Bonsall David, Golubchik Tanya, de Cesare Mariateresa, Limbada Mohammed, Kosloff Barry, MacIntyre-Cockett George, Hall Matthew, Wymant Chris, Ansari M Azim, Abeler-Dörner Lucie, Schaap Ab, Brown Anthony, Barnes Eleanor, Piwowar-Manning Estelle, Eshleman Susan, Wilson Ethan, Emel Lynda, Hayes Richard, Fidler Sarah, Ayles Helen, Bowden Rory, Fraser Christophe
Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
J Clin Microbiol. 2020 Sep 22;58(10). doi: 10.1128/JCM.00382-20.
Viral genetic sequencing can be used to monitor the spread of HIV drug resistance, identify appropriate antiretroviral regimes, and characterize transmission dynamics. Despite decreasing costs, next-generation sequencing (NGS) is still prohibitively costly for routine use in generalized HIV epidemics in low- and middle-income countries. Here, we present veSEQ-HIV, a high-throughput, cost-effective NGS sequencing method and computational pipeline tailored specifically to HIV, which can be performed using leftover blood drawn for routine CD4 cell count testing. This method overcomes several major technical challenges that have prevented HIV sequencing from being used routinely in public health efforts; it is fast, robust, and cost-efficient, and generates full genomic sequences of diverse strains of HIV without bias. The complete veSEQ-HIV pipeline provides viral load estimates and quantitative summaries of drug resistance mutations; it also exploits information on within-host viral diversity to construct directed transmission networks. We evaluated the method's performance using 1,620 plasma samples collected from individuals attending 10 large urban clinics in Zambia as part of the HPTN 071-2 study (PopART Phylogenetics). Whole HIV genomes were recovered from 91% of samples with a viral load of >1,000 copies/ml. The cost of the assay (30 GBP per sample) compares favorably with existing VL and HIV genotyping tests, proving an affordable option for combining HIV clinical monitoring with molecular epidemiology and drug resistance surveillance in low-income settings.
病毒基因测序可用于监测艾滋病毒耐药性的传播、确定合适的抗逆转录病毒治疗方案以及描述传播动态。尽管成本在不断下降，但对于低收入和中等收入国家的广泛艾滋病毒流行情况，下一代测序（NGS）用于常规检测的成本仍然过高。在此，我们介绍veSEQ-HIV，这是一种专门针对艾滋病毒量身定制的高通量、经济高效的NGS测序方法及计算流程，可使用为常规CD4细胞计数检测抽取的剩余血液来进行。该方法克服了几个主要技术挑战，这些挑战曾阻碍艾滋病毒测序在公共卫生工作中的常规应用；它快速、稳健且经济高效，能无偏差地生成多种艾滋病毒毒株的完整基因组序列。完整的veSEQ-HIV流程可提供病毒载量估计以及耐药性突变的定量总结；它还利用宿主内病毒多样性信息构建定向传播网络。我们使用从赞比亚10家大型城市诊所的患者中收集的1620份血浆样本评估了该方法的性能，这些样本是作为HPTN 071-2研究（PopART系统发育学）的一部分。病毒载量>1000拷贝/毫升的样本中有91%成功获得了完整的艾滋病毒基因组。该检测方法的成本（每份样本30英镑）与现有的病毒载量和艾滋病毒基因分型检测相比具有优势，证明了在低收入环境中将艾滋病毒临床监测与分子流行病学及耐药性监测相结合的一种经济实惠的选择。
