Figure 4 | Scientific Reports

Figure 4

From: The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards

Figure 4

The intersequence Hamming distance (HD) distribution (grey bars) of HIV-1 full envelope gene sequences obtained from each subject in the slow (CAP45, CH162, and CH185) and fast GSI dynamics groups (CH042, CH159, CH256, and 703010200) along with the best fit (red curve) of the Shifted Poisson Mixture Model (SPMM)22. The SPMM estimated a single founder variant for all subjects except subject 703010200, whose infection was estimated to originate from six founders (when two putative recombinant strains from subject 703010200 were excluded, the number of founders was estimated to be 4. Here the minimum distance between founder variants was set as 10). The infection duration estimated by SPMM for subject CAP45, CH162, CH185 in the slow group was 24.1 [12.2–35.9] (goodness of fit p < 0.0001), 11.0 [3.4–18.6] (p = 0.07) and 21.4 [13.9–28.8] (p = 0.49) days and for subject CH042, CH159, CH256, and 703010200 in the fast group was 35.7 [19.2–52.2] (p = 0.90), 22.8 [14.4–31.1] (p = 0.002), 21.0 [8.9–33.1] (p = 0.66) and 28.4 [22.2–34.5] (p < 0.0001) days, respectively. The SPMM fits’ sum of squared errors (SSE) and Akaike information criteria (AIC) were 0.33 (291.0), 0.024 (152.9), 0.0017 (966.7), 0.0078 (118.7), 0.022 (761.0), 0.011 (119.2), and 0.0055 (4098.1) for subject CAP45, CH162, CH185, CH042, CH159, CH256 and 703010200, respectively.

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