Im curious your reasoning why not. PCR is a way to amplify specific nucleic acid sequences and is used as one of the primary means to detect bacteria and viruses (as you can detect sequences specific to those pathogens) in all types of samples including and especially clinical samples. It's also how, for example, municipalities test how much dangerous bacteria is in your water. COVID tests are a little more complicated because its an RNA virus so you first need to turn it into DNA (the Reverse Transcription step), but same concept.