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Delafiori J, Navarro LC, Siciliano RF, de Melo GC, Busanello EN, Nicolau JC, Sales GM, de Oliveira AN, Val FFA, de Oliveira DN, Eguti A, dos Santos LA, Dalçóquio TF, Bertolin AJ, Abreu-Netto RL, Salsoso R, Baía-da-Silva D, Marcondes-Braga FG, Sampaio VS, Judice CC, Costa FT, Durán N, Perroud MW, Sabino EC, Lacerda MV, Reis LO, Fávaro WJ, Monteiro WM, Rocha AR, Catharino RR. Covid-19 Automated Diagnosis and Risk Assessment through Metabolomics and Machine Learning. Anal Chem 2021; 93:2471-2479. [PMID: 33471512 PMCID: PMC8023531 DOI: 10.1021/acs.analchem.0c04497] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 01/14/2021] [Indexed: 01/07/2023]
Abstract
COVID-19 is still placing a heavy health and financial burden worldwide. Impairment in patient screening and risk management plays a fundamental role on how governments and authorities are directing resources, planning reopening, as well as sanitary countermeasures, especially in regions where poverty is a major component in the equation. An efficient diagnostic method must be highly accurate, while having a cost-effective profile. We combined a machine learning-based algorithm with mass spectrometry to create an expeditious platform that discriminate COVID-19 in plasma samples within minutes, while also providing tools for risk assessment, to assist healthcare professionals in patient management and decision-making. A cross-sectional study enrolled 815 patients (442 COVID-19, 350 controls and 23 COVID-19 suspicious) from three Brazilian epicenters from April to July 2020. We were able to elect and identify 19 molecules related to the disease's pathophysiology and several discriminating features to patient's health-related outcomes. The method applied for COVID-19 diagnosis showed specificity >96% and sensitivity >83%, and specificity >80% and sensitivity >85% during risk assessment, both from blinded data. Our method introduced a new approach for COVID-19 screening, providing the indirect detection of infection through metabolites and contextualizing the findings with the disease's pathophysiology. The pairwise analysis of biomarkers brought robustness to the model developed using machine learning algorithms, transforming this screening approach in a tool with great potential for real-world application.
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Affiliation(s)
- Jeany Delafiori
- Innovare
Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Cidade Universitária
Zeferino Vaz, Campinas, São Paulo 350-13083-970, Brazil
| | - Luiz Cláudio Navarro
- RECOD
Laboratory, Computing Institute, University
of Campinas, Cidade Universitária Zeferino Vaz,, Campinas, São Paulo 573-13083-852, Brazil
| | - Rinaldo Focaccia Siciliano
- Clinical
Division of Infectious and Parasitic Diseases, University of São Paulo Medical School, São Paulo, São Paulo 01246-903, Brazil
- Instituto
do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, Cerqueira César, São Paulo 44-05403-90, Brazil
| | - Gisely Cardoso de Melo
- Tropical
Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas 69040-000,Brazil
- Amazonas
State University, Manaus, Amazonas 25-69040-000, Brazil
| | - Estela Natacha
Brandt Busanello
- Innovare
Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Cidade Universitária
Zeferino Vaz, Campinas, São Paulo 350-13083-970, Brazil
| | - José Carlos Nicolau
- Instituto
do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, Cerqueira César, São Paulo 44-05403-90, Brazil
| | - Geovana Manzan Sales
- Innovare
Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Cidade Universitária
Zeferino Vaz, Campinas, São Paulo 350-13083-970, Brazil
| | - Arthur Noin de Oliveira
- Innovare
Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Cidade Universitária
Zeferino Vaz, Campinas, São Paulo 350-13083-970, Brazil
| | - Fernando Fonseca Almeida Val
- Tropical
Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas 69040-000,Brazil
- Amazonas
State University, Manaus, Amazonas 25-69040-000, Brazil
| | - Diogo Noin de Oliveira
- Innovare
Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Cidade Universitária
Zeferino Vaz, Campinas, São Paulo 350-13083-970, Brazil
| | - Adriana Eguti
- Sumaré
State Hospital, Sumaré, São Paulo 2400-13175-490, Brazil
| | | | - Talia Falcão Dalçóquio
- Instituto
do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, Cerqueira César, São Paulo 44-05403-90, Brazil
| | - Adriadne Justi Bertolin
- Instituto
do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, Cerqueira César, São Paulo 44-05403-90, Brazil
| | - Rebeca Linhares Abreu-Netto
- Tropical
Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas 69040-000,Brazil
- Amazonas
State University, Manaus, Amazonas 25-69040-000, Brazil
| | - Rocio Salsoso
- Instituto
do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, Cerqueira César, São Paulo 44-05403-90, Brazil
| | - Djane Baía-da-Silva
- Tropical
Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas 69040-000,Brazil
- Amazonas
State University, Manaus, Amazonas 25-69040-000, Brazil
| | - Fabiana G Marcondes-Braga
- Instituto
do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, Cerqueira César, São Paulo 44-05403-90, Brazil
| | - Vanderson Souza Sampaio
- Tropical
Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas 69040-000,Brazil
- Health
Surveillance Foundation of Amazonas State, Manaus, Amazonas, 4010-69093-018 Brazil
| | - Carla Cristina Judice
- Laboratory
of Tropical Diseases, Institute of Biology, University of Campinas, Cidade Universitária Zeferino Vaz, Campinas, São Paulo 13083-970 Brazil
| | - Fabio Trindade
Maranhão Costa
- Laboratory
of Tropical Diseases, Institute of Biology, University of Campinas, Cidade Universitária Zeferino Vaz, Campinas, São Paulo 13083-970 Brazil
| | - Nelson Durán
- Laboratory
of Urogenital Carcinogenesis and Immunotherapy, University of Campinas, Cidade Universitária Zeferino Vaz, Campinas, São Paulo 13083-865, Brazil
| | | | - Ester Cerdeira Sabino
- Institute
of Tropical Medicine, University of São
Paulo, São Paulo, São Paulo 470-05403-000,Brazil
| | - Marcus Vinicius
Guimarães Lacerda
- Tropical
Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas 69040-000,Brazil
- Leônidas and Maria Deane Institute, Manaus, Amazonas, 476-69057-070 Brazil
| | - Leonardo Oliveira Reis
- UroScience
Laboratory, University of Campinas, Cidade
Universitária Zeferino Vaz, Campinas, São Paulo 126-13083-887, Brazil
| | - Wagner José Fávaro
- Laboratory
of Urogenital Carcinogenesis and Immunotherapy, University of Campinas, Cidade Universitária Zeferino Vaz, Campinas, São Paulo 13083-865, Brazil
| | - Wuelton Marcelo Monteiro
- Tropical
Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas 69040-000,Brazil
- Amazonas
State University, Manaus, Amazonas 25-69040-000, Brazil
| | - Anderson Rezende Rocha
- RECOD
Laboratory, Computing Institute, University
of Campinas, Cidade Universitária Zeferino Vaz,, Campinas, São Paulo 573-13083-852, Brazil
| | - Rodrigo Ramos Catharino
- Innovare
Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Cidade Universitária
Zeferino Vaz, Campinas, São Paulo 350-13083-970, Brazil
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