Development of novel approaches for HIV drug resistance detection using nanopore sequencing technology

抗生素耐药性（AMR）是全球最大的健康挑战之一。AMR可以在包括病毒在内的所有病原体中进化。在过去十年中，世界见证了抗逆转录病毒疗法（ART）使用的前所未有的增长，世界卫生组织（WHO）报告称，截至2021年底，全球超过3800万艾滋病毒感染者中有超过2800万人接受治疗。抗逆转录病毒疗法防止出现与艾滋病有关的疾病，改善了数百万艾滋病毒/艾滋病感染者的健康状况，并降低了新的艾滋病毒感染率。在增加使用治疗的同时，出现了艾滋病毒抗药性。全球对关键艾滋病毒药物的耐药性上升具有重大的临床影响，并威胁到在抑制艾滋病毒方面取得的重大进展。在非洲，这一威胁尤其严重，一些国家报告说，艾滋病毒对标准一线治疗的耐药性水平超过10%，这一水平在以前没有使用抗逆转录病毒疗法史的艾滋病毒感染者中也观察到，这可能表明耐药病毒的传播很普遍。此外，世卫组织估计，艾滋病毒阳性母亲所生的婴儿中约有50%对一种或多种一线治疗药物具有艾滋病毒耐药性。该研究由一个在流行病学，病毒学和计算基因组学研究方面具有丰富经验的高度多学科团队监督。这项研究将包括在MRC/LSHTM乌干达单位的实地考察，在那里将采取测试样本。这项工作具有创新性，实现了基因组测序技术和大数据生物信息学。该项目预计将产生科学出版物，并提供新的工具，以支持对耐药性的公共卫生监测。便携式测序技术的出现意味着病毒基因组测序现在可以对耐药性的激增产生更大的公共卫生影响。该项目旨在开发一种基于纳米孔测序的工作流程，用于识别HIV耐药性。这涉及使用加标血浆样本对测序方法进行优化、评估和验证，然后对具有已知耐药性水平的HIV感染患者进行临床评估。最后，将为报告艾滋病毒耐药性开发一个开放源数据处理和分析工作流程。据设想，这一工作流程将支持公共卫生决策，并帮助临床医生和实验室解释基因型耐药性。总之，该项目将作为探索如何在未来最好地利用快速病毒测序的基础，以整合到当地公共卫生监测中，以减少耐药性和进一步传播的发生率。

Antimicrobial resistance (AMR) is one of the greatest global health challenges. AMR can evolve in all groups of pathogens including viruses. Over the past decade, the world has witnessed an unprecedented increase in the use of antiretroviral therapy (ART), The World Health Organisation (WHO) reported over 28 million people receiving treatment globally by the end of 2021, of the over 38 million infected with HIV globally. ART prevents the emergence of AIDS-related illness and has improved the health of millions of people living with HIV/AIDS as well as reduce the rate of new HIV infections. Concurrent with the increased use of treatment has been the emergence of HIV drug resistance. This global rise in resistance to crucial HIV drugs has a significant clinical impact and threatens the significant progress that has been made in suppressing HIV. In Africa, this threat is particularly acute where several countries have reported levels of HIV resistance exceeding 10% to the standard first-line therapy, a level also observed in HIV-infected people who have no previous history of ART use, which may be an indication that transmission of resistant viruses is rife. Also, the WHO estimates that approximately 50% of infants born to HIV positive mothers have HIV drug resistance to one or more of the first-line therapy drugs. The research is supervised by a highly multidisciplinary team with a wealth of experience in epidemiology, virology and computational genomics research. This research will include fieldwork at the MRC/LSHTM Uganda unit where the test specimens will be taken. This work is innovative, implements genome sequencing technologies and big data bioinformatics. This project is expected to yield scientific publications and deliver novel tools to support public health surveillance of drug resistance. The advent of portable sequencing technology means viral genomic sequencing is now positioned to exert a greater public health impact to the upsurge in drug resistance. This project aims to develop a nanopore sequencing-based workflow for identifying HIV drug resistance. This involves optimization, evaluation, and validation of the sequencing method using spiked plasma samples followed by a clinical evaluation from HIV-infected patients with known levels of drug resistance. Lastly, an open-source data processing and analysis workflow will be developed for reporting HIV drug resistance. It is envisaged that this workflow will support public health decisions and aid clinicians and laboratories in interpreting genotypic resistance. Taken together, this project will serve as the underlying basis for exploring how rapid viral sequencing can be best used in the future towards integration into local public health surveillance to decrease the incidence of drug resistance and onward transmission.