Antiretroviral drug resistance in KwaZulu Natal

描述(申请人提供)：自2002年南非采用政府资助的抗逆转录病毒疗法(ART)以来，已有近100万患者接受了ART，艾滋病毒/艾滋病的死亡率有所下降。尽管治疗成功的早期报告报告了很高的依从率和病毒抑制率，但病毒学失败率(VF)已开始接近资源丰富国家的观察结果。由于病毒学监测没有美国那么频繁，在检测到VF和ART切换到二线方案之前，有更多的机会积累耐药性突变。因此，二线治疗的疗效可能会受到影响。到目前为止，还没有对南非一线抗逆转录病毒治疗失败者中与耐药性相关的流行率和风险因素进行全面研究。同样，除了接受单剂量奈韦拉平(NVP)预防HIV-1母婴传播的妇女外，少数耐药变异对基于非核苷逆转录酶抑制剂(NNRTI)的方案疗效的影响尚未得到研究。由于传播性耐药性在南非仍很少见，在该人群中检测到的耐药少数变异可能反映了容易出错的HIV-1 RT所产生的此类突变。我们建议研究南非夸祖鲁-纳塔尔(KZN)一线抗逆转录病毒疗法(VF)后HIV-1耐药性的模式和预测因素，以及在城市和农村地区少数民族耐药少数变异的临床意义。这项建议的具体目的如下：1)确定KZN一线抗逆转录病毒治疗失败时与VF和HIV-1耐药性相关的红细胞抗逆转录病毒水平；2)确定南非KZN省农村和城市周边环境中VF和HIV-1耐药性的风险因素；3)确定自发产生的耐药少数变异对接受一线ART患者VF风险的影响。开始抗逆转录病毒治疗的受试者将从KZN的两个诊所--城市周边和农村--登记。对于经历TDF加拉米夫定和EFV或NVP一线方案病毒学失败的患者的艾滋病毒耐药性突变的数量和模式将与报道的B亚型病毒的耐药性模式进行比较。将使用病例对照设计来确定次优依从性和病毒学失败的风险因素 在KZN省不同的环境中有或没有耐药性。使用Illumina Solexa平台的等位基因特异性聚合酶链式反应和下一代测序将在前处理样本中确定少数耐药变异在病毒群体中的流行率；将确定这些耐药突变对病毒学失败风险的影响。探索性分析将把少数人耐药突变的频率分布与根据群体遗传学理论预测的频率进行比较，以估计在没有药物的情况下，与野生型相比，这些突变的适应成本。少数变异在种群中变得固定并导致抗药性和VF的概率也将被确定。

DESCRIPTION (provided by applicant): Since the introduction in 2002 of government-sponsored antiretroviral therapy (ART) in South Africa in 2002, nearly 1 million patients have received ART, and the death rate from HIV/AIDS has declined. Although early accounts of treatment success reported high rates of adherence and viral suppression, rates of virologic failure (VF) have begun to approximate those observed in resource-rich countries. Because virologic monitoring is less frequent than in the US, there is more opportunity for resistance mutations to accumulate before VF is detected and ART switched to a 2nd-line regimen. As a result, the efficacy of 2nd-line therapy may be compromised. To date, there has not been a comprehensive study of the prevalence and risk factors associated with drug resistance in persons failing 1st-line ART in South Africa. Likewise, the effect of minority drug-resistant variants on the efficacy of non-nucleoside reverse transcriptase inhibitor (NNRTI)-based regimens has not been studied except in women who received single-dose nevirapine (NVP) for prevention of mother-to-child transmission of HIV-1. Because transmitted resistance remains rare in South Africa, drug- resistant minority variants detected in this population may be assumed to reflect the spontaneous generation of such mutants by the error-prone HIV-1 RT. We propose to study the patterns and predictors of HIV-1 drug resistance after VF of 1st-line ART and the clinical significance of minority drug-resistant minority variants in peri-urban and rural settings in KwaZulu-Natal (KZN), South Africa. Specific aims of this proposal are as follows: 1) To determine the red blood cell ARV levels associated with VF and HIV-1 drug resistance at the time of 1st-line ART failure in KZN; 2) To determine the risk factors for VF and HIV-1 drug resistance in rural and peri-urban settings in the KZN province, South Africa; 3) To determine the effect of spontaneously arising drug- resistant minority variants on the risk of VF in patients receiving 1st-line ART. Subjects starting ART will be enrolled from clinics in two settings in KZN-peri-urban and rural. The number and patterns of HIV drug resistance mutations for patients who experience virologic failure of a 1st-line regimen of TDF plus lamivudine and EFV or NVP will be compared to resistance patterns reported for subtype B virus. A case-control design will be used to identify risk factors for suboptimal adherence and virologic failure with or without drug resistance in different settings in KZN province. The prevalence of minority drug resistant variants in the virus population will be determined in pre-treatment samples using allele-specific PCR and next-generation sequencing using the Illumina Solexa platform; the effect of these resistance mutations on the risk of virologic failure will be determined. Exploratory analyses will compare the frequency distribution of minority drug resistance mutations with the frequency predicted from population genetic theory to estimate the fitness cost of these mutations compared to the wildtype in the absence of drugs. The probability that a minority variant becomes fixed in the population and leads to resistance and VF will also be determined.