I am working with sars-cov-2, and we would like to quantify the viral load in clinical specimens (oropharyngeal swab, nasopharyngeal swab, saliva and blood) through absolute qPCR, using viral RNA as reference (obtained from in vitro transcription).

I was advised that the viral load is related to the number of viral particles that are in transit, ie. they are not associated to cells. Therefore, we are going to separate cells from supernatant through centrifugation of each clinical sample (oropharyngeal swab, nasopharyngeal swab, saliva and blood), before the RNA extraction. We are interested in the RNA obtained from the supernatant.

I was not able to find protocols/papers that perform this separation (only for blood).

I am very skeptic that the cellularity of oropharyngeal swab, nasopharyngeal swab and saliva is going to affect the quantification of free-moving viral particles. Is this procedure really necessary? What is your experience about it?

Thank you in advance.