Lieberman 2020.

Study characteristics
Patient Sampling	Single‐group study to estimate sensitivity and specificity: ‐ samples submitted for clinical diagnostic testing (n = 169; not all samples analysed for all tests) Recruitment: not stated Prospective or retrospective: retrospective (residual samples) Number of samples (samples with confirmed SARS‐CoV‐2): 169 (87)
Patient characteristics and setting	Setting: not stated; sampled from laboratory Location: Washington State Public Health Laboratory Country: USA Dates: not stated Symptoms and severity: not stated Demographics: not stated Exposure history: not stated
Index tests	Test name: Xpert Xpress Manufacturer: Cepheid Antigen target: E, N2 Antibody: N/A Test method: rapid PCR Samples used: NP swabs (collection not described) Transport media: 300 μL of VTM sample Sample storage: all same‐sample comparisons were performed on specimens stored at 4 °C for < 72 h with no freeze‐thaws Test operator: not stated; presume laboratory staff Common panel of 26 specimens tested at UW by the UW CDC EUA‐based LDT or at LabCorp Seattle Definition of test positivity: 1 of 2 targets detected was considered positive for all assays; Xpert Xpress data extracted as per IFU definition (positive = both targets or N gene positive; E‐gene‐positive requires retest) Blinding reported: not stated Timing of samples: not stated Also evaluates: [B] Hologic Panther Fusion RUO, [C] Hologic Panther Fusion EUA, [D] Diasorin Simplexa, [E] Roche cobas 6800 in same 26 samples and in additional residual specimens (n = 115) at UW (different N per test)
Target condition and reference standard(s)	Reference standard: RT‐PCR; UW CDC EUA‐based in‐house test (positive if 1 of 2 targets detected ‐ presume at < 40 Ct) Definition of non‐COVID cases: single negative PCR Genetic target(s): NI, N2 Samples used: NP swabs, as for index test Timing of reference standard: not stated Blinded to index test: not stated Incorporated index test: no
Flow and timing	Time interval between index and reference tests: all testing conducted within 72 h All participants received same reference standard: yes Missing data: none reported; review team excluded data for 28 specimens comparing Panther Fusion with DiaSorin Simplexa Uninterpretable results: not stated Indeterminate results (index test): ‘Inconclusive' results (i.e. 1 genetic target detected) were considered positive due to the high specificity of all assays and limited cross‐reactivity seen for SARS‐CoV‐2 primer sets. For Xpert Xpress only 12/13 were positive according to IFU specifications on first test (both targets present, or N gene positive); on retesting the presumptive positive became positive (detection of E‐gene but not N‐gene) Indeterminate results (reference standard): as for index test Unit of analysis: not stated, only refers to samples
Comparative
Notes	Funding: no funding statement reported Publication status: accepted manuscript Source: Journal of Clinical Microbioloby Author COI: no COI statement reported
Methodological quality
Item	Authors' judgement	Risk of bias	Applicability concerns
DOMAIN 1: Patient Selection
Was a consecutive or random sample of patients enrolled?	Unclear
Was a case‐control design avoided?	Yes
Did the study avoid inappropriate exclusions?	Unclear
Did the study avoid inappropriate inclusions?	Unclear
Could the selection of patients have introduced bias?		Unclear risk
Are there concerns that the included patients and setting do not match the review question?			High
DOMAIN 2: Index Test (Antigen tests)
DOMAIN 2: Index Test (Rapid PCR tests)
Were the index test results interpreted without knowledge of the results of the reference standard?	Unclear
If a threshold was used, was it pre‐specified?	Yes
Could the conduct or interpretation of the index test have introduced bias?		Unclear risk
Are there concerns that the index test, its conduct, or interpretation differ from the review question?			Unclear
DOMAIN 3: Reference Standard
Is the reference standards likely to correctly classify the target condition?	No
Were the reference standard results interpreted without knowledge of the results of the index tests?	Unclear
Reference standard does not incorporate result of index test?	Yes
Could the reference standard, its conduct, or its interpretation have introduced bias?		High risk
Are there concerns that the target condition as defined by the reference standard does not match the question?			High
DOMAIN 4: Flow and Timing
Was there an appropriate interval between index test and reference standard?	Yes
Did all patients receive the same reference standard?	Yes
Were all patients included in the analysis?	Unclear
Did all participants receive a reference standard?	Yes
Were results presented per patient?	Unclear
Could the patient flow have introduced bias?		Unclear risk