At the same time, 6 variants containing K103N or K103N were detected, which formed 4 subpopulations. Subpopulation 5 comprised table 1 3 virus sequences while the other 3 each had only one sequence. In all samples ana lyzed from each of the infected monkeys, we consistently found one or two dominant subpopulations, along with many minor subpopulations. Subpopulation dynamics in monkey M03250 Figure 3 shows the fates of selected RT SHIV subpopula tions in M03250, expressed as percentages of the whole viral population at each sampling week and Figure 4 shows the same subpopulations as viral RNA copiesml plasma. As shown in Figures 3 and 4, the dominant sub population found in the original virus challenge stock was also the dominant subpopulation in the first plasma sample collected from M03250.
This variant, however, was not found by week 13 as new subpopulations emerged. It was replaced by two new wild type dominant subpopula tions emerging at week 13 Inhibitors,Modulators,Libraries prior to EFV treatment. The frequency of Inhibitors,Modulators,Libraries sub2 declined significantly between weeks 13 and 17, and the two remained relatively constant throughout a 5 weeks period on combination therapy and a 3 log decline in viremia, even though neither subpopulation carried any known drug resistant mutation. They subsequently became minor species at weeks 23 and 24. During the course of Inhibitors,Modulators,Libraries infection and treatment, many sub populations carrying drug resistant mutations emerged. However, none became dominant before the emergence and expansion of the double mutant K103NM184I, beginning at week 23 and coincident with the onset of virologic failure.
EFV resistance mutations initially were observed at week 17, the first sam ple after EFV monotherapy an AAC allele and an AAT allele. Inhibitors,Modulators,Libraries The AAC subpopulation remained minor until week 22, after which time it became undetectable. The AAT subpopula tion was detected at week 17 and never became dominant. The same was true at weeks 22 and 23 for a variant carry ing two drug resistance mutations K65RK103N, encoding resistance to TNF as well as EFV. Overall, at week 23, 6 weeks after the initiation of ART, 11 out of 23 subpopulations contained K103N and 4 out of 23 subpopulations contained K65R. Subpopulations with a single K103N mutation were 30% of all viral populations of week 23 and none was the dominant subpopulation.
In the neighbor joining tree, Inhibitors,Modulators,Libraries subpopulations contain ing K103N K65R or K103N M184I and sev eral others containing K103N formed a cluster. Several subpopulations containing K103N and K103N formed another cluster. In total, 5 of 9 subpopulations contained K103N inhibitor CHIR99021 at week 24, all existing as minor subpopulations. The subpopulations containing only K103N were 2. 7% of the population at this week, declining from 30. 1% at week 23, a result of the takeover by the doubly resistant sub population 8.