Ultrarapid On-Site Detection of SARS-CoV-2 Infection Using Simple ATR-FTIR Spectroscopy and an Analysis Algorithm: High Sensitivity and Specificity

Abstract

There is an urgent need for ultrarapid testing regimens to detect the severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2] infections in real-time within seconds to stop its spread. Current testing approaches for this RNA virus focus primarily on diagnosis by RT-qPCR, which is time-consuming, costly, often inaccurate, and impractical for general population rollout due to the need for laboratory processing. The latency until the test result arrives with the patient has led to further virus spread. Furthermore, latest antigen rapid tests still require 15–30 min processing time and are challenging to handle. Despite increased polymerase chain reaction (PCR)-test and antigen-test efforts, the pandemic continues to evolve worldwide. Herein, we developed a superfast, reagent-free, and nondestructive approach of attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy with subsequent chemometric analysis toward the prescreening of virus-infected samples. Contrived saliva samples spiked with inactivated γ-irradiated COVID-19 virus particles at levels down to 1582 copies/mL generated infrared (IR) spectra with a good signal-to-noise ratio. Predominant virus spectral peaks are tentatively associated with nucleic acid bands, including RNA. At low copy numbers, the presence of a virus particle was found to be capable of modifying the IR spectral signature of saliva, again with discriminating wavenumbers primarily associated with RNA. Discrimination was also achievable following ATR-FTIR spectral analysis of swabs immersed in saliva variously spiked with virus. Next, we nested our test system in a clinical setting wherein participants were recruited to provide demographic details, symptoms, parallel RT-qPCR testing, and the acquisition of pharyngeal swabs for ATR-FTIR spectral analysis. Initial categorization of swab samples into negative versus positive COVID-19 infection was based on symptoms and PCR results ( n = 111 negatives and 70 positives). Following training and validation (using n = 61 negatives and 20 positives) of a genetic algorithm-linear discriminant analysis (GA-LDA) algorithm, a blind sensitivity of 95% and specificity of 89% was achieved. This prompt approach generates results within 2 min and is applicable in areas with increased people traffic that require sudden test results such as airports, events, or gate controls.

Rapid Classification of COVID-19 Severity by ATR-FTIR Spectroscopy of Plasma Samples

“…The region 1020–1090 cm –1 had VIP scores between 1.85 and 2.05 and may correspond to saccharide C–O stretching 16 , 17 and phosphate (PO 2 – ). 9 The second highest FTIR spectral VIP region 1588–1592 cm –1 with a VIP score of 1.72 has been described as a primary amine peak (N–H bending). 18 These speculative biological assignments remain to be confirmed experimentally.…”

“…To minimize interference from solvent peaks, we acquired spectra after solvents were evaporated from the ATR-FTIR crystal, choosing 75% ethanol as a rapid and practical inactivation and sample preparation. The use of solvent facilitates sample drying on the ATR-FTIR crystal, with the 1 μL sample generally dry within 30 s, compared to the 3–5 min reported by Zhang et al 8 Zhang and colleagues used heating at 65 °C for 30 min to inactivate samples; the inactivation step was not reported by Barauna et al 9 …”

“…Two recent studies reported the potential of ATR-FTIR as a rapid screening test for COVID-19 using plasma 8 or nasopharyngeal swab. 9 Given the reported blood biochemistry changes in severe COVID-19 disease, 6 , 7 we hypothesized that ATR-FTIR spectra of plasma samples would differentiate between severe and non-severe disease. Herein, we developed a predictive algorithm for COVID-19 disease stratification into severe and non-severe COVID-19 using ATR-FTIR spectra, in addition to clinical variables that are available to the physician at the point of admission.…”

Plasmonic Biosensor Augmented by a Genetic Algorithm for Ultra-Rapid, Label-Free, and Multi-Functional Detection of COVID-19

“…Figure 2 b shows the infrared spectrum of COVID-19 virus particles. 11 Among them, the infrared absorption peaks A–E are selected as the typical fingerprint vibration peaks of COVID-19. The fingerprint vibration peaks of the new coronavirus and their respective tentative assignments are shown in Table S3 .…”

“… 9 , 10 Through analysis of the epidemiological characteristics of infected persons and intelligent isolation of risk areas, the impact of the epidemic on the national economy can be minimized and more resources can be allocated to combat the disease more strategically. 11 Therefore, extensive, timely, and accurate identification of new viruses is essential to contain the spread of COVID-19 and control the emerging pandemic.…”