Genomic Miniarrays for HIV-1 Subtyping

描述（由申请人提供）：艾滋病毒/艾滋病是一种前所未有的病毒性流行病，全世界有4200万人感染，每年造成300多万人死亡。该病毒的高突变率导致了多种循环基因型的进化，这赋予了不同的疾病结局、传播率、对治疗的耐药性和对不同疫苗的反应。全世界在疫苗开发和试验评估方面的努力取决于关于目标人群中存在哪些患者HIV-1亚型和循环重组形式的准确信息。目前基于短测序、异双工迁移率测定和实时PCR的检测相对昂贵，只能检测到少数靶点，并且容易产生错误和误导性评估。PI设计了一种新型的微型阵列和基因组探针集系统，用于微阵列平台上的SARS综合检测。这个新系统可以检测和区分任何病毒物种的主要基因，并提供了一个简化的基因组结构剖面。这笔拨款将适应和扩展这项新技术，通过在微型阵列上使用捕获探针集，平行或复制目前在上述短测序，HMA和实时PCR分析中使用的所有主要基因靶标，从而更准确地区分HIV-1亚型。所提出的HIV-1微型阵列将分别为A1、B、C和D四种参考亚型填充约20个大小探针集，其中大多数靶点位于保守的gag和可变的env基因区域。因此，该系统应允许更准确和全面的亚型区分，使用简单，廉价的方案，并对患者样本进行多重处理。拟议的HIV-1微型阵列将包含高特异性的寡核苷酸探针，用于选定的共识区域和更大的目标区域探针，这些探针将具有容错性，并将挑选新的突变和重组变异。这种新型微型阵列和程序正在申请专利。

DESCRIPTION (provided by applicant): HIV/AIDS is an unprecedented viral pandemic with 42 million people infected worldwide and killing more than 3 million people per year. The high mutation rate of this virus has led to the evolution of multiple circulating genotypes, which confer variable disease outcomes, transmission rates, resistance to therapy, and responses to different vaccines. Worldwide efforts at vaccine development and trial evaluations depend on accurate information about which patient HIV-1 subtypes and circulating recombinant forms are present in the targeted populations. Current tests based on short sequencing, the heteroduplex mobility assay and realtime PCR are relatively expensive, can only detect a few targets, and are prone to error and misleading assessments. The PI has devised a novel miniarray and genomic probe set system for comprehensive SARS detection on a microarray platform. This new system can detect and distinguish the major genes of any viral species and provides a simplified profile of the genome structure. This grant Will adapt and extend this new technology to more accurate discrimination of HIV-1 subtypes by employing capture probe sets on the miniarray that parallel or duplicate essentially all the major gene targets which are presently employed in the above mentioned short-sequencing, HMA and real-time PCR assays. The proposed HIV-1 miniarrays will be populated with about 20 large and small probe sets for each of four reference subtypes, A1, B, C and D, with most targets in the conserved gag and the variable env gene regions. This system should therefore allow more exact and comprehensive subtype discrimination with a simple to use, inexpensive protocol, and with multiplex processing of patient samples. The proposed HIV-1 miniarrays will contain high specificity oligo-probes to selected consensus regions and larger target region probes that will be fault tolerant and will pick up new mutations and recombinant variations. The novel miniarrays and procedures are patent pending.