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

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.

Since the start of the Coronavirus Disease 19 (COVID-19) pandemic in Uganda in March 2020, the MRC/UVRI and LSHTM Uganda Research Unit has contributed towards Uganda's response by identifying circulating SARS-CoV-2 variants and importation events. The Unit also functions as a national and regional reference laboratory for SARS-CoV-2 genomic sequencing and supports other neighboring countries that are still developing capacity like South Sudan and Burundi. To date, over 1,000 SARS-CoV-2 genomes from Uganda have been generated to inform pandemic response and over 90% of all SARS-CoV-2 genomes currently submitted in the GISAID database (June 2022) have been contributed by the MRC/UVRI & LSHTM Uganda Research Unit. We have been able to support the national genomic surveillance program by providing timely genomic sequencing reports in part due to our implementation of a high-throughput COVID-19 sequencing protocol (CovidSeq) with the capacity to genotype 96-192 genomes per week when fully operational. Through funds from earlier capital bids, the laboratories have been equipped with modern state of the art thermocyclers for PCR amplification, two sanger sequencers and one Illumina MiSeq Next Generation Sequencing instrument. The onset of the COVID-19 pandemic and the already existing work to support the national HIV drug resistance surveillance activities and other ongoing research that requires genomic sequencing presented a challenge of delayed turnaround time to deliver results and reduced efficiency. These challenges were attributed to the manual nucleic acid extraction and library preparation for next generation sequencing which is tedious, time consuming and impacts on the genomic sequencing capacity and turnaround times of reporting results. This has significantly impacted on the number of genomes that the Unit would have contributed despite the many SARS-COV-2 cases that have been reported. This call gives an opportunity for capacity building.