*Of course step 1 is not needed if you already have the genome fasta file. In such case, make sure you download a GTF file that corresponds to the genome fasta. Otherwise, make sure the listed files in step 1 and 2 belong to your HIV subtype.
You will need to also obtain a transcript annotation file - typically a GTF or a GFF file. From that GTF file and your genome fasta file you can extract the transcript nucleotide sequence as a fasta file using tools such as gffread a tool which incidentially is also included in both the Cufflinks and Stringtie binary releases so it is typically easier to download those binaries and access the program though there.