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28 September 2020 | Story Andre Damons | Photo Supplied
Dr Martin Nyaga, Senior Lecturer and Researcher: NGS, will be heading the World Health Organisation Collaborating Centre (WHO CC).

The University of the Free State (UFS) has been designated a World Health Organisation Collaborating Centre (WHO CC), and the university’s Next Generation Sequencing (NGS) Unit, in partnership with the World Health Organisation (WHO), will for the next four years be conducting genome sequencing of pathogenic organisms, including rotavirus strains from the African continent. 

This centre will be part of the Vaccine Preventable Diseases (VPD) Pathogens Genomics Cluster and will run from September 2020 to September 2024. 

Dr Martin Nyaga, Senior Lecturer and Researcher: NGS/Virology, who will be heading the WHO CC, says an institution is designated as a WHO CC by the WHO Director-General and endorsed by the host country’s minister of health to form part of an international collaborative network, carrying out activities in support of the WHO programmess at all levels. A designation as a WHO CC is a time-limited agreement of collaboration between WHO and the designated institution, through which the latter agrees to implement a series of concrete activities, specifically designed for WHO.

A supreme achievement

Says Dr Nyaga: “In my opinion, a WHO CC designation is one of the supreme achievements an institution can be conferred as a recognition for foregoing exceptional collaborative venture with the WHO and showing future potential to assist the WHO with its global programmes and in our case, the WHO Regional Office for Africa region to offer solutions to the WHO VPD Surveillance and pathogens genomics cluster.”

According to Dr Nyaga this designation was awarded to the UFS after the WHO was content with the outcome of a service contract whereby the UFS-NGS unit undertook a pilot rotavirus surveillance project at whole genome level, using two African countries for the pilot, Rwanda and Zambia.

“From the outcomes of the pilot surveillance project between 2017 and 2019, the WHO/AFRO was satisfied with the genomic data that was generated and partially disseminated in scientific databases and journals as a collaborative venture. 

“It was thus proposed to strengthen its existing collaboration with the UFS-NGS Unit, which initiated the application process to designate the UFS-NGS unit as a WHO CC, an initiative that has taken approximately 20 months to finalise through the different phases of the application and approvals for the designation,” explains Dr Nyaga.

The purpose of the WHO CC

The new WHO CC will upon request by the WHO, implement agreed work plans in a timely manner and to the highest possible standards of quality and must comply with the referred terms of reference and conditions. These include: 
• Conducting genome sequencing of pathogenic organisms causing VPD, including rotavirus strains collected as part of the routine VPD surveillance using NGS technology and analysis of the generated datasets using bioinformatics tools.

• Conducting molecular characterisation of specimens collected during outbreaks and public health emergencies as part of the support for monitoring, preparedness and response to VPD disease outbreaks in Africa.

• Provide technical guidance to WHO on strategies to improve laboratory molecular diagnostics, molecular typing and NGS of rotavirus diarrheal strains and other enteropathogens to detect novel and re-emerging strains. 

• Conduct validation of tools and new molecular diagnostics for detection and characterisation of unusual or rare VPD strains to guide studies and development of new vaccines for VPD.

• Organise capacity-building and training workshops on whole genome sequencing of priority VPD pathogenic organisms.

The impact of the WHO CC on the work of the UFS-NGS 

According to Dr Nyaga, the designation brings extra responsibilities to his work and to the activities of the UFS-NGS unit. “Such initiatives are very welcome to enhance the business aspects, research and academic activities of the UFS-NGS unit, as the benefits are quite holistic since the collaboration enhances co-ownership of data and offers opportunities to train postgraduate students and other scientists.

“It also expands the research infrastructure and most importantly contributes to policy for numerous African governments in important decisions such as vaccine implementation activities, from an informed point of view and managing public health needs that require rapid response like outbreaks that may lead to pandemics.” 
• The current WHO CC designations at South African Institutions of higher learning and research can be found at: 

News Archive

Studies to reveal correlation between terrain, energy use, and giraffe locomotion
2016-11-18



More than half of giraffes in captivity in Europe are afflicted by lameness. This high prevalence represents an important welfare issue, similar to other large zoo animals.

According to Dr Chris Basu, a veterinarian at the Royal Veterinary College in the UK, giraffes in captivity are often afflicted by overgrown hooves, laminitis and joint problems. Diagnosis and treatment is limited by our understanding of anatomy and function, more specifically the locomotion of these animals. Although the giraffe is such a well-known and iconic animal, relatively little has been studied about their locomotor behaviour.

Dr Basu recently visited South Africa to do fieldwork on the locomotion of giraffes as part of his PhD studies under the mentorship of world-renowned Professor of Evolutionary Biomechanics, Prof John Hutchinson. This project is a joint venture between Dr Basu and Dr Francois Deacon, researcher in the Department of Animal, Wildlife, and Grassland Sciences at the UFS. Dr Deacon is a specialist in giraffe habitat-related research. 

Together Prof Hutchinson and Drs Deacon and Basu form a research group, working on studies about giraffe locomotion.

Wild giraffe population decrease by 40% in past decade

“Locomotion is one of the most common animal behaviours and comes with a significant daily energetic cost. Studying locomotion of wild animals aids us in making estimates of this energetic cost. Such estimates are useful in understanding how giraffes fit into ecosystems. Future conservation efforts will be influenced by knowledge of the energy demands in giraffes.

“Understanding aspects of giraffe locomotion also helps us to understand the relationships between anatomy, function and evolution. This is relevant to our basic understanding of the natural world, as well as to conservation and veterinary issues,” said Dr Deacon.

Locomotion study brings strategy for specialist foot care

On face value it seems as if foot disease pathologies are more common in zoo giraffes than in wild giraffes. “However, we need a good sample of data from both populations to prove this assumption,” said Dr Basu. 

This phenomenon is not well understood at the moment, but it’s thought that diet, substrate (e.g. concrete, straw, sand and grass) and genetics play a part in foot disease in giraffes. “Understanding how the feet are mechanically loaded during common activities (standing, walking, running) gives our research group ideas of where the highest strains occur, and later how these can be reduced through corrective foot trimming,” said Dr Basu.

Through the studies on giraffe locomotion, the research group plans to devise strategies for corrective foot trimming. At the moment, foot trimming is done with the best evidence available, which is extrapolation from closely related animals such as cattle. “But we know that giraffes’ specialist anatomy will likely demand specialist foot care,” Dr Basu said.

Studying giraffes in smaller versus larger spaces

The research group has begun to study the biomechanics of giraffe walking by looking at the kinematics (the movement) and the kinetics (the forces involved in movement) during walking strides. For this he studied adult giraffes at three zoological parks in the UK. 

However, due to the close proximity of fencing and buildings, it is not practical to study fast speeds in a zoo setting. 

A setting such as the Willem Pretorius Nature Reserve, near Ventersburg in the Free State, Kwaggafontein Nature Reserve, near Colesberg in the Karoo, and the Woodland Hills Wildlife Estate in Bloemfontein are all ideal for studying crucial aspects such as “faster than walking” speeds and gaits to measure key parameters (such as stride length, step frequency and stride duration). These studies are important to understand how giraffe form and function are adapted to their full range of locomotor behaviours. It also helps to comprehend the limits on athletic capacity in giraffes and how these compare to other animals. 

Drones open up unique opportunities for studying giraffes

The increasing availability of unmanned aerial vehicles (UAVs)/drones opens up unique opportunities for studying locomotion in animals like giraffes. Cameras mounted onto remotely controlled UAVs are a straightforward way to obtain high-quality video footage of giraffes while they run at different speeds.

“Using two UAVs, we have collected high definition slow motion video footage of galloping giraffes from three locations in the Free State. We have also collected detailed information about the terrain that the giraffes walked and ran across. From this we have created 3D maps of the ground. These maps will be used to examine the preferred terrain types for giraffes, and to see how different terrains affect their locomotion and energy use,” said Dr Deacon.

“The raw data (videos) will be digitised to obtain the stride parameters and limb angles of the animals. Later this will be combined with anatomical data and an estimation of limb forces to estimate the power output of the limbs and how that changes between different terrains,” said Dr Basu.


Related articles:

23 August 2016: Research on locomotion of giraffes valuable for conservation of this species
9 March 2016:Giraffe research broadcast on National Geographic channel
18 Sept 2015 Researchers reach out across continents in giraffe research
29 May 2015: Researchers international leaders in satellite tracking in the wildlife environment

 

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