Direct sequencing versus cloned amplicon sequencing in HIV-1 diagnosis

HIV-1-specific sequences could easily be amplified from the DNA of peripheral blood lymphocytes or from the viral RNA present in the plasma. A detailed characterization of the resulting amplicons requires sequencing. Here we have shown that the sequencing strategy depends on the variability of the region of interest. The higher the variability of a distinct region the more a cloning step is necessary prior to sequencing to obtain reliable information. Conversely, direct sequencing analysis is usually sufficient to record changes of conserved viral sequences, e.g. during therapy with reverse transcriptase inhibitors.