Covid-19 Automated Diagnosis and Risk Assessment through Metabolomics and Machine Learning.

Journal: Analytical chemistry
Published Date: Jan 20, 2021

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.

Authors

  • 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.
  • Gisely Cardoso de Melo
    Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas 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.
  • 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.
  • Luiz Augusto Dos Santos
    Paulínia Municipal Hospital, Paulínia, São Paulo 100-13140-000, 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.
  • 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.
  • 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.
  • 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.
  • Mauricio Wesley Perroud
    Sumaré State Hospital, Sumaré, São Paulo 2400-13175-490, 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.
  • 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.
  • 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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