Pathogen Genomics, Phenotype and Immunity (PGPI) & Basic Sciences Programme

该方案的目的是开展研究，使人们更好地了解病原体基因组学，以便确定疾病和流行病的特征，以便更好地加以控制，并调查制定防治艾滋病毒-1和其他感染的有效干预措施所需的病毒学、免疫学和遗传因素。优势将体现在：a)特征良好的队列和生物库；b)干预试验的单位跟踪记录；c)基因组学、免疫分析和生物信息学方面的新技术投资；d)已建立的合作关系。我们建议通过描述循环HIV-1亚型来监测HIV流行，特别是在最近的感染中，并使用全长基因组测序来更好地了解使用更好的生物信息学工具增加的重组病毒。我们将使用分子与社会流行病学和建模方法相结合的方法，为监测流行病趋势和传播动态提供新的途径，并通过确定传播聚集群和热点，为有针对性的干预作出贡献。艾滋病毒耐药性（HIVDR）正在成为在护理和预防方面推广抗逆转录病毒治疗的最重要挑战之一，在资源有限的地区更是如此，这些地区的特点是使用有限的抗逆转录病毒治疗方案、缺货、根据现有供应改变治疗方案以及通常有限地使用病毒载量（VL）检测来监测治疗结果。我们将扩大我们的耐药性研究，为改进干预措施作出贡献。HIV重复感染（SI）调查将利用从高风险人群中收集的大量标本来研究与SI相关的宿主和病毒因素。

This programme aims to conduct research that will lead to better understanding of pathogen genomics in order to characterise diseases and epidemics for better control and to investigate virological, immunological and genetic factors required for the development of effective interventions against HIV-1 and other infections. Advantage will be taken of a) well characterised cohorts and biobanks b) Unit track record in intervention trials c) investment in new technologies in genomics, immunological assays and bioinformatics and d) established collaborations. We propose to monitor the HIV epidemic by characterising the circulating HIV-1 subtypes especially in recent infections and use full length genome sequencing to understand better the increasing recombinant viruses using better bioinformatics tools. We will use molecular in combination with social-epidemiological and modelling approaches to provide novel avenues to monitor epidemic trends and transmission dynamics, and to contribute to targeted interventions through the identification of transmission clusters and hotspots. HIV drug resistance (HIVDR) is emerging as one of the most important challenges to ART roll out for both care and prevention, more so in resource limited areas characterized by the use of limited ARV regimens, stock outs, regimen change based on available supply and often limited use of viral load (VL) testing to monitor treatment outcomes. We will expand our drug resistance studies to contribute to improved interventions. HIV superinfection (SI) investigations will utilise a large collection of specimens from high risk populations to study host and viral factors associated with SI.