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Nasopharyngeal Proteomic Profiles from Patients Hospitalized Due to COVID-19 in Manaus, Amazonas, Brazil
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Cláudia P. M. Araújo, Carolina M. Vieira, Ketlen C. Ohse, Alessandra S. Silva, Sofia A. Cavalcante, Felipe G. Naveca, Fernanda N. Oliveira, James L. Crainey, Marcus V. G. Lacerda, Gisely C. Melo, Vanderson S. Sampaio, Michel Batista, Amanda C. Camillo-Andrade, Marlon D. M. Santos, Diogo B. Lima, Juliana de S. G. Fischer, Paulo C. Carvalho and Priscila F. Aquino
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Abstract
This study investigated proteomic differences in nasopharyngeal swabs of SARS-CoV-2-infected patients from Manaus (Brazil) who were hospitalized during the devastating first wave of the COVID-19 pandemic, before the emergence of the deadly P1 SARS-CoV-2 strain. LC-MS/MS proteomic analysis compared 16 matched COVID-19 patient
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This study investigated proteomic differences in nasopharyngeal swabs of SARS-CoV-2-infected patients from Manaus (Brazil) who were hospitalized during the devastating first wave of the COVID-19 pandemic, before the emergence of the deadly P1 SARS-CoV-2 strain. LC-MS/MS proteomic analysis compared 16 matched COVID-19 patient profiles: eight survivors and eight fatalities. A total of 1604 proteins were identified in fatality swabs, and 981 in the swabs of survivors. Our study provides new insights into the cellular mechanisms underlying first-wave COVID-19 deaths from Manaus and identifies hypoxia-related HYOU1, endothelial injury-associated S100A10, and some viral replication proteins (DDX1/17, XPO1) as potential biomarkers of fatal infections. The proteomic profiles of the swabs taken from patients that died collectively suggest that many of the first wave COVID-19 fatalities in Manaus suffered immune-system collapse. Survivor patient swabs showed elevated levels of immune defense proteins (FN1, C4BPA, IGKV1-5), indicating effective antiviral responses. Gene ontology analysis revealed dysregulated secretory pathways in fatalities and did not detect the defense-response pathways in fatality-group datasets that were observed in survivor protein datasets. Interestingly, the NOS2 protein, previously associated with first-wave fatalities, was found exclusively in our fatality swabs.
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