Nucleoside reverse transcriptase inhibitors (NRTI) were the first antiretroviral drugs available and continue to be a component of anti-retroviral therapy (ART), despite the emergence of drug resistance over time. Few studies have investigated the role of pre-existing drug resistance and response to therapy in children [1–4] compared to similar studies in adults [5, 6]. The largest published drug resistance study of HIV-infected children found a high rate of primary mutations associated with resistance to zidovudine (ZDV), didanosine (ddI) and zalcitabine (ddC), but concluded that none of the baseline drug mutations were associated with a higher rate of virologic failure [2]. It is possible that HIV drug resistance may evolve differently in children because of differences in pharmacokinetics in children, fewer drug options, and higher viral burden, especially in younger children [7, 8] and unique challenges to therapy compliance. Pediatric AIDS Clinical Trials Group (PACTG) 338 was one of the first clinical trials to evaluate highly active anti-retroviral therapy (HAART) which included a protease inhibitor, ritonavir (RTV), in children [9]. We investigated the role of baseline HIV drug resistance mutations and response to therapy.

There were very few primary resistance mutations to PIs in this PI-naïve population, although 88% of the children had polymorphisms that included secondary minor resistance mutations. The most frequent secondary PI mutations were at codons 63 (78%), 77 (37%), 36 (17%) and 10 (12%) (data not shown). Only two children had a primary PI resistance mutation (V82A). Other PI mutations (71, 33 and 20) were present in less than 10% of the study subjects. The most common NRTI mutations occurred at codons 215 (66%), 41 (42%), 67 (37%), 210 (33%), 70 (32%), 69 (22%), 118 (21%) and 219 (21%). The median numbers of baseline NRTI, thymidine analog mutations (TAM), PI and total mutations were 3, 3, 2 and 4.5, respectively (both primary and secondary mutations were included in the analysis for the PI mutations).

After 12 weeks on study, 51 (55%) subjects had viral loads suppressed below 400 copies/ml. The number of subjects with viral suppression dropped to 31 (34%) and 29 (32%) at weeks 24 and 48, respectively.

When the association between the number of baseline resistance mutations and virologic failure after 12 weeks of HAART was investigated, the only significant relationship observed was in the ZDV/lamivudine (3TC)/RTV combination regimen. A higher median number of NRTI mutations at baseline was associated with virologic suppression (1.5 versus 4.0, P = 0.016). There was no apparent association between the number of baseline PI resistance mutations and the level of viral load after 12 weeks of HAART, although as the number of baseline NRTI mutations increased the level of viral load at week 12 decreased (Figure 1). A linear regression with adjustment for censoring of viral loads at the detection limit showed that after 12 weeks on HAART there was a decrease of 0.245 in log₁₀ RNA (copies/mL) associated with each additional NRTI resistance mutation (P = 0.006).

The association between the presence of a specific baseline mutation and virologic suppression during the first 24 weeks on HAART was explored. Viral response was categorized into three ordered levels: full suppression (viral load no more than 400 copies/mL at week 12 or 24), partial suppression (viral load dropped 0.75 log₁₀ copies/mL or more at week 12 or 24 from baseline, but no full suppression), and no suppression. According to this definition, 56 (60%) subjects achieved full viral suppression and an additional 13 (14%) achieved partial viral suppression during the first 24 weeks on HAART. There was no statistically significant (at the unadjusted 5% level) association between any baseline mutation and virologic suppression during the first 24 weeks on HAART.

For the 69 children with full or partial viral suppression as defined above, the association between the presence of a specific baseline mutation and viral rebound between the suppression and week 48 was evaluated. A rebound was declared if there was an increase in RNA of more than one log₁₀ at any time between the time of suppression and week 48 from the nadir viral load value at or before the time of suppression, or if the child came off the assigned protocol treatment at or before week 48. Of the 69 children who achieved full or partial virologic suppression during the first 24 weeks on HAART, 37 (54%) had a viral rebound. In the three-drug arm children with mutation at the NRTI codon 67 seemed to be less likely to have a viral rebound after virologic suppression (unadjusted P = 0.002). There was also the suggestion of a potential association with virologic failure for the presence of any PI mutation (unadjusted P = 0.020) in the three-drug arm and for mutation at the NRTI codon 69 (unadjusted P = 0.028) in the two-drug arm, but these findings need to be treated cautiously due to the problem of multiple comparisons (see statistical analysis section).

We evaluated the association between resistance mutations and their potential effect on the ability of antiviral medications to reduce the viral burden in children with HIV disease. As expected, there was little PI resistance and considerable NRTI resistance in this PI-naïve, NRTI-experienced population. However, contrary to our expectations, we did not find an increase in the rate of viral failure after HAART associated with the presence of resistance mutations at baseline. The two specific associations identified at week 12 in our study (Table 1) were of borderline significance and were in the direction of a decrease, rather than an increase, in the rate of viral failure. As the number of NRTI mutations at baseline increased, the median viral load at week 12 decreased (P = 0.006) and as the baseline level of ZDV resistance increased viral failure decreased after 12 weeks on a ZDV-containing HAART regimen (P = 0.017). Our results were consistent with the drug resistance study of 135 HIV-1 infected children by Eschleman et al. [2]. Neither study produced significant evidence linking a specific baseline drug resistance mutation to a subsequent increase in viral failure. These results suggest that baseline genotyping may not be necessary prior to switching to a PI based regimen. This finding has particular pertinence in resource limited settings.

Possible explanations for these observations include adherence, replicative capacity, and hypersusceptibility to NRTIs. It is likely that children who were adherent to a non-suppressive NRTI regimen and thus developed resistance, were more likely to be adherent to a HAART regimen that contained a brand new class of drugs. Friedland and Williams [10] have suggested that the relationship between the development of resistance and adherence to the drugs is bell-shaped, such that both high and low degrees of adherence decrease the likelihood of the development of resistance. This concept has been supported by several recent studies [11–13]. The RNA results from PACTG 338, where most children had detectable, even high viral loads at baseline, suggest that the drug(s) they were taking were less effective in suppressing viral replication, resulting in ongoing viral production in the presence of ART. Thus, children who were more adherent may have been more likely to develop resistance to their non-suppressive initial therapy regimens The children's viral loads rapidly became undetectable once they were placed on drugs that were more suppressive and to which they had no baseline resistance (RTV and 3TC). Only 5 of the children had the M184V and only 2 had the V82A mutations at baseline. The effect would be less striking in children in the two drug regimen since the mutations associated with stavudine (d4T) resistance are primarily those seen with ZDV, ddI and ddC to which the children had been previously exposed (codons 41, 67, 70, 210, 215, and 219).

Another explanation for these results might be reduced replication capacity of the virus found in the children at baseline. The NRTI mutations typically associated with reduced fitness are M184V [14] and K65R [15]; however, only 1 child had the K65R mutation and only 5 had the M184V mutation at baseline. In addition, viral loads at baseline were relatively high: the median baseline viral load was 20,500 copies/mL and 20% of the children had baseline viral loads of 100,000–1,000,000 copies/mL.

Lastly, it has been shown that the L74V and M184V mutations confer hypersusceptibility to ZDV [16, 17]. However, in the 338 data set only 5 of the 47 children randomized to ZDV/3TC/RTV for whom we have data, had the 74V mutation. This could, however, be an explanation for why children on the ZDV/3TC/RTV arm who had more baseline NRTI mutations were more likely to have a viral load <400 copies/mL at 12 weeks than those with fewer mutations.

Limitations of our study include the fact that we have baseline resistance data on only a subset of children from the entire study and lack of information on adherence to the drug regimens, replicative capacity and hypersusceptibility of the viruses. We did not determine the occurrence of new resistance mutations after the initiation of HAART or investigate the virologic impact of these subsequent resistance mutations.

Despite considerable baseline NRTI resistance, the children in PACTG 338 who were treated with a brand new class of drugs (e.g. ritonavir, the protease inhibitor) in combination therapy responded favorably and rapidly. We did not observe an increase in the rate of viral failure after HAART linked to the presence of resistance mutations at baseline. In fact, viral loads at the 12 week time point were inversely correlated with the number of baseline NRTI mutations. It is important to remember that resistance is not an all-or-none phenomenon, and treatment failure is not defined by a resistance test. In order to better understand both the virology of mutated viruses in vivo and their response to anti-retroviral drugs as well as the use of resistance testing, prospective randomized clinical trials linked with pathogenesis-related in vitro analysis should be performed in children.