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

该方案的目的是进行研究，以便更好地了解病原体基因组学，从而更好地控制疾病和流行病，并调查病毒学、免疫学和遗传学因素，以便制定防治艾滋病毒-1和其他感染的有效干预措施。将利用a）充分表征的队列和生物库B）干预试验的单位跟踪记录c）对基因组学、免疫测定和生物信息学新技术的投资和d）已建立的合作。我们建议监测艾滋病毒流行的特点，特别是在最近的感染，并使用全长基因组测序，以更好地了解越来越多的重组病毒，使用更好的生物信息学工具的循环HIV-1亚型。我们将使用分子结合社会流行病学和建模方法，以提供新的途径来监测流行趋势和传播动态，并通过确定传播集群和热点来促进有针对性的干预措施。艾滋病毒耐药性（HIV drug resistance，HIV DR）正在成为抗逆转录病毒疗法（ART）在护理和预防两方面的最重要挑战之一，在资源有限的地区尤其如此，这些地区的特点是使用有限的抗逆转录病毒药物治疗方案、缺货、根据现有供应改变治疗方案以及经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，以促进改善干预措施。HIV重叠感染（SI）调查将利用来自高危人群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.