Are there complete viruses with protein coat or only pieces of genes in the coronavirus research in sewage?

The technique (RT-PCR) measures RNA fragments (genes from SARS-CoV-2 virus). Finding intact RNA fragments indicates indirectly the possible presence of the virus. This is the same technique as used by hospitals to establish COVID-19 infection. Particularly in sewage water it is highly unlikely that unprotected viruses (pieces of RNA without protein coat) would be found. In the biologically active environment of sewage, the fragments of virus-RNA would rapidly become degraded. The RNA is stable for some days when it is protected by the protein coat, meaning that it is present as whole virus particle.