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

这份一般信息概述了向MRC Capital Equipment申请资金，以采购高通量的图书馆准备设备，以加强MRC/UVRI和LSHTM乌干达研究单位的下一代测序能力。该单位在2002年引入了基因组测序设施，当时我们收购了Sanger Beckman Coulter Sequencer Sequencer，该测序仪用于支持第一个艾滋病毒耐药(HIVDR)临床试验“非洲抗逆转录病毒治疗交付试验”(DART)。自那以后，基因组学设施进行了重大升级，包括采购了两台应用生物系统公司的桑格测序仪，以及最近一台Illumina MiSeq下一代测序仪和几台牛津纳米孔测序仪。乌干达病毒研究所有另一台MiSeq测序仪，在工作量增加或我们的MiSeq需要维护的情况下用作备份。我们还计划获得一个离子洪流平台，以便在试剂供应和设备维护面临挑战的情况下为我们提供更多选择，就像新冠肺炎疫情期间所经历的那样。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/艾滋病监测、艾滋病毒分子流行病学研究、艾滋病毒双重感染、艾滋病毒疫苗工作，以及目前利用元基因组学进行的病毒发现和监测研究。我们目前正在支持乌干达政府支持的SARS-CoV-2疫苗发现工作。该单位是国家和地区艾滋病毒耐药性和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，是扩大免疫方案下新出现和重新出现的病毒和可免疫疾病参考实验室的一部分。多年来，该股支持了几个项目和国家基因组监测方案，然而，在2020年，所有这些都发生了变化，因为SARS-CoV-2基因组监测的需求被列为优先事项，由于全球旅行限制和封锁，需要在当地完成。尽管为SARS-CoV-2建立了本地基因组学能力，但对这些服务的需求非常高，这需要自动化来增加结果的周转时间。为了解决这个问题，我们购买了一台自动化的EMAG BioMerieux仪器，用于DNA/RNA提取和下游序列分析。一项主要挑战是为随后的下游下一代测序手工准备测序库，这构成了这项工作的一个主要瓶颈。因此，这项应用是为了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，并在SARS-CoV-2之后应对大流行。通过与合作伙伴的广泛协商，强烈推荐以下平台用于高通量生成下一代测序、汉密尔顿、贝克曼库尔特和埃彭多夫的文库。我们的一些员工之前曾在南非的Tulio de Oliveira教授的实验室接受过汉密尔顿平台的培训，考虑到南非授权分销商提供的试剂和技术支持，这是首选平台。在这份申请中，我们只设法从汉密尔顿平台经销商那里获得了报价，他们很容易就提供了报价。我们无法从其他经销商那里得到报价，因为我们的询问从未得到回应，尽管有几封电子邮件提醒我们。这是在我们的环境中工作的一个重大挑战，因为获取有关试剂、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，探讨其他可行方案，以作出明智的决定，以确保物有所值。

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.