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Kazmer ST, Hartel G, Robinson H, Richards RS, Yan K, van Hal SJ, Chan R, Hind A, Bradley D, Zieschang F, Rawle DJ, Le TT, Reid DW, Suhrbier A, Hill MM. Pathophysiological Response to SARS-CoV-2 Infection Detected by Infrared Spectroscopy Enables Rapid and Robust Saliva Screening for COVID-19. Biomedicines 2022; 10:biomedicines10020351. [PMID: 35203562 PMCID: PMC8962262 DOI: 10.3390/biomedicines10020351] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/10/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
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.
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Affiliation(s)
- Seth T. Kazmer
- Precision & Systems Biomedicine Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (S.T.K.); (H.R.); (R.S.R.)
| | - Gunter Hartel
- Biostatistics Unit, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia;
| | - Harley Robinson
- Precision & Systems Biomedicine Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (S.T.K.); (H.R.); (R.S.R.)
| | - Renee S. Richards
- Precision & Systems Biomedicine Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (S.T.K.); (H.R.); (R.S.R.)
| | - Kexin Yan
- Inflammation Biology Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (K.Y.); (D.J.R.); (T.T.L.); (A.S.)
| | - Sebastiaan J. van Hal
- New South Wales Health Pathology-Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; (S.J.v.H.); (R.C.)
| | - Raymond Chan
- New South Wales Health Pathology-Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; (S.J.v.H.); (R.C.)
| | - Andrew Hind
- Agilent Technologies Australia, Mulgrave, VIC 3170, Australia; (A.H.); (D.B.); (F.Z.)
| | - David Bradley
- Agilent Technologies Australia, Mulgrave, VIC 3170, Australia; (A.H.); (D.B.); (F.Z.)
| | - Fabian Zieschang
- Agilent Technologies Australia, Mulgrave, VIC 3170, Australia; (A.H.); (D.B.); (F.Z.)
| | - Daniel J. Rawle
- Inflammation Biology Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (K.Y.); (D.J.R.); (T.T.L.); (A.S.)
| | - Thuy T. Le
- Inflammation Biology Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (K.Y.); (D.J.R.); (T.T.L.); (A.S.)
| | - David W. Reid
- Lung Inflammation & Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia;
- The Prince Charles Hospital, Chermside, QLD 4032, Australia
| | - Andreas Suhrbier
- Inflammation Biology Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (K.Y.); (D.J.R.); (T.T.L.); (A.S.)
- Australian Infectious Disease Research Centre, GVN Centre of Excellence, Brisbane, QLD 4029, Australia
| | - Michelle M. Hill
- Precision & Systems Biomedicine Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (S.T.K.); (H.R.); (R.S.R.)
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD 4006, Australia
- Correspondence:
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