Antiretroviral drug resistance in KwaZulu Natal

描述（申请人提供）：自2002年在南非引入政府资助的抗逆转录病毒疗法（ART）以来，近100万患者接受了ART治疗，艾滋病毒/艾滋病死亡率下降。虽然早期的治疗成功报告了高依从率和病毒抑制率，但病毒学失败（VF）率已开始接近资源丰富国家的水平。由于病毒学监测频率低于美国，因此在检测到VF和ART转换为二线方案之前，耐药突变有更多的机会积累。因此，二线治疗的疗效可能会受到影响。迄今为止，尚未对南非一线抗逆转录病毒治疗失败者的耐药性流行率和相关风险因素进行全面研究。同样，少数耐药变异对非核苷类逆转录酶抑制剂（NNRTI）为基础的方案的疗效的影响尚未研究，但接受单剂量奈韦拉平（NVP）预防母婴传播HIV-1的女性除外。因为在南非传播的抗药性仍然很罕见，在这一人群中检测到的耐药少数变异体可能被认为反映了易出错的HIV-1 RT自发产生的这种突变体。我们建议研究一线ART VF后HIV-1耐药的模式和预测因素，以及夸祖鲁省城乡结合部少数耐药少数变异体的临床意义。南非，纳塔尔（KZN）。该提案的具体目标如下：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ARV水平; 2）确定南非KZN省农村和城郊环境中VF和HIV-1耐药性的风险因素; 3）确定在接受一线ART的患者中自发产生的耐药少数变异体对VF风险的影响。开始ART的受试者将从KZN-KZ的两个环境（城市和农村）的诊所招募。将比较TDF+拉米夫定+EFV或NVP一线治疗方案病毒学失败患者的HIV耐药突变数量和模式与报告的B亚型病毒耐药模式。病例对照设计将用于确定次优依从性和病毒学失败的风险因素 在KZN省的不同环境中有或没有耐药性。将使用等位基因特异性PCR和下一代测序（使用Illumina Solexa平台）在治疗前样本中确定病毒群体中少数耐药变异的患病率;将确定这些耐药突变对病毒学失败风险的影响。探索性分析将比较少数耐药突变的频率分布与群体遗传学理论预测的频率，以估计这些突变在不存在药物的情况下与野生型相比的适应度成本。还将确定少数变异体在群体中固定并导致耐药性和VF的概率。

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.