ABG-Net


African Biosecurity and Genomics Network
As a result of the recent 2013 to 2016 West African Ebola Virus Disease (EVD) outbreak and the ongoing menace of endemic Lassa Haemorrhagic Fever (LF), several African academic institutions, civil society organizations and their international collaborators, came together to form a coalition that has emerged into the African Biosafety and Genomics Network or ABG-Net. The research mandate was conceptualized at the 2nd African Conference on EID and Biosecurity. (http://www.getafrica.org/index.php/about-us/conferences)

The ABG-Net is comprised of the following leading institutions:

  • Stellenbosch University, Faculty of Medicine & Health Sciences, Cape Town, South Africa. PI Prof Akin Abayomi
  • University of Sierra Leone College of Medicine and Allied Sciences, Freetown, Sierra Leone and Kenema general Hospital. PIs: Prof Sahr Gevao and Dr Donald Grant.
  • Irrua Specialist Teaching Hospital Nigeria, Institute of Lassa Fever Research & Control. PI Prof George Akpede
  • University of Laval, Quebec City, Canada. PI: Prof Gary Kobinger
     Collaborating with:
    • University of Western Cape, South African National Bioinformatics Institute. PI Prof Alan Christoffels
    • University College London, Center for Biodiversity and Environmental Research. Prof Kate Jones
    • Sierra Leone 34 Military Medical Corp. Prof F Sahr
    • Liberia Institute of Biomedical Research. Dr Stephen Kennedy
    • Lagos State University Teaching Hospital, Department of Virology. Prof S Omilabu
    • Tshwane University of Technology, Pretoria South Africa. Prof Paul Bartels

Project 1: Stellenbosch University (SU). Applying biopreservation research, and adapting biosecurity governance to enable culturally acceptable genomic studies in the setting of public health crises caused by highly infectious pathogens.

Stellenbosch University will function as the coordinating institute and will conduct the following research: Biobanking science as it relates to sample management logistics, Room Temperature Storage (RTS), Quality Management Systems (QMS) and Quality Control (QC) thus providing evidence based validations of various biospecimens integrity and storage conditions. SU will also introduce the concepts of adding value through cell line creation derived from individuals within the respective cohorts of the project. Specifically the processing and storage of biospecimens for future cell culture applications through collaboration with ISENET and RUCDR Infinite Biologics. SU will transfer biobanking capacity and expertise generated through involvement in the H3Africa and B3Africa consortia across the ABG-Net and to include biosecurity regulatory considerations for biocontainment. Collaborating with the Center for Biodiversity and Environmental Research University at the University College London (UCL) to improve mathematical modelling using parameters derived from the field work in Sierra Leone and Nigeria for both LF and EVD. These models would be used to generate spatial and temporal predictions under different future scenarios. SU will also explore the sustainability of biobanking and the additional expense of increased biosecurity required for biocontainment facilities. Lastly, SU will explore the ELSI and CE principles of banking and researching EID’s during PHEIC across the ABG-Net and also define and coordinate the training needs of the ABG-Net in conjunction with the collaborating PIs and shared core leads. Su will also be collaborating with the University of Ibadan Research Foundation to build capacity across the region in public crises management and surveillance.

PI: Prof Akin Abayomi - Chief Pathologist and Head of Division of Haematology, Associate Professor, Faculty of Health Sciences, Tygerberg Hospital, Stellenbosch University, Cape Town, South Africa.
Contact:
Dr Carmen Swanepoel – This email address is being protected from spambots. You need JavaScript enabled to view it.  
                   

Project 2: Irrua Specialist Teaching Hospital Nigeria: Delineating the environmental factors, host-pathogen determinants and viral evolution driving Lassa fever (LF) distribution and severity in West Africa using genomics and bioinformatics.

LF, one of the severe VHF’s, has plagued West African countries for decades, perhaps centuries, causing much human suffering and loss of lives and livelihood. It is an important factor in the widespread poverty, and poor maternal and child health indices that characterize countries in the sub-region. Caused by an arena virus LASV, the main vector and reservoir of infection is the commensal rodent Mastomys natalensis. LASV is also transmitted from human to human and may cause nosocomial (hospital-acquired) outbreaks. Case-fatality rates during outbreaks are sometimes up to 60 – 80%. As with Ebola, health systems in endemic countries are often times overwhelmed by the magnitude of the outbreak, lack of health care personnel, diagnostic and treatment facilities and loss of health workers due to nosocomial exposure to infection. Thus understanding the dynamics of interaction between environmental factors, the vector, the pathogen and the host in the transmission and severity of infection could offer the opportunity for development of new avenues for the interruption of transmission of infection.

PI: Prof George Akpede - Professor of Paediatrics, College of Medicine, Ambrose Alli University
Contact:
Prof George Akpede - This email address is being protected from spambots. You need JavaScript enabled to view it.
 

Project 3: University of Sierra Leone: Understanding the host-pathogen determinants of the spectrum of morbidity, mortality and recovery seen in Ebola Virus (EBOV) Disease using genomics and bioinformatics.

University of Sierra Leone (USL), 34 Military Hospital and Kenema Government Hospital are putting in place biocontainment infrastructure and biosecurity frameworks which will enable them to continue their investigations of the genomics of the EBOV host- pathogen interactions, using existing Biospecimens and their respective data that have been collected in SL. Prospective biospecimens from survivors and members of communities are also accessible for determining correlates of resistance and non-outbreak transmission dynamics from the survivor clinics in Freetown. Once the right ELSI, infrastructure and regulatory frameworks are in place, these centers will generate libraries and renewable biological material, representative of the outbreak that will facilitate genomic studies on EVD clinical scenarios.

PI: Prof Sahr Gevao - Full Professor, College of Medicine and Allied Health Sciences, Sierra Leone
Contact:
Prof Sahr Gevao - This email address is being protected from spambots. You need JavaScript enabled to view it.
 

Project 4: Laval University: Environmental surveillance of the genomic footprint of Viral Haemorrhagic Fever viruses to improve the understanding of the ecological sanctuaries, vector dynamics and their emergence.

Both LF and EVD outbreaks are sporadic and no model capable of accurately predicting either EBOV or LASV outbreaks exists. A better understanding of the ecology of VHF causing viruses is desperately needed in order to develop accurate predictive models of VHF outbreaks. Being able to predict LASV and EBOV migration in susceptible animals as well as future outbreaks, would allow the deployment of preventive measures including vaccination and education of at risk populations as well as early detection of initial cases. These measures could significantly reduce the size of future VHF outbreaks and therefore reduce the cost associate with outbreak response, and the economic burden associated with VHF outbreaks. After the initial capacity building and training phase field studies, teams will perform year-round fieldwork to achieve the objectives of this proposal. A concerted effort to identify the host reservoir of EBOV will be part of this projects mandate.

PI: Prof Gary Kobinger - Director of Infectious disease research center, University of Laval
Contact:
Dr Gary Kobinger - This email address is being protected from spambots. You need JavaScript enabled to view it.
 

Admin and Training Core: Development of a project management plan for the ABG-Net

The Administration and Training Core will be responsible for all administrative activities including administrative, fiscal management; central data management and quality assurance. It is also the duty of the Core to organize workshops and training for the respective research groups and consultants that form part of the ABG-Net schedule and arrange annual meetings and regular progress meetings via internet communications. We will schedule the Science Advisory Committee meetings, preparation of progress reports, and communication with administrators and PIs at the other centers. We have defined a hierarchical organizational structure consisting of the Center Directors, a Center Steering Committee, and an external Science Advisory Committee.

PI: Mr Faghri February – Senior Technical Officer, Department of Haematology, Stellenbosch University.
Contact:
 

Biosecurity Core: Improving the health-security-legal interface, to ensure adoption of a biosecurity framework that promotes peaceful custodianship and research on dangerous category “A” infectious pathogens in Africa

This core proposal addresses the cross-cutting principles that need to be developed in the countries involved in this research proposal to address the gaps in biosecurity and technical resources necessary to conduct indigenous research on Emerging Infectious Diseases (EID). This is particularly true of pathogens that pose a threat to communities, public peace and stability, and are capable of extending beyond national borders to cause Public Health Emergency of International Concern (PHEIC). The countries involved in this collaboration that will provide the source of the research material- Sierra Leone, Liberia, and Nigeria, all have predominantly undeveloped governance procedures and infrastructure necessary to effectively conduct research on samples and data derived during such outbreaks

Biosecurity in Practice: Members of the ABG-Net are working with the governments to provide a series of services focused on key areas (below) to build national instruments to support research capacity on dangerous pathogens. Without such frameworks academic enquiry and research will be retarded.

PI: Prof Akin Abayomi - Chief Pathologist and Head of Division of Haematology, Associate Professor, Faculty of Health Sciences, Tygerberg Hospital, Stellenbosch University, Cape Town, South Africa. Assisted by Prof Rebecca Katz (Georgetown University) and Mr Scott Spence (VERTIC).
 Contact:
 Prof Akin Abayomi - This email address is being protected from spambots. You need JavaScript enabled to view it.
 Rebecca Katz - This email address is being protected from spambots. You need JavaScript enabled to view it.
 

Bioinformatics Core: Building indigenous capacity to carry out environmental surveillance and identifying biomarkers of prognosis using bioinformatics of genomic derived data from emerging infectious diseases.

The African biosecurity and genomics network (ABG-Net) comprise multiple research centres with overlapping computational needs. Yet, the ABG-Net benefits from bioinformatics expertise distributed throughout the network (Big Data Research Centre at Laval University, Canada; South African National Bioinformatics Institute and Center for Biodiversity and Environment Research, University College London). The vision of the bioinformatics core is to ensure that we harness this extensive network of computational expertise to the benefit of ABG-Net deliverables.

PI: Prof Alan Christoffels – Professor and Director, South African National Bioinformatics Institute, University of the Western Cape.
Contact:
Prof Alan Christoffels – This email address is being protected from spambots. You need JavaScript enabled to view it.
 

Modelling and Prediction Core: Using genetic and ecological data to predict the future distribution of viral haemorrhagic fevers.

The VHF Disease Forecasting proposal directly addresses the gap by developing a single forecasting framework (environmental-mechanistic modelling) that operates across large-spatial scales. We will develop this approach with Lassa Fever (LF) and Ebola Virus Disease (EVD), collating both existing literature and explicitly using data collected by coordinating centres on reservoir and amplifying host genetics, phylogeography, ecology and viral seroprevalance. The proposal has three specific aims:

Understand the phylogenetic and environmental correlates of reservoir host seroprevalance across Africa.

Understanding the seasonal and climatic cycles that influence the dynamics and abundance of reservoir hosts.

Building on our knowledge of host and pathogen distributions and abundance dynamics we will calculate the force of zoonotic infection to input into landscape-scale human epidemiological models to calculate current risk. We will then change underlying climatic, environmental and human demographic conditions in line with global future scenarios, and possible intervention strategies to understand how the distribution and probability of zoonotic spillover and transmission will change over time

PI: Prof Kate Jones – Full Professor of Ecology and Biodiversity, University College London (UK)
Contact:
Prof Kate Jones - This email address is being protected from spambots. You need JavaScript enabled to view it.
Dr Dave Redding - This email address is being protected from spambots. You need JavaScript enabled to view it.
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