A Capital Business Case to Enhance Pathogen Genomic Surveillance in Sub-Saharan Africa through Laboratory Infrastructure Capacity Building

通过实验室基础设施能力建设加强撒哈拉以南非洲病原体基因组监测的资本商业案例

• 批准号: MR/X01343X/1
• 负责人: Deogratius Ssemwanga
• 金额: $ 32.1万
• 依托单位: London School of Hygiene & Tropical Medicine
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2023
• 资助国家: 英国
• 起止时间: 2023 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=MR%2FX01343X%2F1
• 关键词: Capital; Business; Case; Enhance; Pathogen

This general information outlines the application to the MRC Capital Equipment for funds to procure a high throughput library preparation equipment to strengthen the capacity for next generation sequencing at the MRC/UVRI & LSHTM Uganda Research Unit. The Unit introduced the genomics sequencing facility in 2002 when we acquired a Sanger Beckman Coulter Sequencer that was used to support the first HIV drug resistance (HIVDR) clinical trial the 'Delivery of Antiretroviral Therapy in Africa Trial, (DART). The genomics facility has since undergone major upgrades to include the procurement of two Applied Biosystems sanger sequencers and most recently an Illumina MiSeq next generation sequencer and several Oxford Nanopore sequencers. Another MiSeq sequencer is available at the Uganda Virus Research Institute that has been used as a backup in the event of increased workload or when our MiSeq is due for maintenance. We further have plans to get an Ion Torrent platform to provide us with more options in the event of reagent supply and equipment maintenance challenges as experienced during the COVID-19 pandemic. Since 2002, this genomics facility has supported several projects including the national HIVDR surveillance, HIV molecular epidemiology studies, HIV superinfection, HIV vaccine work and currently the virus discovery and surveillance studies using metagenomics. We are currently supporting the SARS-CoV-2 vaccine discovery work that is supported by the Uganda Government. The Unit is host to the National and Regional HIV Drug Resistance and SARS-CoV-2 diagnostics and genomics reference laboratory. Additionally, working with partners at the Uganda Virus Research Institute, we are part of the other reference laboratories for emerging and re-emerging viruses and immunisable diseases under the Expanded Programme on Immunisation. Over the years, the Unit has supported several projects and national genomics surveillance programmes, however, in 2020, all this changed as the demand for SARS-CoV-2 genomic surveillance was prioritised and needed to be done locally due to the global travel restrictions and lockdowns. Although local genomics capacity for SARS-CoV-2 was set up, the demand for these services was very high and this required the need for automation to increase results turn around time. To address this issue, we acquired an automated EMAG bioMerieux instrument for DNA/RNA extraction and the downstream sequence analysis. One major challenge was the manual preparation of sequencing libraries for the subsequent downstream next generation sequencing which posed a major bottleneck in this work. This application is therefore to procure an automated platform to increase the capacity for library preparation and therefore increase the turnaround time to improve on our efficiency and pandemic response beyond SARS-CoV-2. Through wide consultation from partners, the following platforms have highly been recommended for high throughput generation of libraries for next generation sequencing, Hamilton, Beckman Coulter and Eppendorf. Some of our staff have previously been trained on the Hamilton platform in Prof. Tulio de Oliveira's laboratory in South Africa and this is the platform of choice given the availability of reagents and technical support from the authorised distributor in South Africa. In this application, we have only managed to get a quotation from the Hamilton Platform distributor who readily provided a quotation. We were unable to get a quotation from the other distributors as our enquiries were never responded to despite several email reminders. This is a major challenge working in our environment as access to information on reagents, equipment and maintenance remains a major challenge. If funding is awarded, we will still explore other available options for consideration in consultation with other partners to make an informed decision to ensure value for money.

本一般信息概述了向MRC资本设备申请资金，以采购高通量文库制备设备，以加强MRC/UVRI & LSHTM乌干达研究单位的下一代测序能力。该部门于2002年引进了基因组测序设施，当时我们购买了一台桑格贝克曼库尔特测序仪，用于支持第一个艾滋病毒耐药性（HIV DR）临床试验，即“非洲抗逆转录病毒治疗试验”（DART）。此后，基因组学设施进行了重大升级，包括采购两台Applied Biosystems桑格测序仪，最近采购了Illumina MiSeq下一代测序仪和几台Oxford Nanopore测序仪。另一个MiSeq测序仪可在乌干达病毒研究所使用，在工作量增加或MiSeq需要维护时用作备份。我们还计划获得Ion Torrent平台，以便在COVID-19疫情期间遇到试剂供应和设备维护挑战时为我们提供更多选择。自2002年以来，该基因组学设施支持了几个项目，包括国家艾滋病毒监测、艾滋病毒分子流行病学研究、艾滋病毒重叠感染、艾滋病毒疫苗工作以及目前使用宏基因组学的病毒发现和监测研究。我们目前正在支持由乌干达政府支持的SARS-CoV-2疫苗发现工作。该股是国家和区域艾滋病毒耐药性和SARS-CoV-2诊断和基因组学参考实验室的所在地。此外，我们与乌干达病毒研究所的合作伙伴合作，是扩大免疫计划下新出现和重新出现的病毒和可免疫疾病的其他参考实验室的一部分。多年来，该部门支持了多个项目和国家基因组监测计划，然而，在2020年，由于全球旅行限制和封锁，对SARS-CoV-2基因组监测的需求被优先考虑，需要在当地进行，这一切都发生了变化。虽然建立了SARS-CoV-2的本地基因组学能力，但对这些服务的需求非常高，这需要自动化以增加结果周转时间。为了解决这个问题，我们购买了一台自动化的埃马克bioMerieux仪器，用于DNA/RNA提取和下游序列分析。一个主要挑战是手动制备测序文库以用于随后的下游下一代测序，这在这项工作中构成了主要瓶颈。因此，这项申请旨在采购一个自动化平台，以增加图书馆准备的能力，从而增加周转时间，以提高我们的效率和SARS-CoV-2之后的大流行应对能力。通过与合作伙伴的广泛咨询，以下平台被高度推荐用于下一代测序的高通量文库生成，汉密尔顿，贝克曼库尔特和Eppendorf。我们的一些员工之前曾在南非Tulio de Oliveira教授的实验室接受过汉密尔顿平台的培训，考虑到南非授权经销商提供的试剂和技术支持，这是首选平台。在此应用程序中，我们只设法从汉密尔顿平台分销商那里获得报价，该分销商随时提供报价。我们无法从其他分销商那里得到报价，因为尽管有几封电子邮件提醒，我们的询问从未得到回应。这是在我们的环境中工作的一个重大挑战，因为获得有关试剂、设备和维护的信息仍然是一个重大挑战。如果获得拨款，我们仍会与其他伙伴磋商，探讨其他可行的方案，以作出明智的决定，确保物有所值。