Abstract
Fourier transform infrared (FTIR) spectroscopy provides a (bio)chemical snapshot of the sample, and was recently used in proof-of-concept cohort studies for COVID-19 saliva screening. However, the biological basis of the proposed technology has not been established. To investigate underlying pathophysiology, we conducted controlled infection experiments on Vero E6 cells in vitro and K18-hACE2 mice in vivo. Potentially infectious culture supernatant or mouse oral lavage samples were treated with ethanol or 75% (v/v) Trizol for attenuated total reflectance (ATR)-FTIR spectroscopy and proteomics, or RT-PCR, respectively. Controlled infection with UV-inactivated SARS-CoV-2 elicited strong biochemical changes in culture supernatant/oral lavage despite a lack of viral replication, determined by RT-PCR or a cell culture infectious dose 50% assay. Nevertheless, SARS-CoV-2 infection induced additional FTIR signals over UV-inactivated SARS-CoV-2 infection in both cell and mouse models, which correspond to aggregated proteins and RNA. Proteomics of mouse oral lavage revealed increased secretion of kallikreins and immune modulatory proteins. Next, we collected saliva from a cohort of human participants (n = 104) and developed a predictive model for COVID-19 using partial least squares discriminant analysis. While high sensitivity of 93.48% was achieved through leave-one-out cross-validation, COVID-19 patients testing negative on follow-up on the day of saliva sampling using RT-PCR was poorly predicted in this model. Importantly, COVID-19 vaccination did not lead to the misclassification of COVID-19 negatives. Finally, meta-analysis revealed that SARS-CoV-2 induced increases in the amide II band in all arms of this study and in recently published cohort studies, indicative of altered β-sheet structures in secreted proteins. In conclusion, this study reveals a consistent secretory pathophysiological response to SARS-CoV-2, as well as a simple, robust method for COVID-19 saliva screening using ATR-FTIR.
Highlights
Following the initial alarm of a cluster of atypical viral pneumonia in the city of Wuhan, China, on 31 December 2019, severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) rapidly spread around the world, leading the World Health Organization to declare coronavirus disease 2019 (COVID-19) a public health emergency of international concern (PHEIC) on 30 January 2020, and a global pandemic on 11 March 2020 [1,2]
For biosafe attenuated total reflectance (ATR)-Fourier transform infrared (FTIR) spectroscopy, we recently reported a decontamination procedure with the addition of 100% ethanol to plasma to obtain 75% final (v/v), and used this method in developing ATR-FTIR for predicting COVID-19 severity using plasma samples [12]
A media control and an ultraviolet light (UV)-inactivated SARS-CoV-2, the latter of which could not replicate as UV destroys RNA
Summary
(SARS-CoV-2) rapidly spread around the world, leading the World Health Organization to declare coronavirus disease 2019 (COVID-19) a public health emergency of international concern (PHEIC) on 30 January 2020, and a global pandemic on 11 March 2020 [1,2]. While the current gold standard, reverse transcriptase quantitative polymerase chain reaction (RT-qPCR), is highly sensitive in detecting SARS-CoV-2 RNA, the technical requirements, time-to-result, and the accumulated testing costs are prohibitive in developing countries and disadvantaged communities. Equipment-free rapid antigen tests with immobilized anti-SARS-CoV-2 antibodies in lateral flow devices are widely used in some countries. These tests can be performed at home with self-collected samples and generate results in 5–20 min, with the caveats of potential sampling errors and unknown reactivity to new variants. With the global research community actively investigating the use of novel nanomaterials and chemistries for rapid antigen tests, sensitivities and ease of use will likely improve in the near future
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