key: cord-0684759-isswwnzn authors: Ward, Stephanie; Lindsley, Andrew; Courter, Josh; Assa’ad, Amal title: Clinical Testing For Covid-19 date: 2020-05-20 journal: J Allergy Clin Immunol DOI: 10.1016/j.jaci.2020.05.012 sha: 39e45782a1d30136cc04498a2ee30d34cf98a9a0 doc_id: 684759 cord_uid: isswwnzn Abstract As the novel coronavirus SARS-CoV-2 caused COVID-19 cases in the United States the initial test was developed and performed at the Center for Disease Control (CDC). As the number of cases increased the demand for tests multiplied, leading the CDC to utilize the Emergency Utilization Authorization to allow clinical and commercial laboratories to develop tests to detect the presence of the virus. Many nucleic acid tests based on reverse transcriptase-polymerase chain reaction (RT-PCR) were developed, each with different techniques, specifications and turnaround time. As the illnesses turned into a pandemic, testing became more crucial. The test supply became inadequate to meet the need that it had to be prioritized according to guidance. For surveillance, the need for serologic tests emerged. Here we review the timeline of test development, the turn-around times, the various approved tests and compare them as regards the genes they detect. We concentrate on the point-of-care tests and discuss the basis for new serologic tests. We discuss the testing guidance for prioritization and their application in a hospital setting. As SARS-CoV-2 virus arrived in the USA causing the COVID-19 illness, one of the most talked about issues in the management of the disease and the resulting pandemic has been clinical testing. A unique situation arose of a communicable and highly contagious disease necessitating the rapid diagnosis of patients and the identification of non-symptomatic infected persons. Unfortunately, the USA did not have a Food and Drug Administration (FDA) approved laboratory test for the illness. The FDA ultimately utilized its Emergency Use Authorizations (EUA) on February 4, 2020 to allow for more rapid and widespread development and implementation of in-vitro testing.1 Indeed, companies and organizations utilized the EUA to file applications for new tests based on different methodologies, amounting to 48 applications in the span of 3 months from the beginning of February to the end of April 2020. In addition, multiple other tests were put in place under a separate authorization by a Presidential memorandum in early March allowing laboratories that carry Clinical Laboratory Improvement Amendment (CLIA) certification to put tests in place without an EUA from the FDA. This created an unprecedented situation where the medical community and the public may not be familiar with the various new tests for COVID-19 that are offered to patients and hospitals. The purpose of this review is to provide information, up-to-date as of the date of submission of the manuscript to the journal, on the various tests that have been developed, their scientific basis and their interpretation. We give a real-world example demonstrating the time lag in the return of test results and review testing prioritization guidance since the supply of tests remains below the perceived need. As part of the quality assessment of each assay, the FDA requires demonstration of 199 specificity and exclusivity. Exclusivity means that no other viruses or bacteria from a 200 specified list is detected by the test. These are infectious organisms that may be close 201 genetically to the SARS-Co V2, or would be expected to be present in patients 202 presenting with the same symptoms of COVID-19 (Table 4) . 2) A few tests report cross reactivity with other coronaviruses, specifically viruses that 221 cause infections in animals, such as bats. Because of the relatively infrequent 222 occurrence of these zoonotic coronaviruses "jumping species" into humans (once a 223 decade over the last 20 years), this form of false positive results is unlikely to occur 224 again during the current pandemic (Table 2) . (Tables 1 and 2 ). Viral quantification is also highly dependent upon sampling 238 technique and the accurate measure/estimation of the amount of input material. Beyond sampling issues, the clinical utility of a quantitative SARS-CoV-2 test is unclear Cepheid has an EUA for its point of care Xpert Xpress SARS-CoV-2 testThis The 253 system requires the use of single-use disposable cartridges that hold the RT-PCR 254 reagents and host the RT-PCR process. Biofire Defense has an EAU for the BioFire COVID-19 Test which is a disposable, 256 closed system that stores all the necessary reagents for sample preparation for RT-257 PCR and detection in order to isolate, amplify, and detect nucleic acid from the SARS- Abbott has an EUA for its ID NOW which is a rapid, 13 minutes or less, instrument- that the test be read out as "inconclusive" and repeated. If US CDC kit used one 304 gene/amplicon (N2) with the most efficient RNA extraction system tested, the kit's LOD 305 would be 316 copies/ml. Of note, the US CDC kit also utilizes an extraction positive 306 control which detects the human RNase P gene. In summary, a test that does not utilize a concurrent sample-derived positive control 308 would have a higher false negative rate than a test with a human gene positive However, other coronavirus protein sequences are much less conserved in the N and 332 S2 proteins. The S1 subunit is less conserved and more highly specific to SARS-CoV-2. Genomics Laboratory (Table 3) (Table 5) . 28 Highest priority is recommended for vulnerable populations who 549 may require hospital-level care for COVID-19, heath care workers including non-clinical 550 staff, and the first symptomatic patients in a closed setting such as long-term living 551 facilities. Prioritizing these specific populations allow for more rapid interventions for the 552 most vulnerable patients, decrease the risk of transmission between and from health 553 care providers and to more rapidly identify and limit outbreaks in contained settings. The 554 CDC has updated its guidance on testing on March 24, 2020 ( Table 6 ). The highest 555 priority groups for testing include hospitalized patients and symptomatic healthcare 556 workers, to reduce spread of infection in the healthcare system and optimize care for 557 those patients requiring hospital care. Lower priority test groups include symptomatic 558 patients who reside in a long-term care facility, are aged 65 years of age or older, 559 patients with underlying medical conditions or first responders, as these groups may be In the setting of limited resources in areas with community transmission, prioritization for testing should be given to: • People who are at risk of developing severe disease and vulnerable populations, who will require hospitalization and advanced care for COVID-19. • Health workers (including emergency services and non-clinical staff) regardless of whether they are a contact of a confirmed case (to protect health workers and reduce the risk of nosocomial transmission) • The first symptomatic individuals in a closed setting (e.g. schools, long-term living facilities, prisons, hospitals) to quickly identify outbreaks and ensure containment measures. All other individuals with symptoms related to the close settings may be considered probable cases and isolated without additional testing if testing capacity is limited. Ensure optimal care options for all hospitalized patients, lessen the risk of nosocomial infections, and maintain the integrity of the healthcare system • Hospitalized patients • Symptomatic healthcare workers PRIORITY 2 Ensure that those who are at highest risk of complication of infection are rapidly identified and appropriately triaged • Patients in long-term care facilities with symptoms • Patients 65 years of age and older with symptoms • Patients with underlying conditions with symptoms • First responders with symptoms PRIORITY 3 As resources allow, test individuals in the surrounding community of rapidly increasing hospital cases to decrease community spread, and ensure health of essential workers • Critical infrastructure workers with symptoms • Individuals who do not meet any of the above categories with symptoms • Health care workers and first responders • Individuals with mild symptoms in communities experiencing high COVID-19 hospitalizations • Individuals without symptoms Other inpatients or those being admitted: • 2 or more of the following symptoms with no alternative diagnosis: o Fever, Cough, Sore throat, Difficulty breathing, myalgia, loss of smell Symptomatic outpatients: • Oncology patients in ED who are discharged home. • Non-high risk surgical procedure scheduled in next 96 hours. Asymptomatic patients: • Pre-transplant with an organ offer (need ASAP turn-around) • Pre-surgical high-risk procedures (ideally obtain test prior to procedure day) • Pre-admission for chemotherapy or BMT (ideally obtain test prior to therapy day) • Solid organ transplants with acute rejection requiring biologic therapies (i.e. ATG) • Neonates with a COVID-19 positive mother (@ 24 and 48 hours) *This is a recitation of general scientific principles, intended for broad and general physician understanding and knowledge and is offered solely for educational and informational purposes as an academic service of Cincinnati Children's Hospital Medical Center. This should in no way be considered as an establishment of any type of standard of care, nor is it offering medical advice for a particular patient or as constituting medical consultation services, either formal or informal. While this may be consulted for guidance, it is not intended for use as a substitute for independent professional medical judgment, advice, diagnosis, or treatment. 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