusGovPHLN20" /> They have also added collection recommendations for serology, in separate guidance, indicating that "serological testing before two weeks from the onset of symptoms may result in false negative results."<ref name="AusGovPHLN-Serology20">{{cite web |url=https://www.health.gov.au/sites/default/files/documents/2020/09/phln-guidance-for-serological-testing-in-covid-19-phln-guidance-on-serological-testing-in-covid-19.docx |format=Word |title=PHLN guidance for serological testing in COVID-19 |author=Public Health Laboratory Network |publisher=Department of Health, Australian Government |date=03 September 2020 |accessdate=06 September 2021}}</ref>
:Finally, and more recently, potential evidence of saliva having diagnostic value for detecting SARS-CoV-2 has arisen. Xu ''et al.'' noted in published April 2020 research that the "diagnostic value of saliva specimens for ... nucleic acid examination remains limited but promising."<ref name="XuSaliva20">{{cite journal |title=Saliva: Potential diagnostic value and transmission of 2019-nCoV |journal=International Journal of Oral Science |author=Xu, R.; Cui, B.; Duan, X. et al. |volume=12 |at=11 |year=2020 |doi=10.1038/s41368-020-0080-z}}</ref> Another paper published in September 2020 provided similar thoughts, though was generally more optimistic than the paper published by Xu ''et al.'', suggesting saliva from the opening of the mouth (in contrast to Xu ''et al.'' and their finding of better results from saliva in the throat) may be viable specimen.<ref name="WyllieSaliva20">{{cite journal |title=Saliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2 |journal=New England Journal of Medicine |author=Wyllie, A.L.; Fournier, J.; Casanovas-Massana, A. et al. |volume=383 |pages=1283–6 |year=2020 |doi=10.1056/NEJMc2016359 |pmid=32857487 |pmc=PMC7484747}}</ref> In fact, an April 2020 EUA by the FDA had been made for the first saliva-based COVID-19 test, produced by Vault Health, Inc.<ref name="VHVault20">{{cite web |url=https://www.prnewswire.com/news-releases/vault-health-launches-first-of-its-kind-saliva-based-fda-eua-approved-test-for-covid-19-301039633.html |title=Vault Health Launches First-of-its-Kind Saliva-based FDA EUA Approved Test for COVID-19 |author=Vault Health |work=PR Newswire |date=14 April 2020 |accessdate=01 May 2020}}</ref>
:As these and similar studies have been peer reviewed and methods validated, saliva has increasingly looked like a viable sample type. The CDC updated their guidance in October 2020 regarding saliva as a testing substrate. The CDC now notes: "Collect 1-5 ml of saliva in a sterile, leak-proof screw cap container. No preservative is required."<ref name="CDCInterimGuidC19_20" /> This is presumably in conjunction with tests approved for the use of saliva. Australia's PHLN updated their guidance in 2021 to include a full section on saliva testing and how to approach it, though cautioning it "does not advise routine use of saliva for diagnostic testing except in specific situations."<ref name="AusGovPHLN20" />
* Conduct testing. NAAT methods like qRT-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 "RT-PCR or TMA are the methods of choice to detect SARS-CoV-2 during the acute illness."<ref name="AusGovPHLN20" /> Viral cultures are little mentioned, though the PHLN underscores the idea that viral cultures for routine diagnoses are "of limited utility" and, if attempted, should only be performed in Biosafety Level 3 (BSL-3) laboratories.<ref name="AusGovPHLN20" /> As of August 2020, only the PHLN has made any specific recommendations for how serological testing should be conducted for testing ''past cases'' of COVID-19.<ref name="AusGovPHLN20" /> The current set of approved serology tests from around the world appear to use lateral flow immunoassay, ELISA, or [[Neutralisation (immunology)|neutralization]] methods.<ref name="JHSerology20" /> Also note that at least in the U.S., the FDA in October 2020 discontinued review and approval of laboratory developed tests (LDTs), in favor of tests that would be more likely to increase access to testing or overall test capacity.<ref name="FoxEUAs20">{{cite web |url=https://www.jdsupra.com/legalnews/euas-for-laboratory-developed-covid-19-91593/ |title=EUAs for Laboratory Developed COVID-19 Tests Will No Longer Be Reviewed by the FDA |author=Fox, A. |work=JDSupra |date=12 October 2020 |accessdate=18 November 2020}}</ref>
* Confirm the results. The WHO notes that optimally a positive result should come from a NAAT method "with at least two independent targets on the SARS-CoV-2 genome." However, they recognize that "in areas with widespread transmission of SARS-CoV-2, a simple algorithm might be adopted with one single discriminatory target," though monitoring of potential mutations is recommended.<ref name="WHOLabMar20" /> Most guidance notes that 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 to limit the chance of incorrect results.
* 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 [https://www.cdc.gov/coronavirus/2019-ncov/php/reporting-pui.html CDC's COVID-19 Worksheet]. In Canada, reports are sent to the Public Health Agency of Canada (PHAC) via their [https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection/health-professionals/interim-guidance-surveillance-human-infection.html Coronavirus Diseases (COVID-19) Case Report Form].
'''Additional considerations for point-of-care testing and self-collection'''
One of the long-term goals of healthcare professionals, governments, and test kit manufacturers has been to develop and increase access to point-of-care (POC) testing solutions for COVID-19. This has come with many challenges, but it is largely being realized. The CDC continues to update its ''Guidance for SARS-CoV-2 Point-of-Care and Rapid Testing''<ref name="CDCGuidancePOC20">{{cite web |url=https://www.cdc.gov/coronavirus/2019-ncov/lab/point-of-care-testing.html |title=Guidance for SARS-CoV-2 Point-of-Care Testing |author=Centers for Disease Control and Prevention |publisher=Centers for Disease Control and Prevention |date=13 November 2020 |accessdate=07 September 2021}}</ref>, and, after the first "collect and test" at-home kit—the Lucira COVID-19 All-In-One Test Kit—was approved by the FDA in November 2020<ref name="RomoFDAApproves20">{{cite web |url=https://www.npr.org/sections/coronavirus-live-updates/2020/11/17/936055284/fda-approves-first-at-home-coronavirus-test |title=FDA Approves 1st At-Home Coronavirus Test |author=Romo, V. |work=NPR |date=17 November 2020 |accessdate=18 November 2020}}</ref>, many more were eventually approved for emergency use.<ref name="FDAInVitAntigen21">{{cite web |url=https://www.fda.gov/medical-devices/coronavirus-disease-2019-covid-19-emergency-use-authorizations-medical-devices/in-vitro-diagnostics-euas-antigen-diagnostic-tests-sars-cov-2 |title=In Vitro Diagnostics EUAs - Antigen Diagnostic Tests for SARS-CoV-2 |publisher=U.S. Food and Drug Administration |date=07 September 2021 |accessdate=07 September 2021}}</ref> However, while these easy-use or quick-result tests are promising and welcome, a few additional testing considerations come with them. For example, the CDC has indicated that though FDA-authorized POC tests are approved for symptomatic individuals, "CLIA will temporarily allow CLIA-certified laboratories and other testing sites to use SARS-CoV-2 point-of-care and rapid antigen tests on asymptomatic people for the duration of the COVID-19 public health emergency."<ref name="CDCGuidancePOC20" /> Other recommendations include not reusing test devices or components, changing gloves at strategic points, and limiting opening of test materials until ready to begin testing.<ref name="CDCGuidancePOC20" />
In some cases, such as drive-through testing sites, patient self-collection of a sample may be required. In these cases, it's vital that the patient is given clear and concise instructions on how to collect the sample before they begin the process. The American Association for Clinical Chemistry (AACC) notes that false-negative results are more likely with poor instruction and recommends healthcare providers provide patients with written or video instructions, along with any verbal instructions. Less invasive nasal swabs are typically being used in this case. During self-collection, the patient inserts the entire swab tip in one nasal cavity, makes four to five sweeping circles along the nasal wall for about 10 to 15 seconds, and then repeats the process in the opposite nostril.<ref name="AACCProperSelf20">{{cite web |url=https://labtestsonline.org/news/proper-self-collection-nasal-swabs-critical-accurate-covid-19-testing |title=Proper Self-collection of Nasal Swabs Critical for Accurate COVID-19 Testing |author=American Association for Clinical Chemistry |work=Lab Tests Online |publisher=American Association for Clinical Chemistry |date=12 November 2020 |accessdate=18 November 2020}}</ref>
In the case of at-home test kits, instructions for sample collection and system use should be followed carefully. For example, the Lucira All-In-One Test Kit can be used in a CLIA-certified lab or "for prescription home use," meaning a healthcare provide must approve a prescription in order for the patient can use the test at home. Additionally, the healthcare provider will still be held responsible for reporting the test results they receive from the patient using the kit at home.<ref name="LuciraCOVIDInst20">{{cite web |url=https://www.fda.gov/media/143808/download |format=PDF |title=Lucira COVID-19 All-In-One Test Kit - Instruction for Use |publisher=Lucira Health |date=2020 |accessdate=18 November 2020}}</ref>
'''Mitigating risk associated with false negatives'''
Before moving on, words of caution should be issued in regard to any COVID-19 testing conducted: false-negative results can be problematic.<ref name="BealeMultiple20">{{cite web |url=https://www.darkdaily.com/2020/06/29/multiple-studies-raise-questions-about-reliability-of-clinical-laboratory-covid-19-diagnostic-tests/ |title=Multiple Studies Raise Questions About Reliability of Clinical Laboratory COVID-19 Diagnostic Tests |author=Beale, S. |work=Dark Daily |date=29 June 2020 |accessdate=07 September 2021}}</ref><ref name="WestCOVID20">{{cite journal |title=COVID-19 Testing: The Threat of False-Negative Results |journal=Mayo Clinic Proceedings |author=West, C.P.; Montori, V.M.; Sampathkumar, P. |volume=95 |issue=6 |pages=1127–29 |year=2020 |doi=10.1016/j.mayocp.2020.04.004 |pmid=32376102 |pmc=PMC7151274}}</ref> One of the primary reasons they are problematic is that it may leave an otherwise asymptomatic individual to continue to unknowingly spread the virus further. Those individuals may relax physical distancing measures and become lax with their mask wearing, affecting others outside the clinical setting. Inside a clinical setting, a patient with a false negative "may be sent to the frontlines of care and inadvertently transmit the virus to patients and colleagues, further straining the already precarious ability of the health care system to respond to the pandemic."<ref name="WestCOVID20" />
In a perspective piece published in ''Mayo Clinic Proceedings'', West ''et al.'' of the Mayo Clinic offer four critical recommendations for society as we attempt to mitigate the risk associated with false negatives when performing clinical testing for COVID-19. Those recommendations are<ref name="WestCOVID20" />:
:1. Continue protective and preventative measures inside and outside the testing facility. This includes efforts such as physical distancing, regular hand-washing, regular disinfection of surfaces, and adequate personal protective equipment (PPE) for clinical staff (as well as the encouragement of proper mask wearing by others).
:2. Develop and improve PCR and serological assays to be more sensitive and specific. The development and improvement process must include methodologically rigorous studies designed to limit the risk of biased results, as well as clearly reported test performance characteristics.
:3. Assess patients carefully for their potential risk level for being infected. Confidence in negative test results may need to be lowered for health care workers and individuals in other high-risk groups. In general, given the uncertainty around viral load, asymptomatic transmission, and other disease characteristics, caution should be used with negative results in general.
:4. Establish risk-based protocols for managing negative COVID-19 results. Truly low-risk individuals may not be a major concern when results come back negative. However, individuals in higher-risk categories may require more judicious protocols, e.g., delaying a return to a workplace (for self-isolation) despite receiving a negative and having no symptoms. (This may require a more sensitive follow-up test or at least a second negative in a repeat test, particularly among clinical workers.)


==References==
==References==
{{Reflist|colwidth=30em}}
{{Reflist|colwidth=30em}}

Revision as of 18:10, 3 February 2022

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)

Early in the COVID-19 pandemic, laboratory guidance for testing for SARS-CoV-2 was relatively quick to evolve. The timely development and organized use of accurate assays and meaningful screening protocols, however, has been inconsistent but improving worldwide, with some countries more urgently and agilely responding than others.[1][2][3] 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.[4] 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.[5][6] In fact, the WHO had draft guidance for laboratory testing out as early as January 10, 2020, before gene sequencing was even completed.[7] 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 has largely been the predominant diagnostic method used in guidance for detecting SARS-CoV-2's RNA in specimens and thus laboratory confirmation of COVID-19 cases. Other diagnostic methods such as isothermal amplification (e.g., LAMP) and antigen testing have also emerged as the pandemic has progressed. 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. It also has other uses; in its September 2020 guidance, the WHO said: "If negative NAAT results are obtained from a patient in whom SARS-CoV-2 infection is strongly suspected, a paired serum specimen could be collected."[8] On April 3, the U.S. Food and Drug Administration (FDA) approved the country's 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[9] As of September 2021, the U.S. FDA has granted emergency use authorizations (EUA) for 88 serology/antibody tests.[10] (Note: Johns Hopkins also appears to be maintaining a page tracking approved serology tests around the world.)

Primary testing guidance

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)[8][11][12][13][14]:

  • Determine that the patient is indicating clinical and/or epidemiological evidence of COVID-19 (meets case definitions). Early on in the pandemic, case definitions and testing criteria were initially strict due to lack of test kits[15][16][17], but test kit availability has ramped up since, allowing for testing a wider group of symptomatic patients, as well as asymptomatic patients. However, clinicians are still encouraged to consider other causes for respiratory illness.[11]
  • Collect at a minimum an upper respiratory tract (URT) specimen. Some guidance like that found in the U.K. also suggests collecting lower respiratory tract (LRT) specimens, whenever possible.[13] Broadly, it appears lower respiratory tract specimens such as sputum and bronchoalveolar lavage fluid are a more 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.[18][19] In most cases, a URT will be sufficient; however, an LRT is especially useful when a patient tests negative with a URT but is still high suspicious of having COVID-19. Yet, as Wang et al. point out, "testing of specimens from multiple sites may improve the sensitivity and reduce false-negative test results,"[18] 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."[12] 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."[14] Nasopharyngeal aspiration is also an acceptable sample collection method for the upper respiratory tract according to all mentioned entities except the PHLN, which appears to have removed mention of nasopharyngeal aspirate from its guidance sometime in 2021.[14]
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 used to suggest hospital patients have "a sample for acute serology" taken, but that appears to have been removed from 2021 guidance.[13] The PHLN initially provided similar advice as the WHO, but in late April they expanded their guidance to discuss the value of serology.[14] They have also added collection recommendations for serology, in separate guidance, indicating that "serological testing before two weeks from the onset of symptoms may result in false negative results."[20]
Finally, and more recently, potential evidence of saliva having diagnostic value for detecting SARS-CoV-2 has arisen. Xu et al. noted in published April 2020 research that the "diagnostic value of saliva specimens for ... nucleic acid examination remains limited but promising."[21] Another paper published in September 2020 provided similar thoughts, though was generally more optimistic than the paper published by Xu et al., suggesting saliva from the opening of the mouth (in contrast to Xu et al. and their finding of better results from saliva in the throat) may be viable specimen.[22] In fact, an April 2020 EUA by the FDA had been made for the first saliva-based COVID-19 test, produced by Vault Health, Inc.[23]
As these and similar studies have been peer reviewed and methods validated, saliva has increasingly looked like a viable sample type. The CDC updated their guidance in October 2020 regarding saliva as a testing substrate. The CDC now notes: "Collect 1-5 ml of saliva in a sterile, leak-proof screw cap container. No preservative is required."[12] This is presumably in conjunction with tests approved for the use of saliva. Australia's PHLN updated their guidance in 2021 to include a full section on saliva testing and how to approach it, though cautioning it "does not advise routine use of saliva for diagnostic testing except in specific situations."[14]
  • Conduct testing. NAAT methods like qRT-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 "RT-PCR or TMA are the methods of choice to detect SARS-CoV-2 during the acute illness."[14] Viral cultures are little mentioned, though the PHLN underscores the idea that viral cultures for routine diagnoses are "of limited utility" and, if attempted, should only be performed in Biosafety Level 3 (BSL-3) laboratories.[14] As of August 2020, only the PHLN has made any specific recommendations for how serological testing should be conducted for testing past cases of COVID-19.[14] The current set of approved serology tests from around the world appear to use lateral flow immunoassay, ELISA, or neutralization methods.[17] Also note that at least in the U.S., the FDA in October 2020 discontinued review and approval of laboratory developed tests (LDTs), in favor of tests that would be more likely to increase access to testing or overall test capacity.[24]
  • Confirm the results. The WHO notes that optimally a positive result should come from a NAAT method "with at least two independent targets on the SARS-CoV-2 genome." However, they recognize that "in areas with widespread transmission of SARS-CoV-2, a simple algorithm might be adopted with one single discriminatory target," though monitoring of potential mutations is recommended.[8] Most guidance notes that 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 to limit the chance of incorrect results.
  • 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 COVID-19 Worksheet. In Canada, reports are sent to the Public Health Agency of Canada (PHAC) via their Coronavirus Diseases (COVID-19) Case Report Form.

Additional considerations for point-of-care testing and self-collection

One of the long-term goals of healthcare professionals, governments, and test kit manufacturers has been to develop and increase access to point-of-care (POC) testing solutions for COVID-19. This has come with many challenges, but it is largely being realized. The CDC continues to update its Guidance for SARS-CoV-2 Point-of-Care and Rapid Testing[25], and, after the first "collect and test" at-home kit—the Lucira COVID-19 All-In-One Test Kit—was approved by the FDA in November 2020[26], many more were eventually approved for emergency use.[27] However, while these easy-use or quick-result tests are promising and welcome, a few additional testing considerations come with them. For example, the CDC has indicated that though FDA-authorized POC tests are approved for symptomatic individuals, "CLIA will temporarily allow CLIA-certified laboratories and other testing sites to use SARS-CoV-2 point-of-care and rapid antigen tests on asymptomatic people for the duration of the COVID-19 public health emergency."[25] Other recommendations include not reusing test devices or components, changing gloves at strategic points, and limiting opening of test materials until ready to begin testing.[25]

In some cases, such as drive-through testing sites, patient self-collection of a sample may be required. In these cases, it's vital that the patient is given clear and concise instructions on how to collect the sample before they begin the process. The American Association for Clinical Chemistry (AACC) notes that false-negative results are more likely with poor instruction and recommends healthcare providers provide patients with written or video instructions, along with any verbal instructions. Less invasive nasal swabs are typically being used in this case. During self-collection, the patient inserts the entire swab tip in one nasal cavity, makes four to five sweeping circles along the nasal wall for about 10 to 15 seconds, and then repeats the process in the opposite nostril.[28]

In the case of at-home test kits, instructions for sample collection and system use should be followed carefully. For example, the Lucira All-In-One Test Kit can be used in a CLIA-certified lab or "for prescription home use," meaning a healthcare provide must approve a prescription in order for the patient can use the test at home. Additionally, the healthcare provider will still be held responsible for reporting the test results they receive from the patient using the kit at home.[29]

Mitigating risk associated with false negatives

Before moving on, words of caution should be issued in regard to any COVID-19 testing conducted: false-negative results can be problematic.[30][31] One of the primary reasons they are problematic is that it may leave an otherwise asymptomatic individual to continue to unknowingly spread the virus further. Those individuals may relax physical distancing measures and become lax with their mask wearing, affecting others outside the clinical setting. Inside a clinical setting, a patient with a false negative "may be sent to the frontlines of care and inadvertently transmit the virus to patients and colleagues, further straining the already precarious ability of the health care system to respond to the pandemic."[31]

In a perspective piece published in Mayo Clinic Proceedings, West et al. of the Mayo Clinic offer four critical recommendations for society as we attempt to mitigate the risk associated with false negatives when performing clinical testing for COVID-19. Those recommendations are[31]:

1. Continue protective and preventative measures inside and outside the testing facility. This includes efforts such as physical distancing, regular hand-washing, regular disinfection of surfaces, and adequate personal protective equipment (PPE) for clinical staff (as well as the encouragement of proper mask wearing by others).
2. Develop and improve PCR and serological assays to be more sensitive and specific. The development and improvement process must include methodologically rigorous studies designed to limit the risk of biased results, as well as clearly reported test performance characteristics.
3. Assess patients carefully for their potential risk level for being infected. Confidence in negative test results may need to be lowered for health care workers and individuals in other high-risk groups. In general, given the uncertainty around viral load, asymptomatic transmission, and other disease characteristics, caution should be used with negative results in general.
4. Establish risk-based protocols for managing negative COVID-19 results. Truly low-risk individuals may not be a major concern when results come back negative. However, individuals in higher-risk categories may require more judicious protocols, e.g., delaying a return to a workplace (for self-isolation) despite receiving a negative and having no symptoms. (This may require a more sensitive follow-up test or at least a second negative in a repeat test, particularly among clinical workers.)

References

  1. Subbaraman, N.; Callaway, E. (23 March 2020). "Coronavirus tests: Researchers chase new diagnostics to fight the pandemic". Nature - News Explainer. doi:10.1038/d41586-020-00827-6. https://www.nature.com/articles/d41586-020-00827-6. Retrieved 05 April 2020. 
  2. Apuzzo, M.; Gebrekidan, S. (20 March 2020). "Can’t Get Tested? Maybe You’re in the Wrong Country". The New York Times. https://www.nytimes.com/2020/03/20/world/europe/coronavirus-testing-world-countries-cities-states.html. Retrieved 05 April 2020. 
  3. Hindsley, G. (28 March 2020). "The Lost Month: How a Failure to Test Blinded the U.S. to COVID-19". The New York Times. https://www.nytimes.com/2020/03/28/us/testing-coronavirus-pandemic.html. Retrieved 05 April 2020. 
  4. Denison, M.R. (2004). "Coronavirus Research: Keys to Diagnosis, Treatment, and Prevention of SARS". Learning from SARS: Preparing for the Next Disease Outbreak. Institute of Medicine. pp. 137–72. doi:10.17226/10915. ISBN 9780309182157. https://www.nap.edu/read/10915/chapter/5. 
  5. Ceccarelli, M.; Berretta, M.; Venanzi Rullo, E. et al. (2020). "Differences and similarities between Severe Acute Respiratory Syndrome (SARS)-CoronaVirus (CoV) and SARS-CoV-2. Would a rose by another name smell as sweet?". European Review for Medical and Pharmacological Sciences 24 (5): 2781-2783. doi:10.26355/eurrev_202003_20551. PMID 32196628. 
  6. Wilder-Smith, A.; Chiew, C.J.; Lee, V.J. (2020). "Can we contain the COVID-19 outbreak with the same measures as for SARS?". The Lancet Infectious Diseases. doi:10.1016/S1473-3099(20)30129-8. PMC PMC7102636. PMID 32145768. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102636. 
  7. World Health Organization (10 January 2020). "Laboratory testing of human suspected cases of novel coronavirus (nCoV) infection: Interim guidance 10 January 2020". WHO/2019-nCoV/laboratory/2020.1. World Health Organization. https://apps.who.int/iris/bitstream/handle/10665/330374/WHO-2019-nCoV-laboratory-2020.1-eng.pdf. Retrieved 05 April 2020. 
  8. 8.0 8.1 8.2 World Health Organization, et al. (11 September 2020). "Diagnostic testing for SARS-CoV-2". WHO/2019-nCoV/laboratory/2020.6. World Health Organization. https://apps.who.int/iris/handle/10665/334254. Retrieved 18 November 2020. 
  9. Terry, M. (3 April 2020). "Cellex and Mayo Clinic Launch Tests to Determine COVID-19 Immunity from Previous Exposure". BioSpace. https://www.biospace.com/article/fda-approves-1st-covid-19-antibody-test/. Retrieved 05 April 2020. 
  10. "In Vitro Diagnostics EUAs". U.S. Food and Drug Administration. 20 August 2020. https://www.fda.gov/medical-devices/coronavirus-disease-2019-covid-19-emergency-use-authorizations-medical-devices/vitro-diagnostics-euas#individual-serological. Retrieved 23 August 2020. 
  11. 11.0 11.1 Centers for Disease Control and Prevention (2 August 2021). "Overview of Testing for SARS-CoV-2". Centers for Disease Control and Prevention. https://www.cdc.gov/coronavirus/2019-ncov/hcp/testing-overview.html. Retrieved 06 September 2021. 
  12. 12.0 12.1 12.2 Centers for Disease Control and Prevention (26 February 2021). "Interim Guidelines for Collecting and Handling of Clinical Specimens for COVID-19 Testing". Centers for Disease Control and Prevention. https://www.cdc.gov/coronavirus/2019-nCoV/lab/guidelines-clinical-specimens.html. Retrieved 06 September 2021. 
  13. 13.0 13.1 13.2 Public Health England (29 March 2021). "COVID-19: Guidance for sampling and for diagnostic laboratories". U.K Government. https://www.gov.uk/government/publications/wuhan-novel-coronavirus-guidance-for-clinical-diagnostic-laboratories. Retrieved 06 September 2021. 
  14. 14.0 14.1 14.2 14.3 14.4 14.5 14.6 14.7 Public Health Laboratory Network (22 June 2021). "PHLN guidance on laboratory testing for SARS-CoV-2 (the virus that causes COVID-19)". Department of Health, Australian Government. https://www.health.gov.au/resources/publications/phln-guidance-on-laboratory-testing-for-sars-cov-2-the-virus-that-causes-covid-19. Retrieved 06 September 2021. 
  15. Centers for Disease Control and Prevention (27 April 2020). "Evaluating and Testing Persons for Coronavirus Disease 2019 (COVID-19)". Centers for Disease Control and Prevention. Archived from the original on 01 May 2020. https://web.archive.org/web/20200501002841/https://www.cdc.gov/coronavirus/2019-ncov/hcp/clinical-criteria.html. Retrieved 08 July 2020. 
  16. Branswell, H. (4 April 2020). "CDC launches studies to get more precise count of undetected Covid-19 cases". STAT. https://www.statnews.com/2020/04/04/cdc-launches-studies-to-get-more-precise-count-of-undetected-covid-19-cases/. Retrieved 05 April 2020. 
  17. 17.0 17.1 Center for Health Security (26 August 2021). "Serology tests for COVID-19". Johns Hopkins University. https://www.centerforhealthsecurity.org/covid-19TestingToolkit/serology/Serology-based-tests-for-COVID-19.html. Retrieved 06 September 2021. 
  18. 18.0 18.1 Wang, W.; Xu, Y.; Gao, R. et al. (2020). "Detection of SARS-CoV-2 in Different Types of Clinical Specimens". JAMA. doi:10.1001/jama.2020.3786. PMC PMC7066521. PMID 32159775. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7066521. 
  19. Yu, F.; Yan, L.; Wang, N. et al. (2020). "Quantitative Detection and Viral Load Analysis of SARS-CoV-2 in Infected Patients". Clinical Infectious Diseases: ciaa345. doi:10.1093/cid/ciaa345. PMID 32221523. 
  20. Public Health Laboratory Network (3 September 2020). "PHLN guidance for serological testing in COVID-19" (Word). Department of Health, Australian Government. https://www.health.gov.au/sites/default/files/documents/2020/09/phln-guidance-for-serological-testing-in-covid-19-phln-guidance-on-serological-testing-in-covid-19.docx. Retrieved 06 September 2021. 
  21. Xu, R.; Cui, B.; Duan, X. et al. (2020). "Saliva: Potential diagnostic value and transmission of 2019-nCoV". International Journal of Oral Science 12: 11. doi:10.1038/s41368-020-0080-z. 
  22. Wyllie, A.L.; Fournier, J.; Casanovas-Massana, A. et al. (2020). "Saliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2". New England Journal of Medicine 383: 1283–6. doi:10.1056/NEJMc2016359. PMC PMC7484747. PMID 32857487. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7484747. 
  23. Vault Health (14 April 2020). "Vault Health Launches First-of-its-Kind Saliva-based FDA EUA Approved Test for COVID-19". PR Newswire. https://www.prnewswire.com/news-releases/vault-health-launches-first-of-its-kind-saliva-based-fda-eua-approved-test-for-covid-19-301039633.html. Retrieved 01 May 2020. 
  24. Fox, A. (12 October 2020). "EUAs for Laboratory Developed COVID-19 Tests Will No Longer Be Reviewed by the FDA". JDSupra. https://www.jdsupra.com/legalnews/euas-for-laboratory-developed-covid-19-91593/. Retrieved 18 November 2020. 
  25. 25.0 25.1 25.2 Centers for Disease Control and Prevention (13 November 2020). "Guidance for SARS-CoV-2 Point-of-Care Testing". Centers for Disease Control and Prevention. https://www.cdc.gov/coronavirus/2019-ncov/lab/point-of-care-testing.html. Retrieved 07 September 2021. 
  26. Romo, V. (17 November 2020). "FDA Approves 1st At-Home Coronavirus Test". NPR. https://www.npr.org/sections/coronavirus-live-updates/2020/11/17/936055284/fda-approves-first-at-home-coronavirus-test. Retrieved 18 November 2020. 
  27. "In Vitro Diagnostics EUAs - Antigen Diagnostic Tests for SARS-CoV-2". U.S. Food and Drug Administration. 7 September 2021. https://www.fda.gov/medical-devices/coronavirus-disease-2019-covid-19-emergency-use-authorizations-medical-devices/in-vitro-diagnostics-euas-antigen-diagnostic-tests-sars-cov-2. Retrieved 07 September 2021. 
  28. American Association for Clinical Chemistry (12 November 2020). "Proper Self-collection of Nasal Swabs Critical for Accurate COVID-19 Testing". Lab Tests Online. American Association for Clinical Chemistry. https://labtestsonline.org/news/proper-self-collection-nasal-swabs-critical-accurate-covid-19-testing. Retrieved 18 November 2020. 
  29. "Lucira COVID-19 All-In-One Test Kit - Instruction for Use" (PDF). Lucira Health. 2020. https://www.fda.gov/media/143808/download. Retrieved 18 November 2020. 
  30. Beale, S. (29 June 2020). "Multiple Studies Raise Questions About Reliability of Clinical Laboratory COVID-19 Diagnostic Tests". Dark Daily. https://www.darkdaily.com/2020/06/29/multiple-studies-raise-questions-about-reliability-of-clinical-laboratory-covid-19-diagnostic-tests/. Retrieved 07 September 2021. 
  31. 31.0 31.1 31.2 West, C.P.; Montori, V.M.; Sampathkumar, P. (2020). "COVID-19 Testing: The Threat of False-Negative Results". Mayo Clinic Proceedings 95 (6): 1127–29. doi:10.1016/j.mayocp.2020.04.004. PMC PMC7151274. PMID 32376102. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151274.