V3 loop sequence (A), coreceptor usage (B) and distribution (C) of viruses in macaques infected with R5 SHIV
molecular clones. (A) V3 loop sequence comparison of the inoculating clonal virus and representative lymph node viruses in macaques EN31 (clone 11; colonic), FF94 (clone 8; mesenteric) and FD83 (clone 8; colonic) at time of necropsy. Dashes stand for identity in sequences, and the net positive charge of this region is shown on the right. Positions 11 and 25 within the V3 loop are indicated by triangles, with brackets highlighting the presence of positively charged amino acids at these positions. The numbers in parentheses represent the numbers of clones matching the indicated sequence per total number of clones sequenced. (B) Infection of U87.CD4.CCR5 and U87.CD4.CXCR4 indicator cells with pseudovirions bearing S11R, D25K or WT V3 sequences. RLU, relative light units. Data are the means and standard deviations from triplicate wells and are representative of at least two independent experiments. (C) Distribution of viruses in Inguinal LN, PBMC and plasma of FF94 over time as determined by clonal sequence analysis. Numbers in parentheses indicate number of gp120 clones sequenced at each time point.