FIG. 4.

Phylogenetic analysis of V1/V2 clones. RT-PCR products from separate reactions independently cloned after gel purification. Variant clones were identified by HTA screening. Where possible, at least two independent clones of each variant were sequenced. For two subjects, Z06 and Z24, the single variant was independently cloned and sequenced 6 to 10 times from each RT-PCR product. The neighbor-joining tree was made with aligned sequences with gaps ignored. All sequences are from the blood. Identifiers indicate subject (e.g., Z10), clone (e.g., g3), and HTA band (e.g., 0.1, 0.2, etc.), respectively. For subjects Z06 and Z24, which each had a single variant, the HTA band number is indicated as “0.” For these two subjects, the number of clones with identical sequences is shown in parentheses.