Genomic Miniarrays for HIV-1 Subtyping

描述(申请人提供)：艾滋病毒/艾滋病是一种史无前例的病毒大流行，全世界有4200万人感染，每年有300多万人死亡。这种病毒的高突变率导致了多种循环基因型的进化，这些基因型导致了不同的疾病结局、传播率、对治疗的抵抗力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亚型和流通中的重组形式的准确信息。目前基于短测序、异源双链迁移率分析和实时定量聚合酶链式反应的检测方法相对昂贵，只能检测到少数几个靶点，而且容易产生错误和误导性的评估。PI设计了一种新型的微型阵列和基因组探针集系统，用于在微阵列平台上全面检测SARS。这一新系统可以检测和区分任何病毒物种的主要基因，并提供简化的基因组结构。这笔赠款将使这项新技术适应并扩展到更准确地区分HIV-1亚型，方法是在微型阵列上使用捕获探针组，这些探针组基本上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。拟议的HIV-1微型阵列将填充大约20个大小探针集，分别用于A1、B、C和D四个参考亚型，大多数靶点位于保守的Gag和可变env基因区。因此，这个系统应该允许更准确和全面的亚型识别，使用简单，廉价的方案，并通过对患者样本的多路处理。建议的HIV-1微型阵列将包含针对选定共识区域的高特异性寡核苷酸探针和更大的目标区域探针，这些探针将具有容错能力，并将检测到新的突变和重组变异。这种新颖的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.