Whitman 2020a [A].

Study characteristics
Patient Sampling	Purpose: Diagnosis of current acute or convalescent‐phase infection Design: Multi‐group study to assess sensitivity and specificity [1] Covid patients (n = 128 samples from 79 patients) [2] Non‐Covid patients (n = 159) [2a] Pre‐pandemic (n = 108) [2b] Cross‐reactivity, concurrent (n = 41) [2c] Concurrent, SARS‐COV‐2 PCR‐negative, no other viruses detected (n = 10) Recruitment: [1] Patients diagnosed at University of California, San Francisco (UCSF) hospital system or Zuckerberg San Francisco General (ZSFG) Hospital. Not admitted, admitted or ICU [2a] Blood donors before 2019 [2b] Patients with other respiratory pathogen testing at University of California, San Francisco (UCSF) hospital system or Zuckerberg San Francisco General (ZSFG) Hospital [2c] Patients at University of California, San Francisco (UCSF) hospital system or Zuckerberg San Francisco General (ZSFG) Hospital Recruitment method not stated. Prospective or retrospective: Retrospective Sample size: 287 (128) Further detail: [1] Inclusion: In or outpatients at University of California, San Francisco (UCSF) hospital system or Zuckerberg San Francisco General (ZSFG) Hospital with symptomatic infection and positive SARS‐CoV‐2 RT–PCR testing of nasopharyngeal or oropharyngeal swabs and remnant plasma and serum samples in associated laboratories Exclusion: If an individual had more than one specimen for a given time interval, only the later specimen was included. [2a] Inclusion: Blood donors before July 2018. Exclusion: Not stated [2b] Inclusion: Concurrent patients from 2020 with detection of other respiratory viruses. Exclusion: Not stated [2c] Inclusion: Concurrent patients from 2020, RT‐PCR‐negative for SARS‐CoV‐2 by RT–PCR. Exclusion: Not stated Exclusions: Data that did not fit our study design were excluded after the fact. This included all data and statistics derived from specimens from individuals who were mis‐assigned to a data analysis group (including time interval of days from symptom onset, or RT‐PCR status), duplicate patient specimens not originally identified prior to obtaining results or data from confirmatory spot testing described in the manuscript.
Patient characteristics and setting	Setting: Hospital inpatients (82%) and outpatients (ambulatory) (18%) Location: University of California, San Francisco (UCSF) hospital system or Zuckerberg San Francisco General (ZSFG) Hospital, San Francisco, CA Country: USA Dates: Not stated Symptoms and severity: 18% (14/79) not admitted, 46% (36/79) inpatients without ICU care, 37% (29/79) required ICU care Demographics: Age range 22‐90 years, mean 52.9 (SD 15) years 68% Hispanic/Latino 9% Asian 9% White 8% Black 6% Other/not reported Male sex 54/79 (68%) Exposure history: Not stated. Non‐Covid group 1: [2a] Pre‐pandemic Source: Blood donors before July 2019. From University of California, San Francisco (UCSF) hospital system or Zuckerberg San Francisco General (ZSFG) Hospital Characteristics: Healthy Non‐Covid group 2: [2b] Cross‐reactivity [2c] RT‐PCR‐negative, no other respiratory viruses detected Source: [2b] [2c] University of California, San Francisco (UCSF) hospital system or Zuckerberg San Francisco General (ZSFG) Hospital, in 2020 Characteristics: [2b] Influenza A (n = 2), human rhinovirus/enterovirus (n = 17), human metapneumovirus (n = 54), respiratory syncytial virus (n = 9), parainfluenza (n = 3), adenovirus (n = 2), other coronaviruses (n = 4) [2c] Not other respiratory viruses
Index tests	Test name: [A] COVID‐19 IgM‐IgG Rapid Test (51‐002‐20) [B] Perfect POC Novel Corona Virus (SARS‐CoV‐2) IgM/IgG Rapid Test Kit (SC30201 W) [C] Novel Coronavirus (SARS‐CoV‐2) IgM/IgG Combo Rapid Test‐Cassette [D] COVID‐19 (SARS‐CoV‐2) IgG/IgM Antibody Test Kit (Colloidal Gold) [E] Novel Coronavirus (2019‐nCoV) Ab Test (Colloidal Gold) IgM [F] COVID‐19 IgG/IgM Rapid Test Cassette (INGMMC42S) (RightSign assay from Hangzhou Biotest) [G] SARS‐CoV‐2 IgM/IgG Antibody Rapid Test (VC01210 3) [H] Coronavirus IgG/IgM Antibody (COVID‐19) Test Cassette (U‐CoV102) [I] VivaDiag SARS‐CoV‐2 IgM/IgG Rapid Test (VID35‐08‐011) [J] SARS‐CoV‐2 Antibody Test (W195) [K] EDI Novel Coronavirus COVID‐19 IgM or IgG ELISA (KT‐1033; KT‐1032) [Addional in‐House ELISA reported; not included in review] Manufacturer: [A] BioMedomics Inc, Morrisville, NC, USA [B] Bioperfectus Technologies Co Ltd, Jiangsu, China [C] DecomBio Biotechnology Co Ltd, Beijing, China [D] DeepBlue Medical Technology Co Ltd, Anhui, China [E] Innovita Biological Technology Co Ltd, Qian'an, China [F] Premier Biotech, Minneapolis, MN, USA (RightSign assay from Hangzhou Biotest, marketed by Premier Biotech under a different name) [G] Sure Biotech, New York, USA; Wan Chai, Hong Kong [H] UCP Biosciences, San Jose, CA, USA [I] VivaChek Biotech Co, Hangzhou, China [J] Wondfo Biotech Co Ltd, Guagzhou, China [K] Epitope Diagnostics, San Diego, USA Antibody: [A]‐[I] IgM and/or IgG [J] Total Ab [K] IgM, or IgG Antigen target: [A] RBD [B] N and S [C] Not stated [D] Not stated [E] N and S [F] Not stated [G] N and S [H] Not stated [I] Not stated [J] Not stated [K] N Evaluation setting: [A]‐[J] POCT, performed in lab [K] Laboratory Test method: [C] [F]‐[J] Lateral flow assays [D] [E] Colloidal gold [K] ELISA Timing of samples: 0‐ > 20 days pso 1‐5 days pso: n = 28 6‐10 days pso: n = 36 11‐15 days pso: n = 34 16‐20 days pso: n = 19 > 20 days pso: n = 11 Samples used: Plasma or serum Test operator: Laboratory staff Definition of test positivity: [A]‐[J] All visual‐based tests, each cartridge was assigned an integer score (0 for negative, 1–6 for positive) for test line intensity by two independent readers blinded to specimen status and to each other’s scores. [K] IgM positive cut‐off = 1.1 × ((average of negative control readings) + 0.10). Values less than or equal to the positive cut‐off were interpreted as negative; IgG positive cut‐off = 1.1 × ((average of negative control readings) + 0.18). Values less than or equal to the positive cut‐off were interpreted as negative. Blinding reported: [A]‐[J] two independent readers blinded to specimen status and to each other’s scores [K] Not stated Threshold predefined: [A]‐[L] Yes
Target condition and reference standard(s)	Reference standard: RT‐PCR, threshold not stated Samples used: Nasopharyngeal or oropharyngeal swabs Timing of reference standard: Not stated Blinded to index test: Yes, prior Incorporated index test: No Definition of non‐COVID cases: [2a] Pre‐pandemic [2b] RT‐PCR‐negative or none [2c] RT‐PCR‐negative Samples used: [2a] NA, pre‐pandemic [2b] Nasopharyngeal or oropharyngeal swabs or none [2c] Nasopharyngeal or oropharyngeal swabs Timing of reference standard: Not stated 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: Some specimens were exhausted during the analysis and were not included in all tests. One test result missing for test [E], IgM, 11‐15 days Uninterpretable results: Not stated Indeterminate results: Not stated. Unit of analysis: Samples but only 1 sample per patient per time‐split included. If an individual had more than one specimen for a given time interval, only the later specimen was included.
Comparative
Notes	Funding: This work was supported by gifts from Anthem Blue Cross Blue Shield, the Chan Zuckerberg Biohub and anonymous philanthropy. We thank the following sources for donation of test kits: the manufacturers of Bioperfectus, DecomBio, Sure Biotech, UCP Biosciences; D. Friedberg, J. Hering and H. Schein. The Wilson lab has received support from the Rachleff Family Foundation. The Hsu lab has received support from S. Altman, V. and N. Khosla, D. and S. Deb, the Curci Foundation and Emergent Ventures. The Marson lab has received gifts from J. Aronov, G. Hoskin, K. Jordan, B. Bakar, the Caufield family and funds from the Innovative Genomics Institute, the Northern California JDRF Center of Excellence and the Parker Institute for Cancer Immunotherapy. We thank the National Institutes of Health for its support (to J.D.W., R38HL143581; to A.E.G., F30AI150061; to D.N.N., L40 AI140341; to S.P.B., NHLBI R38HL143581, to G.M.G., NHLBI R38HL143581; to T.A.M., 1F30HD093116; to D.W., 1F31NS106868‐01; to J.G.C., R01 AI40098; to E.T.R. and R.C.C., CDC U01CK000490; MSTP students were supported by T32GM007618). R.Y. was supported by an AP Giannini Postdoctoral Fellowship. J.A.S. was supported by the Larry L. Hillblom Foundation (2019‐D‐006‐FEL). A.M. holds a Career Award for Medical Scientists from the Burroughs Wellcome Fund, is an investigator at the Chan Zuckerberg Biohub and is a recipient of the Cancer Research Institute Lloyd J. Old STAR grant. C.Y.C. is the director of the UCSF‐Abbott Viral Diagnostics and Discovery Center, receives research support funding from Abbott Laboratories and is on the scientific advisory board of Mammoth Biosciences. C.J.Y. is co‐founder of DropPrint Genomics and serves as an advisor to them. M.S.A. holds stock in Medtronic and Merck. P.D.H. is a co‐founder of Spotlight Therapeutics and serves on the board of directors and scientific advisory board and is an advisor to Serotiny. P.D.H. holds stock in Spotlight Therapeutics and Editas Medicine. A.M. is a co‐founder of Spotlight Therapeutics and Arsenal Biosciences and serves on their board of directors and scientific advisory board. A.M. has served as an advisor to Juno Therapeutics, was a member of the scientific advisory board at PACT Pharma and was an advisor to Trizell. A.M. owns stock in Arsenal Biosciences, Spotlight Therapeutics and PACT Pharma. R.Y. owns stock in AbbVie, Bluebird Bio, Bristol‐Myers Squibb, Cara Therapeutics, Editas Medicine, Esperion and Gilead Sciences. Unrelated to this current work, the Marson lab has received sponsored research support from Juno Therapeutics, Epinomics, Sanofi and GlaxoSmithKline and a gift from Gilead. Publication status: Published paper Source: Nature Biotechnology Author COI: C.Y.C. is the director of the UCSF‐Abbott Viral Diagnostics and Discovery Center, receives research support funding from Abbott Laboratories and is on the scientific advisory board of Mammoth Biosciences. C.J.Y. is co‐founder of DropPrint Genomics and serves as an advisor to them. M.S.A. holds stock in Medtronic and Merck. P.D.H. is a co‐founder of Spotlight Therapeutics and serves on the board of directors and scientific advisory board and is an advisor to Serotiny. P.D.H. holds stock in Spotlight Therapeutics and Editas Medicine. A.M. is a co‐founder of Spotlight Therapeutics and Arsenal Biosciences and serves on their board of directors and scientific advisory board. A.M. has served as an advisor to Juno Therapeutics, was a member of the scientific advisory board at PACT Pharma and was an advisor to Trizell. A.M. owns stock in Arsenal Biosciences, Spotlight Therapeutics and PACT Pharma. R.Y. owns stock in AbbVie, Bluebird Bio, Bristol‐Myers Squibb, Cara Therapeutics, Editas Medicine, Esperion and Gilead Sciences. Unrelated to this current work, the Marson lab has received sponsored research support from Juno Therapeutics, Epinomics, Sanofi and GlaxoSmithKline and a gift from Gilead.
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?	No
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?	No
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?		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?	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?	No
Were results presented per patient?	Yes
Could the patient flow have introduced bias?		High risk