How to identify HIV variants in blood population or semen components - (Jun/04/2007 )

Hello can you please suggest me how to identify hiv variants in blood population or semen components is their any methods to identify different variants

RNA/DNA-extraction, (RT-)PCR, cloning and sequencing of different clones. Align them and check for mutations/insertions/deletions, make phylogenetic trees if you have enough clones/differences.

Or do "population based sequencing" if you just want to see if there is a major difference between the population in semen vs the population in blood. (RNA/DNA-extraction, amplification, sequencing of samples of blood and on samples of semen).