Depends if it is a DNA or RNA virus. If it is an RNA virus you will need to make cDNA from the RNA before you can do PCR amplification. Your reverse transcription protocol might not be compatible with your method for removing the viral coat which would prevent a one-pot approach.

Hello,

For me the real question is that having an RNA that is not pure does not influence reverse transcription and the efficiency of reverse transcriptase to synthesize cDNA.

We can do potentially if it is a DNA, for example we can directly amplify the DNA on bacterial colonies without isolating it but in this case it is a DNA and not the RNA and it is the taq polymerase which carries out the synthesis of the new molecule and not reverse transcriptase.