Fig. 3

Analysis of major antigenic subdomains on the transmitted/founder HIV-1 envelope based on the positive yeast clones selected by the sequential plasma samples from P08 and P11. a, c Overlapping sequences of the positive yeast clones selected by the sequential plasma samples and aligned to the original full-length P08-gp160 and P11-gp160 sequence used in the construction of combinatorial yeast library. Vertical dashed lines highlight the V1V2, V3C3V4, and the ectodomain of gp41 in which the selected fragments are predominantly located. The four red horizontal lines from each subdomain represent the selected clones for studying avidity maturation of plasma antibodies during infection (see Fig. 5). b, d Quantitative measurement of antibody recognition against distinct subdomains on transmitted/founder HIV-1 envelope during natural infection. Each subdomain was identified based on the frequency of amino acid residues among the selected fragments and colored coded. The locations of the most frequently recognized residues within V1V2, V3C3V4 and ectodomain of gp41 are indicated in parentheses according to HXB2 and highlighted in red, blue, and green, respectively. The percentages represent the area under the curve (AUC) of each antigenic subdomain verse the total AUC (shaded area). The hypervarible regions V1–V5, interspersed conserved regions C1–C5 in gp120, immune dominant (ID), MPER and transmembrane domain (TM) in gp41 are also indicated