GCRF_NF118: Capacity building reliable diagnostic & epidemiological tools to confront the spectre of a COVID-19 epidemic in refugee communities...

Lead Research Organisation: University of Salford
Department Name: Sch of Science,Engineering & Environment

Abstract

Evidence-led policymaking for COVID-19 control relies on accurate understanding the epidemiology of SARS-CoV-2 infections by correlating diagnostics, molecular fingerprinting and patient metadata (intrinsic (e.g. age), and extrinsic (e.g. travel history)). Efforts to correlate these data in Uganda are stalling, despite available local expertise, because laboratories designated for diagnosing and tracking COVID-19 are under-resourced, and widespread mistrust of diagnostic workflows. Current policy is therefore shaped by data from industrialised countries, which may be misleading due to significant differences in the population demographics and underlying health status.

Laboratory facilities in northern Uganda are lacking: i) reagents and experience of reliable workflows for processing of COVID-19 diagnostics; ii) whole genome sequencing equipment and consumables for providing robust epidemiological information. We will address these needs by bringing together UK-based academics and industrial partners with Ugandan biologists and policymakers to rapidly build local capacity for
SARS-CoV-2 diagnostics and real-time epidemiology. Specifically:

Transfer knowledge of SARS-CoV-2 diagnostic workflows from leading UK testing centres (NHS, Lighthouse Labs) to Uganda.

Establish Nanopore sequencing and bioinformatics in northern Uganda, supported by Salford/Liverpool/COG-UK partners, and facilitate their long-term adoption by Ugandan laboratories (UVRI, Makerere University).

Combine WGS with new survey-based patient metadata to provide real-time SARS-CoV-2 genomics, including strains circulating around refugee settlements, to support the Ugandan Ministry of Health and Prime Minister's Office to promptly mitigate local and national COVID-19 spread.

Bring together industry and logistics partners with Ugandan policymakers, to identify and address bottlenecks in the equipment and consumable supply chain, to support cost-effective, future Ugandan bioscience.

Publications

10 25 50
 
Description The project resulted in a diagnostic service for COVID19 diagnosis serving northern Uganda beginning operation in spring 2021 (slightly delayed while waiting for accreditation from the Ugandan Ministry of Health). This service was free at the point of care. Many local people turned up in person to get tested and a sample collection network for health care centres across northern Uganda was established resulting in samples being received from across the region. Over the next 9 months the service performed an average of about 300 samples a week (max was 1000 samples in early summer 2021). Demand for the service declined in late 2021 as Ugandan government COVID19 control policy changed by spring 2022 most testing was of healthy citizens needing documentation for travel. This usage continues today. In total about 13000 samples were processed up to May 2022. Genome sequencing capacity was also established at Gulu University and was used to attempt WGS of 500 SARS-CoV2 strains obtained from the diagnostic laboratory. Trained Gulu technical staff were able to complete sequencing reactions in Gulu and bioinformatic analysis of data was performed in collaboration with a project partner at Makerere University in Kampala. Thus all data generated in situ. Only reliance on external resources was access to data storage capacity on remote computer servers (e.g. Univ of Salford). Approximately half the samples tested yielded data of sufficient quality to be shared on the international SARS-CoV2 genome database (GISAID). Our data tracked the dynamics of the pandemic in northern Uganda as Alpha, Delta then Omicron waves swept the region. These data were shared with the Ugandan Ministry of Health and represent about 20% of all SARS-CoV2 WGS data generated for Uganda to date. The final objective was identifying and addressing barriers to diagnostic reagent supply in Uganda. For this objective we included suppliers, logistics providers and end users in a survey of current practice, from which it is clear that the system is not fit for purpose and represents a major barrier to the progress of laboratory science in Uganda. We explored practical solutions to this, specifically working with Oxford Nanopore Technologies and a non-for-profit logistics charity in Uganda to establish a practical and sustainable supply chain for ONT reagents (for genomics) into the country that did not require expensive intermediaries. This supply chain worked reasonably well (still some issues with timely customs clearance and in-country distribution) for the duration of the project and remains in place for future use.
Exploitation Route Our diagnostic data are being used by various research consortia to explore the epidemiology of the COVID19 pandemic on a regional and continental scale (work in progress). Our WGS data have been deposited in the international SARS-CoV2 genome database (GISAID) thereby contributing to global surveillance of the pandemic. We established molecular diagnostics and ONT-based genomics expertise in Gulu University that is now being exploited for non-COVID19 research at this Institution. We established a sustainable supply chain into Uganda for some molecular biology reagents, which are being exploited by us and Ugandan scientists to support other relevant projects in the country.
Sectors Agriculture, Food and Drink,Healthcare,Pharmaceuticals and Medical Biotechnology
 
Description A diagnostic service for COVID19 diagnosis began operation in spring 2021 (slightly delayed while waiting for accreditation from the Ugandan Ministry of Health). This service was free at the point of care. Many local people turned up in person to get tested and a sample collection network for health care centres across northern Uganda was established resulting in samples being received from across the region. Over the next 9 months the service performed an average of about 300 samples a week (max was 1000 samples in early summer 2021). Demand for the service declined in late 2021 as Ugandan government COVID19 control policy changed by spring 2022 most testing was of healthy citizens needing documentation for travel. This usage continues today. In total about 13000 samples were processed up to May 2022. The results produced by the laboratory were used to inform local/regional COVID19 control planning. For example, closure of Gulu University and local schools to restrict spread of virus. Genome sequencing capacity was also established at Gulu University and was used to attempt WGS of 500 SARS-CoV2 strains obtained from the diagnostic laboratory. Trained Gulu technical staff were able to complete sequencing reactions in Gulu and bioinformatic analysis of data was performed in collaboration with a project partner at Makerere University in Kampala. Thus all data generated in situ. Only reliance on external resources was access to data storage capacity on remote computer servers (e.g. Univ of Salford). Approximately half the samples tested yielded data of sufficient quality to be shared on the international SARS-CoV2 genome database (GISAID). Our data tracked the dynamics of the pandemic in northern Uganda as Alpha, Delta then Omicron waves swept the region. These data were shared with the Ugandan Ministry of Health and represent about 20% of all SARS-CoV2 WGS data generated for Uganda to date. The final objective was identifying and addressing barriers to diagnostic reagent supply in Uganda. For this objective we included suppliers, logistics providers and end users in a survey of current practice, from which it is clear that the system is not fit for purpose and represents a major barrier to the progress of laboratory science in Uganda. We explored practical solutions to this, specifically working with Oxford Nanopore Technologies and a non-for-profit logistics charity in Uganda to establish a practical and sustainable supply chain for ONT reagents (for genomics) into the country that did not require expensive intermediaries. This supply chain worked reasonably well (still some issues with timely customs clearance and in-country distribution) for the duration of the project and remains in place for future use.
First Year Of Impact 2022
Sector Education,Healthcare
Impact Types Societal,Economic,Policy & public services
 
Description COVID19 control measures
Geographic Reach Africa 
Policy Influence Type Participation in a guidance/advisory committee
Impact Our results helped convince decision-makers that Universities and schools should be closed, resulting in reduced transmission of SARS-CoV2 and likely less illness/death.
 
Title creation of expertise in molecular diagnostics and WGS in Uganda 
Description Knowledge exchange resulted in 8 research staff at Gulu University acquiring in depth expertise in PCR-based diagnostics and ONT-based whole genome sequencing. 
Type Of Material Improvements to research infrastructure 
Year Produced 2023 
Provided To Others? No  
Impact The expertise developed by Gulu staff during the project is now being exploited for research in tropical health across the University and for training of additional staff members. 
 
Description MOU with Gulu University 
Organisation Gulu University
Country Uganda 
Sector Academic/University 
PI Contribution Work described within the project proposal
Collaborator Contribution Additional resources to cope with high demand for COVID19 diagnostics
Impact Gulu University provided additional technical staff for the molecular diagnostics service established by this project when we realised demand for our service was much greater than we anticipated.
Start Year 2021
 
Title provision of molecular diagnostic services 
Description With the support of this funding alone we have established a fully-functioning molecular diagnostic laboratory for covid19 in northern Uganda. This facility has now performed over 12,000 tests. The laboratory has been nationally (Ugandan Ministry of Health) and internationally (East African COVID19 Common Pass and Oneworld Accuracy) and, since May 2021 has been fully integrated into national and international COVID19 reporting networks. The lab is now managed and staffed entirely by Ugandan scientists, who received their training in situ as part of this project. Improvements in the laboratory's efficiency over the past 12 months has resulted in test turn-around time dropping from 3-5 days to 3-5 hours. 
Type Diagnostic Tool - Non-Imaging
Current Stage Of Development Wide-scale adoption
Year Development Stage Completed 2021
Development Status Under active development/distribution
Impact Training in covid19 molecular diagnostics has been offered to Ugandan staff beyond those employed by the project as a means of demonstrating the applicability of this approach to other infectious diseases, particular NTDs. Numerous academic staff have had hands-on experience of these methods for the first time and thus are now far more aware of their simplicity and broad applicability. 
 
Title provision of whole genome sequencing capability 
Description The project has established whole genome sequencing capability at the University of Gulu and applied it to characterising SARS-CoV2 strains circulating in northern Uganda. The project provided in situ training for Ugandan scientists on ONT-based sequencing technologies and the equipment and reagents to do the sequencing. The project also established a sustainable supply chain for ONT reagents into Uganda/Gulu. The project has attempted to sequence the genomes of all strains detected by the routine molecular diagnostic service run in the Gulu laboratory, resulting in almost 200 genomes submitted to GISAID to date. WGS is now carried out by Ugandan scientists. The project enhanced bioinformatic capability in Uganda, specifically training Ugandan scientists in the use of pipelines for analysis of SARS-CoV2 WGS data. 
Type Diagnostic Tool - Non-Imaging
Current Stage Of Development Wide-scale adoption
Year Development Stage Completed 2021
Development Status Under active development/distribution
Impact Training on ONT-based genomics has been delivered to scientists in Gulu who are not part of the COVID19 laboratory as a means of increasing awareness of the broad applicability of the technology. This has led to new collaborations with Gulu staff utilising ONT sequencing to address non-COVID19 questions, increasing the likelihood that this expertise will be sustained in northern Uganda.