Costa 2020.

Study characteristics
Patient Sampling	Purpose: Diagnosis of current acute‐phase infection and current convalescent‐phase infection (only time split 4‐13 days pso was eligible for our review though) Design: Two‐group study to estimate sensitivity and specificity [1] Confirmed COVID patients (n = 122) [1a] rt‐PCR‐positive (n = 106) [1b] negative RT‐PCR but a clinical COVID‐19 diagnosis (n = 16) [2] Non‐COVID samples (96 historical blood donation samples, Table 3 specified 100 though) Recruitment: [1] Not stated (2 Brazilian hospitals) [2] Not stated Prospective or retrospective: [1] Prospective [2] Retrospective Sample size: 218 (122) of which 134 (38) are eligible for our review. Further detail: [1a] rt‐PCR‐positive [1b] rt‐PCR‐negative with clinical COVID diagnosis based on highly suggestive symptoms and chest computed tomography (CT) findings [2] historical (February 2019) blood donors Exclusion criteria not stated
Patient characteristics and setting	Setting: Mixed (inpatients and outpatients) Location: 2 Brazilian hospitals: Hospital das Clínicas da Faculdade de Medicina da Universidade de S˜ao Paulo (HC‐FMUSP; [1b]) and Hospital Sírio‐Libanes (HSL; [1a, inpatients]). Both hospitals are located in Sao Paulo. Country: Brazil Dates: Not stated Symptoms and severity: 75 inpatients and 47 outpatients Numbers (%) for 59 PCR+ inpatients, 47 PCT+ outpatients and 16 PCR‐ inpatients: Fever 34 (60); 27 (61); 13 (81) Cough 38 (67); 35 (79); 16 (100) Coryza 7 (12); 10 (23); 1 (6) Sore throat 6 (11;) 16 (36); 1 (6) Dyspnoea 30 (53); 12 (27); 15 (94) Myalgia 6 (11); 18 (41); 3 (19) Asthenia 6 (11); 8 (18); NA Headache 4 (7); 27 (61); 2 (13) GI symptoms* 5 (9); 17 (38); 3 (19) Haemoptysis 3 (5); NA; NA Dysgeusia 1 (1.8); 2 (4.5); 2 (13) Anosmia NA; 7 (15; ) 2(13) All 16 RT‐PCR‐negative patients had pneumonia, 6/16 (38%) were intubated. Demographics: [1a] 59 PCR+ inpatients Age median 61 (range 32‐90) years Male 41 (70%) [1a] 47 PCR+ outpatients (healthcare workers) Age median 44 (range 21‐62) years Male 20 (43%) [1b] 16 PCR‐ inpatients Age median 55 (range 36‐77) years Male 6 (38%) Exposure history: [1a] 47/106 were healthcare workers [1b] Not stated Non‐Covid group 1: [2] Pre‐pandemic controls Source: Blood donors; February 2019 Characteristics: Not stated (blood donors, so possibly healthy)
Index tests	Test name: [A] Not stated [B] Not stated Manufacturer: [A] Euroimmun‐ Lübeck, Germany [B] Wondfo‐China Antibody: [A] IgA and IgG [B] IgG and IgM Antigen target: [A] anti‐SARS‐CoV‐2 S1 IgG and IgA [B] Not stated Evaluation setting: [A] Lab test performed in lab [B] POCT, unclear where performed (plasma samples) Test method: [A] ELISA [B] Rapid chromatographic immunoassays; Anti‐SARS‐CoV‐2 antibodies present in the sample bind to recombinant antigens coated on colloidal gold particles and form an antigen‐antibody/colloidal gold complex. Timing of samples: [1a] PCR+ inpatients Mean 10.7 (range 4‐23) days pso PCR+ outpatients Mean 32.0 (range 16‐42) days pso All PCR+ patients: < 14 days: 38/106 14+ days pso: 59/106 Unknown: 9/106 [1b] PCR‐ inpatients Mean 8 (range 2‐15 ) days pso Samples used: Plasma Test operator: Not stated Definition of test positivity: [A] Results were interpreted according to the manufacturer’s recommendation: a ratio < 0.8 as negative, between 0.8 and 1.1 as borderline, and ≥ 1.1 as positive. [B] The result was read in 15 minutes by three people that had received appropriate training. The colour change was compared to the assay standard. Blinding reported: not stated Threshold predefined: [A] yes, according to the manufacturer's recommendation [B] yes, visual‐based
Target condition and reference standard(s)	Reference standard: [1] RT‐PCR. RNA was extracted from clinical samples with an automated method using magnetic beads (sample Preparation System RNA, Abbott, Illinois, USA). SARS‐CoV‐2 RNA reverse transcription, amplification, and detection were performed using an adapted protocol, as described elsewhere. An assay detecting the E gene was used as the first‐line screening tool, followed by confirmatory testing with an assay detecting the N gene. Threshold not stated. [1b] 14/16 RT‐PCR‐negative patients had a second negative RT‐PCR. Clinical COVID‐19 diagnosis based on highly suggestive symptoms and chest computed tomography (CT) findings. Samples used: [1] Respiratory samples were obtained from both the nasopharynx and oropharynx using rayon swabs. Timing of reference standard: Not stated Blinded to index test: yes, prior Incorporated index test: no Definition of non‐COVID cases: Pre‐pandemic Samples used: Pre‐pandemic Timing of reference standard: Pre‐pandemic (February 2019) Blinded to index test: yes, prior Incorporated index test: no
Flow and timing	Time interval between index and reference tests: Not stated All patients received same reference standard: no Missing data: yes as only 38/122 COVID cases included in our review Uninterpretable results: Not stated Indeterminate results: Not stated (there seemed to be some borderline results for test [A] in Figure 1, see supplement) Unit of analysis: [1] Patients [2] Unclear
Comparative
Notes	Funding: Internal funding from the Hospital das Clínicas of University of S˜ao Paulo, Brazil. Publication status: Published paper (Short Communication) Source: Journal of Clinical Virology Author COI: The authors reported no declarations of interest.
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?	No
Did the study avoid inappropriate exclusions?	Unclear
Did the study avoid inappropriate inclusions?	Unclear
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 (All tests)
DOMAIN 2: Index Test (Antibody 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?	Unclear
Were the reference standard results interpreted without knowledge of the results of the index tests?	Yes
The reference standard does not incorporate the index test	Yes
Could the reference standard, its conduct, or its interpretation have introduced bias?		Unclear 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?	Unclear
Did all patients receive the same reference standard?	No
Were all patients included in the analysis?	No
Did all participants receive a reference standard?	Yes
Were results presented per patient?	Unclear
Could the patient flow have introduced bias?		High risk