Depends from your sample, biopsy tissue, cell culture, supernatant, plasma, serum. In patients normally we take peripherical blood and we find positive strain (remember that virus is outside the cell) when we have biopsy liver tissue we can find both postive and negative strain (virus is inside cells and we have replication and translation processes).
But dont worry, there are primers described for each one. i have found some papers if you want it i will give you some!!