Background: The HIVNET 012 trial in Uganda demonstrated that single-dose nevirapine (NVP) prophylaxis can prevent HIV-1 mother-to-child transmission. NVP resistance (NVPR) mutations were detected in 21 (19%) of 111 women in HIVNET 012 6–8 weeks (wks) after single-dose NVP. The most common NVPR mutation was K103N.

Methods: To examine the emergence of NVPR in this setting, we analyzed samples collected 7 days after NVP administration from a subset of women in HIVNET 012. Genotyping was performed with the Applied Biosystems ViroSeq HIV-1 Genotyping System. The rate of detection of K103N and Y181C at 7 days vs 6–8 wks post-NVP was compared using a McNemar’s test for paired samples.

Results: Genotypes from 7 days and 6–8 wks post-NVP were obtained for 66 women (paired samples). NVPR mutations were typically detected as mixtures of mutant and wild-type sequences. A similar number of women had NVPR mutations detected at the 2 time points. However, the pattern of mutations was different. Y181C was detected in 13 (87%) of 15 women with NVPR at 7 days, but in only 4 (22%) of 18 women with NVPR at 6–8 wks. In contrast, K103N was detected in 6 (40%) of 15 women with NVPR at 7 days, but was detected in all 18 women with NVPR at 6–8 wks. Analysis of paired samples suggests that Y181C is selected early, but fades in most women by 6–8 wks (p = 0.0117). In contrast, K103N is more likely to be detected at 6–8 wks than at 7 days, which is consistent with delayed selection of HIV-1 with this mutation (p = 0.0005). V106A and G190A were also detected in some 7 day samples. Eight (8) women had > 1 NVPR mutation at 7 days. Analysis of cloned variants from representative samples revealed complex mixtures of variants with different mutation patterns. In some samples, variants with > 1 NVPR mutation were identified, and additional NVPR mutations were identified that were not detected by population sequencing.

Conclusions: The pattern of NVPR mutations detected after single-dose NVP depends on the timing of sample collection. Y181C is frequently detected at 7 days, but often fades from detection by 6–8 wks. K103N emerges more slowly, but remains detectable in most women at 6–8 wks. The more rapid emergence and fading of Y181C vs K103N may reflect differences in the NVP susceptibility and fitness of HIV-1 with these mutations. Analysis of cloned variants reveals that diverse populations of HIV-1 variants with NVPR mutations are selected as early as 7 days following single dose NVP.