Szymczak 2020.

Study characteristics
Patient Sampling	Single group study to estimate sensitivity and specificity: ‐ remnant samples from patients with symptomatic diarrhea submitted for routine diagnostic testing (n=79 from 77 patients) Recruitment: Convenience Prospective or retrospective: Retrospective
Patient characteristics and setting	Setting: Unclear Location: Clinical Microbiology Laboratory at Montefiore Medical Center, New York Country: USA Dates: Apr 21 to May 15 2020 Symptoms and severity: All symptomatic for diarrhoea Demographics: Not stated Exposure history: Not stated
Index tests	Test name: Xpert Xpress (no product code reported) Manufacturer: Cepheid Inc Target gene(s): N2 and E Antigen target: n/a Test method: Automated RT‐PCR Samples used: Stool, collection not reported Transport media: Not stated; coated swabs transferred to 1 ml 0.85% saline for testing Sample storage: Stored at 2 to 8C for up to 7 days prior to testing Test operator: Not stated Definition of test positivity: Describes 'following the package insert instructions' ‐ presumptive positives not reported Blinding reported: Yes; conducted first Timing of samples: PCR +ve stool samples collected 0 to 33 days from initial respiratory PCR; 8/27 collected at >=14 days and 6/27 collected at >=21 days
Target condition and reference standard(s)	Reference standard: RT‐PCR; Hologic Panther Fusion Definition of non‐COVID cases: As for cases (single PCR negative) Genetic target(s): two ORF1a regions Samples used: Stool, as for index Timing of reference standard: Some samples frozen at ‐80oC prior to testing with Hologic Panther Fusion Blinded to index test: Unclear Incorporated index test: No
Flow and timing	Time interval between index and reference tests: Simultaneous; same swabs All patients received same reference standard: Yes Missing data: None reported, no participant flow diagram reported Uninterpretable results: None reported Indeterminate results (index test): discrepant results re‐tested with both index and reference test using both a new aliquot and a shared aliquot tested on both instruments on the same day Indeterminate results (reference standard): discrepant results re‐tested with both index and reference test using both a new aliquot and a shared aliquot tested on both instruments on the same day Unit of analysis: Samples (79 from 77 patients)
Comparative
Notes	Funding: No funding statement reported Publication status: Published Source: J Clin Microbiol 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?	No
Was a case‐control design avoided?	Unclear
Did the study avoid inappropriate exclusions?	Unclear
Did the study avoid inappropriate inclusions?	Yes
Could the selection of patients have introduced bias?		High 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 molecular tests)
Were the index test results interpreted without knowledge of the results of the reference standard?	Yes
If a threshold was used, was it pre‐specified?	Yes
Could the conduct or interpretation of the index test have introduced bias?		Low risk
Are there concerns that the index test, its conduct, or interpretation differ from the review question?			High
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?	No
Could the patient flow have introduced bias?		Unclear risk