Pharyngeal cotton swabs (FirstLab, Brazil) were from individuals who came to one of the six hospitals participating in the study and met the criteria for suspected cases according to the State Health Secretary and World Health Organization (WHO) guidelines between June and September 2020. For all participants, demographic data (age, gender, pre-existing medical conditions, symptoms, and date of symptoms’ onset) were collected (see the Supporting Information). Exclusion criteria from this study were those with inconclusive RT-qPCR results after two rounds of RT-qPCR.

For the gold-standard protocol via diagnosis by RT-qPCR, a nasopharyngeal swab was collected from participants by inserting a rayon swab with a plastic shaft into the nostril parallel to the palate. The swab was inserted to a location equidistant from the nostril and the outer opening of the ear and was gently scraped for a few seconds to absorb secretions. The swab was then placed immediately into a sterile tube containing a viral transport medium. RT-qPCR was performed in the Central Laboratory from the Health Secretary of Espírito Santo (LACEN-SESA) to allow definitive diagnosis of COVID-19 infection.

For ATR-FTIR spectroscopy, a pharyngeal swab was collected from participants by inserting a cotton swab into the mouth and scrapping the tonsils, the tongue, and the inner part of the cheek. The swab was then placed immediately into a sterile tube and stored on ice until analysis.

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