TITLE: Copy of COVID 19 testing using ATR spectrometer and AI.
AUTHORS: Driss LAHLOU KITANE, Salma LOUKMAN, Nabila Marchoudi, Nawfel Azami

[STEPS]
?. [Sample collection and RNA extraction]
Sample collection A sample of saliva swab or Naso-pharyngeal swab is collected using only swab with a synthetic tip. Swab is immediately inserted into sterile tubes containing 1ml of viral transport mediathe VTM used is the VTM-N of Citoswab
[Saliva Swab or NP Swab]
?. [Sample collection and RNA extraction]
RNA extraction and Spectrometer preparationwe use extraction Genrui extraction kits and machine.Take out a 96-well plate, wait for its temperature to equilibrate to room temperature, flick the liquid to concentrate on the bottom of the tube, tear the aluminum foil for use. Add 25μL of the binding solution (well and mix before use) to wells 1 and 7 of the 96-well plate, and then add 125μL of sample in sequence, and mix by suction and returning until the magnetic beads are cloudyPlace the 96-well plate on the reagent disk of the nucleic acid extraction instrument, install the magnetic rod cover (special for the instrument), and close the front cover;Select the corresponding item parameters and click RunAfter the operation is completed, remove the 96-well plate from the instrument, and the liquid in wells 6 and 12 can be directly used for detection or transferred to an EP tube without DNA/RN enzyme at -80℃for storage, discard the magnetic rod cover, place the instrument, close the front cover, open and disinfect A nanodrop can be used to verify if the RNA was extracted properly.
?. [Sample collection and RNA extraction]
Validation using 40 clinical reference samples, which are 20 known positive RNA extract and 20 negative extractfor the 40 clinical samples proceed as below: run Steps 3.1 and 3.2if the result is concordant with the clinical sample type continue to the next sample, elsepush the "rebuild model" button by adding the precedent spectrum and continue to the next sample. After validation step, and if concordance is less then 90% go to step 6 and redo calibration else redo background with distilled water for next spectrometer use.
?. [Genetic extract spectra measurement and classification ]
18 °C
?. [Genetic extract spectra measurement and classification ]
with a micro pipette take   ,on the ATR spectrometer using covid-model parameters and a background taken of distilled water, put the drop on the cleaned crystal  , use the pressure of 700kg/cm^2, lock the crystal cover and launch the spectra measurement
[ of the RNA homogenized extract]
?. [Genetic extract spectra measurement and classification ]
Save the measurement file,   export the file to a CSV format and launch the machine learning sub routine for sample classification, push the classification button and save the results
?. [Genetic extract spectra measurement and classification ]
clean the spectrometer surfaces with an Hydro-Alcoholic solution and Optical lens paper for the next use.
?. [Genetic extract spectra measurement and classification ]
Extract conservationfor the conservation of the remaining extract we place it under
-80 °C
?. [Genetic extract spectra measurement and classification ]
If any change in the experiments conditions( ATR spectrometer, HW transport, the VTM matrix, the RNA extraction kit) a new model calibration is needed based on the new reference data. Reference data is a set of at least 160 spectra collected from known representative clinical samples(80 positives with differents CTs and 80 negatives), and taken in the same new conditions.Positive and negative spectra should be saved in their corresponding folders, before rebuilding the model. HW calibration of the spectrometer should be verified according to the NIST(National Institute of Standards and Technology) standards.