HIV-1 variant decay.

aBased on the region of env (V1/V2 or V4/V5) that was the most reproducible by two independent HTA replicates.bReported half-lives are the average calculated from decay analyses of two independent HTA replicates. N/A = not applicable.cPercent difference values between plasma and CSF viral populations as measured by HTA. Reported values are the average calculated from two independent HTA replicates (see refs. [39],[41] for methods).dTotal CSF viral load increased initially for subject 5002.eTotal plasma viral decay for subject 5003 was calculated for the drop in viral load from days 3 to 6 on HAART. There was a slight increase in plasma viral load from days 6 to 10 on HAART, which can be seen in Figure 2B, but this increase does not seem to be significant. Although the baseline samples were not available for analysis, we know that the baseline plasma viral load was 126,000 copies/ml, and this subject had undetectable viral loads in both plasma and CSF by 2 months post-HAART, so there was an overall good response to antiretroviral therapy. The small variation in plasma viral load from days 6 to 10 on therapy could be explained by a number of technical, pharmacological, and/or biological factors.fA compartmentalized variant was detected for subject 4021 in the day 5 CSF sample; however, the relative abundance of this variant was less than other bands detected that were not reproducible by HTA, indicating that the detection of this band may be due to inefficient sampling and low viral load. It is equally possible that this band represents a reproducible compartmentalized variant that is decaying more slowly than the other variants detected by HTA. Therefore, the half-life for the CSF-compartmentalized variants is listed as >1.59 days (a half-life of 1.59 days was measured for CSF shared variants).

a. 本分析选取两组独立异源双链追踪分析（HTA）重复实验中重复性最优的包膜基因（env）区域（V1/V2或V4/V5）开展。b. 报告的半衰期为两组独立HTA重复实验衰变分析的平均值，N/A表示不适用。c. 血浆与脑脊液病毒群体间的百分比差值通过HTA测定，报告值为两组独立HTA重复实验的计算平均值，具体方法参见文献[39]、[41]。d. 受试者5002的脑脊液总病毒载量初始阶段呈上升趋势。e. 受试者5003的血浆总病毒衰变情况基于高效抗逆转录病毒治疗（HAART）第3日至第6日的病毒载量降幅计算得出。尽管HAART治疗第6日至第10日期间，其血浆病毒载量略有上升（详见图2B），但该上升趋势并不显著。虽未获取基线样本用于分析，但已知该受试者的基线血浆病毒载量为126000拷贝/毫升，且在HAART治疗2个月后，其血浆与脑脊液中的病毒载量均已无法检出，整体对抗逆转录病毒治疗应答良好。治疗期间第6日至第10日的血浆病毒载量小幅波动，可由多种技术、药理学及/或生物学因素解释。f. 受试者4021在第5日的脑脊液样本中检测到区室化变异株；但该变异株的相对丰度低于其他无法通过HTA重复检出的条带，提示该条带的检出可能源于采样不充分及病毒载量较低。同样存在另一种可能性：该条带代表的是一种可重复的区室化变异株，其衰变速度慢于HTA检测到的其他变异株。因此，脑脊液区室化变异株的半衰期被记为>1.59天（脑脊液共享变异株的半衰期测定值为1.59天）。