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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

Power interruptions: Information for internal communication
2008-01-31

As part of the UFS’s commitment to address load shedding, the management would like to communicate the following:

The UFS mainly deals with the power interruptions by way of (a) the possible installation of equipment (e.g. generators) and (b) operational arrangements to ensure the functioning of the UFS in spite of power interruptions.

During the past week progress was made on both fronts. The information that follows resulted from a meeting of a task team of Physical Resources led by Mr Nico Janse van Rensburg, which took place on Monday 28 January (this task team naturally focuses on physical solutions) and a discussion by Exco on Wednesday 30 January 2008. Exco discussed the recommendations of the mentioned task team in respect of physical aspects, as well as the operational arrangements proposed by faculties.

Physical solutions

A Main Campus

1. New emergency power installations already approved:

Last week Exco gave its approval for the design and installation of emergency power equipment in all the large lecture-hall complexes to proceed immediately.

In all these cases

  • load surveys have been completed and a start has been made with the ordering of equipment and the process of appointing contractors. (Exco approved the adjustment of normal tender procedures in an attempt to expedite completion.)
  • generators with 20-30% more capacity than required for the current load are being ordered.
  • provision is being made for the connection of lights and at least one wall plug to the emergency power.
  • the expected construction time is 16 weeks (except in the case of the Flippie Groenewoud Building where it is 6 weeks).

The above-mentioned concerns lecture halls/ venues in the following buildings: Examination Centre, Flippie Groenewoud Building, Stabilis, Genmin and the Agriculture Building.

As far as the Agriculture Building is concerned, a larger generator (larger than required for lecture venues only) is being ordered in view of simultaneously providing essential research equipment (refrigerators, ovens, glasshouses) with emergency power within 16 weeks.

2. Investigation into the optimal utilisation of present emergency power installations

All the emergency power systems are being investigated on the basis of a list compiled in 2006 to determine whether excess capacity is available and whether it is possible to connect additional essential equipment or lights to it.

The electrical engineer warns as follows:
“Staff members must under no circumstances overload present emergency power points.

A typical example of this is a laboratory with 10 power points of which 2 points are emergency power outlets. Normally a fridge and freezer would, for example, be plugged into the two emergency power points, but now, with long load-shedding interruptions, a considerably larger number of appliances are being plugged into the power point by means of multi-sockets and extension cords. In the end the effect of such connections will accumulate at the emergency generator, which will then create a greater danger of it being overloaded and tripping, in other words, no emergency power will then be available.”

3. Requests and needs addressed directly to Physical Resources or reported to Exco via the line managers.

All the physical needs and requests addressed directly to Physical Resources or submitted to Exco via the line managers are being listed, classified and considered technically in view of their being discussed by the task team on Monday 11 February.
The information will (a) lead to recommendations to Exco regarding possible additional urgent emergency power installations, and (b) be used in the comprehensive investigation into the UFS’s preparedness for and management of long power interruptions.

Requests that can easily be complied with immediately and that fit into the general strategy will indeed be dealt with as soon as possible.

4. Purchase of loose-standing equipment: light, small, loose-standing generators, UPSs as solutions to/ aids during power interruptions

Exco approved that

a) faculties and support services accept responsibility themselves for the funding and purchase of loose equipment such as, for example battery lights, should they regard these as essential.
b) UPSs (uninterruptible power supplies) that faculties and support services wish to purchase to combat the detrimental effect of unexpected power interruptions on computer equipment) can (as at present) be purchased from own funds via Computer Services.
c) UPSs (uninterruptible power supplies) that faculties and support services wish to purchase to combat the detrimental effect of unexpected power interruptions on other types of equipment can normally be purchased from own funds with the consent of the line manager concerned.
Note: Please just make sure of the appropriateness of the equipment for a specific situation: it is not a power supply that can bridge a two-hour power interruption.)
d) small, loose-standing generators can be purchased from own funds via Physical Resources and installed under their supervision.
e) laptop computers can , where necessary, be purchased from own budgets. The availability of second-hand laptop computers must be taken into account.

B Vista

No major problems have been reported to date. The situation is being monitored and will be managed according to need. The same guidelines that apply to the Main Campus will naturally also apply to the Vista Campus.

C Qwaqwa

The situation is receiving attentions and solutions have already been found for most problems.

D General

1. All-inclusive project
A comprehensive investigation into the UFS’s preparedness for and management of long power interruptions will be launched as soon as possible. Available capacity will be utilised first to alleviate the immediate need. The needs assessment to which all faculties and support services have already contributed is already an important building block of the larger project.

2. Building and construction projects currently in the planning and implementation phase
The need for emergency power for projects such as the new Computer Laboratory is being investigated proactively and will be addressed in a suitable manner.

3. Liaison with Centlec
Attempts at direct and continuous liaison are continuing in an attempt to accommodate the unique needs of the UFS.

4. HESA meeting and liaison with other universities
A representative of the UFS will attend a meeting of all higher education institutions on 11 February. The meeting is being arranged by HESA (Higher Education South Africa) to discuss the implications for the sector, the management of risks and the sector’s response to government.

5. Internal communication
It is the intention to communicate internally after every meeting of the task team, which will take place on Mondays. Strategic Communication will assist in this regard.


 

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