I want to use ELISA to detect inactivated SARS-CoV-2 propagated in Vero cells using aptamers, what solution will you recommend for me to use after centrifugation of the sample, is it the supernatant liquid or the pellets.
I'd use the supernatant. The pellet is insoluble/denatured material. If you are able to solubilize it without adding detergents (which will saturate your ELISA plate before much protein can bind to them), you can check both.
In addition, for quantification, you might be better off with a sandwich system, using two antibodies, one for analyte capture and one for analyte detection. Direct coating of the plate with the analyte IMHO is ok for qualitative testing, but not for quantification, as the surface of the plate is not really homogenous, and you'll usually observe a wide variation when replicating samples at saturating conditions..