Periodic Reporting for period 1 - GREAT-LIFE (Linking Infectious disease Front-liners’ control Efforts with central public health authorities in The African Great Lakes Region)
Okres sprawozdawczy: 2023-07-01 do 2024-12-31
The African Great Lakes region is one of the most densely populated areas in Africa and also one of the areas globally with the highest biodiversity, and forced or voluntary migrations. Very limited information is available on the prevalence and epidemiology of infectious diseases, especially gastrointestinal diseases and antimicrobial resistance that has been very understudied.
Logistically it is difficult to sample and conventionally study infectious diseases in the area and such studies have limited real-time value locally. In this study we will take full advantage of the potential offered by combining field-deployable nanopore sequencing combined with metagenomics and lap-top bioinformatics, to establish frontline sequencing at remote sites and linking this with central sharing of analytic output. Newly developed bioinformatics solutions by us have made it possible to perform simple bioinformatics analyses in real-time using laptops and subsequently share the analytic output simply using the mobile net, avoiding the need of transferring large amounts of data and access to high performance computing.
In GREAT-LIFE we will establish sequencing across six countries in the region and use this to study the abundances of AMR in villages and refugee camps. Linking this with spatial and temporal epidemiological data will enable us to identify locally relevant drivers for AMR and provide data for changing empiric treatment and policies. In addition, we will utilize sequencing directly on GI samples to identify the causative agents (and their AMR) both to provide data for policies, but also to provide immediate results for direct patient care in the frontline. We will educate a number of people in the very frontline to utilize field-sequencing and bioinformatics, as well as more advanced bioinformaticians and epidemiologist centrally. The data generated will be linked in real-time through a central hub in Tanzania to public health authorities for actions.
Logistically it is difficult to sample and conventionally study infectious diseases in the area and such studies have limited real-time value locally. In this study we will take full advantage of the potential offered by combining field-deployable nanopore sequencing combined with metagenomics and lap-top bioinformatics, to establish frontline sequencing at remote sites and linking this with central sharing of analytic output. Newly developed bioinformatics solutions by us have made it possible to perform simple bioinformatics analyses in real-time using laptops and subsequently share the analytic output simply using the mobile net, avoiding the need of transferring large amounts of data and access to high performance computing.
In GREAT-LIFE we will establish sequencing across six countries in the region and use this to study the abundances of AMR in villages and refugee camps. Linking this with spatial and temporal epidemiological data will enable us to identify locally relevant drivers for AMR and provide data for changing empiric treatment and policies. In addition, we will utilize sequencing directly on GI samples to identify the causative agents (and their AMR) both to provide data for policies, but also to provide immediate results for direct patient care in the frontline. We will educate a number of people in the very frontline to utilize field-sequencing and bioinformatics, as well as more advanced bioinformaticians and epidemiologist centrally. The data generated will be linked in real-time through a central hub in Tanzania to public health authorities for actions.
The initial focus of the first project period has been on creating a common understanding and collaboration facilitating the sharing and co-analyses of data between institutions and countries, as well as ensuring the necessary training of people and access to equipment, reagents and bioinformatic and epidemiological analyses. We have successfully performed training, created a workflow for reagents and developed laptop based bioinformatic tools for (semi-) automatic analyses of whole genome sequencing data from bacteria and viruses, as well as metagenomes. Thus, we were capable of initiating the investigations into the usefulness of genomics for studying AMR and diarrheal cases, according to the plan of work. This will now be the priority for the next period.
The start of the project did, however, become more complex and work-intensive than expected, since according to our application and grant agreement, we are obliged to respond to any Disease X event that emerges/re-emerges during the project implementation. Already in October 2023, GREAT-LIFE was requested by our affiliated partner in Kamituga, The Democratic Republic of Congo (DRC), to assist in elucidating what at that time seemed like an initial outbreak of mpox with an epidemiology that was potentially worse than seen in previous outbreaks. GREAT-LIFE has since helped, in a very complicated political landscape with multiple stakeholders, local health authorities in South Kivu, DRC, Burundi, Rwanda, Uganda, Kenya and Tanzania, including training courses, assistance with epidemiological and laboratory protocols, reagents and analytic expertise. Due to national policies, it is not possible to share all results, but GREAT-LIFE has amongst other contributions done the following:
• Identified a novel clade Ib as the cause of the outbreak in South Kivu (https://pubmed.ncbi.nlm.nih.gov/38487886/(odnośnik otworzy się w nowym oknie))
• Developed a PCR test for specific identification of this clade (https://pubmed.ncbi.nlm.nih.gov/39119722/(odnośnik otworzy się w nowym oknie))
• Elucidated the epidemiological transmission of clade Ib in South Kivu and identified risk factors (https://pubmed.ncbi.nlm.nih.gov/39933565/(odnośnik otworzy się w nowym oknie))
• Shown the transmission into Burundi (https://pubmed.ncbi.nlm.nih.gov/39421956/(odnośnik otworzy się w nowym oknie))
Of unpublished contributions, GREAT-LIFE has also contributed to the first detection of clade Ib in Rwanda, Kenya, Tanzania and Uganda. Most mpox activities are now continuing a sister project, JUA KIVU, which involves several GREAT-LIFE partners.
The start of the project did, however, become more complex and work-intensive than expected, since according to our application and grant agreement, we are obliged to respond to any Disease X event that emerges/re-emerges during the project implementation. Already in October 2023, GREAT-LIFE was requested by our affiliated partner in Kamituga, The Democratic Republic of Congo (DRC), to assist in elucidating what at that time seemed like an initial outbreak of mpox with an epidemiology that was potentially worse than seen in previous outbreaks. GREAT-LIFE has since helped, in a very complicated political landscape with multiple stakeholders, local health authorities in South Kivu, DRC, Burundi, Rwanda, Uganda, Kenya and Tanzania, including training courses, assistance with epidemiological and laboratory protocols, reagents and analytic expertise. Due to national policies, it is not possible to share all results, but GREAT-LIFE has amongst other contributions done the following:
• Identified a novel clade Ib as the cause of the outbreak in South Kivu (https://pubmed.ncbi.nlm.nih.gov/38487886/(odnośnik otworzy się w nowym oknie))
• Developed a PCR test for specific identification of this clade (https://pubmed.ncbi.nlm.nih.gov/39119722/(odnośnik otworzy się w nowym oknie))
• Elucidated the epidemiological transmission of clade Ib in South Kivu and identified risk factors (https://pubmed.ncbi.nlm.nih.gov/39933565/(odnośnik otworzy się w nowym oknie))
• Shown the transmission into Burundi (https://pubmed.ncbi.nlm.nih.gov/39421956/(odnośnik otworzy się w nowym oknie))
Of unpublished contributions, GREAT-LIFE has also contributed to the first detection of clade Ib in Rwanda, Kenya, Tanzania and Uganda. Most mpox activities are now continuing a sister project, JUA KIVU, which involves several GREAT-LIFE partners.
GreatLife has already in the first period implemented genomic sequencing as a core resource for all 6 African institutions involved in the project. Furthermore, all institutions are actively using this for both project specific and other activities and thus, continuously expanding their expertise.
In addition, GreatLife was pivotal in the identification and early elucidation of the mpox outbreak in Eastern DRC. The GreatLife led identification of a novel clade of mpox namely clade Ib, has had a major impact on the surveillance performed by WHO, public health authoritis in DRC and beyond as well as initiation of projects and research by others. GreatLife have identified the novel clade, developed PCR tests for specific detection thereof and described the genomic epidemiology including identification of risk factors for transmission in South Kivu, DRC and Burundi. In addition, GreatLife assisted in the det4ction and characterization in Rwanda, Uganda, Kenya and Tanzania, and even though we have not been allowed to perform the actual investigations we have assisted the authorities in those countries. Mpox activities among the GreatLife partners is now mainly continuing in other projects, but we are sure we have assisted a lot, even though it is difficult to quantify the exact impact.
GreatLife has also already in the first capacity building phase provided novel knowledge on rift valley fever and cholerae, but it is difficult to see the impact yet.
In addition, GreatLife was pivotal in the identification and early elucidation of the mpox outbreak in Eastern DRC. The GreatLife led identification of a novel clade of mpox namely clade Ib, has had a major impact on the surveillance performed by WHO, public health authoritis in DRC and beyond as well as initiation of projects and research by others. GreatLife have identified the novel clade, developed PCR tests for specific detection thereof and described the genomic epidemiology including identification of risk factors for transmission in South Kivu, DRC and Burundi. In addition, GreatLife assisted in the det4ction and characterization in Rwanda, Uganda, Kenya and Tanzania, and even though we have not been allowed to perform the actual investigations we have assisted the authorities in those countries. Mpox activities among the GreatLife partners is now mainly continuing in other projects, but we are sure we have assisted a lot, even though it is difficult to quantify the exact impact.
GreatLife has also already in the first capacity building phase provided novel knowledge on rift valley fever and cholerae, but it is difficult to see the impact yet.