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. Author manuscript; available in PMC: 2018 Feb 1.
Published in final edited form as: J Virol Methods. 2016 Nov 16;240:32–41. doi: 10.1016/j.jviromet.2016.11.004

Figure 1. Location of universal forward primers for Vpu amplification.

Figure 1

Alignment of HIV-1 group M reference sequences (www.hiv.lanl.gov) spanning HIV-1 genomic nucleotides 5970-6095 (HIV-1 HXB2 genomic reference numbering convention) illustrates the extensive genetic diversity within and upstream of Vpu's initial 5' transmembrane domain. NL4.3 is used as the alignment reference; others are identified by their subtype and Genbank Accession number. At each position in the alignment, “.” indicates an identical base to the reference, letters identify bases that differ from it, and “-” indicates a deleted base. The sequences of universal forward primers located 90 and 38 bases upstream of Vpu, and a forward primer matching the first 25 bases of NL43 Vpu (“0”) are indicated above the alignment. Universal primer sequences contain degenerate bases designated by IUPAC ambiguity codes. Locations of the HIV-1 Rev and Vpu start codons are also shown.