Figure 2

Highlighter analyses of HIV sequences from infant plasma and maternal breast milk. (A) Multiple 5’-half and 3’-half genome sequences derived from infant plasma at the time of HIV diagnosis are aligned below the infant consensus sequence (Con). Nucleotide differences from the inferred T/F consensus sequence are indicated by tic marks color-coded for each base. IUPAC denotes International Union of Pure and Applied Chemistry ambiguous base assignments caused by Taq polymerase-induced nucleotide misincorporation occurring in the first two cycles of the PCR amplification. Flanking gray boxes indicate regions not amplified. Gray tics indicate deletions. The arrow indicates the location of the K103N mutation in the RT gene in consensus and all SGA sequences (AAA to AAC mutation). The horizontal axis indicates nucleotide positions based on HXB2 reference sequence numbering. Consensus sequence begins at nucleotide position 484 in the 5’ long terminal repeat (LTR) U5 and extend to position 9,606 in the 3’ LTR R. (B) Two 9 Kb amplicons, and multiple pol and rev/env fragments representing low-diversity breast milk sequences collected at four weeks postpartum (shown at the left of the blue bars in Figure 1) are aligned below the consensus sequence (identical to Con from Figure 1A). The arrow represents the location of the K103N mutation. Clustered mutations enclosed in elipses reflect recombination with more divergent maternal sequences. The horizontal axis indicates HXB2 nucleotide positions. Sequences begin at nucleotide position 582 in the 5’ LTR U5 and extend to position 9,606 in the 3’ LTR R. Boxes corresponding to LTRs and 9 major protein coding regions of the HIV genome are shown at the bottom.