Figure 2

Analysis of the patients’ human immunodeficiency virus-1 sequences . A highly-conserved 255 base pair region of the human immunodeficiency virus-1 gag gene was sequenced. (A) Shown are the nucleotide sequences obtained from FF and MM, as compared with the consensus human immunodeficiency virus-1 clade C sequence. Standard ambiguity codes are used (R = G or A; Y = T or C). (B) The human immunodeficiency virus-1 gag sequences from MM and FF, along with 27 human immunodeficiency virus-1 clade C sequences from South Africa, were aligned and then analyzed with the PhyML tool [8]. Shown is a phylogenetic tree made with the maximum likelihood method. The human immunodeficiency virus-1 clade B HXB2 gag sequence is included as an outgroup. GenBank accession numbers are given for the comparison sequences. (C) The human immunodeficiency virus-1 gag sequence from MM was compared with other human immunodeficiency virus-1 clade C viruses published in the Los Alamos human immunodeficiency virus-1 database using the QuickAlign tool [8]. Shown is a frequency histogram of the published clade C sequences based on the number of nucleotides that differ from the MM human immunodeficiency virus-1 gag sequence.