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08 June 2021 | Story André Damons | Photo Charl Devenish
African solidarity through medical research
Left: Prof Martin Nyaga, an Associate Professor: Next Generation Sequencing (UFS-NGS) and Director of the WHO Collaborating Centre (WHO CC), says there is a need to invest heavily in medical research, especially in next-generation sequencing facilities. Right: Dr Peter Mwangi is a Postdoctoral Research Fellow: NGS and Research Scientist in the WHO Collaborating Centre (WHO CC) at the University of the Free State (UFS).

South Africa is at the forefront of SARS-CoV-2 genomics surveillance in Africa, and the University of the Free State (UFS) Next Generation Sequencing (UFS-NGS) Unit is playing a major role in responding rapidly to public health threats in South Africa and other African countries.

Prof Martin Nyaga, Associate Professor in the UFS-NGS Unit and Director of the World Health Organization Collaborating Centre (WHO CC), and Dr Peter Mwangi, a Postdoctoral Research Fellow in the UFS-NGS Unit, say medical research in Africa is seriously deficient when benchmarked against other developed continents in terms of the capacity to perform SARS-CoV-2 genomics. According to them, an article published in a nature science journal provided evidence that African nations were largely uninvolved in clinical trials for the development of a COVID-19 vaccine.

“If African leaders are to learn one thing from the current pandemic, it is the need to provide adequate resources and funding for medical research, especially in next-generation sequencing facilities. Anyone keen on real-time data and information on the COVID-19 pandemic understands how fundamental sequencing the SARS-CoV-2 genome is. Rapid sequencing of the SARS-CoV-2 genome has played a key role in accelerating the development of emergency vaccines against this devastating disease,” say the two researchers.

Genome sequencing projects are collaborative efforts
Prof Nyaga is heading the WHO CC after the UFS was designated as a collaborating centre for vaccine-preventable diseases (VPD) surveillance and pathogen genomics last year. The centre is located in the Division of Virology in the Faculty of Health Sciences. It is also part of the Network for Genomic Surveillance in South Africa (NGS-SA), a genomics network/consortium established to respond rapidly to public health threats in South Africa.

Genome sequencing projects are usually collaborative efforts involving different stakeholders, including the national government through the Ministry of Health, scientists, and clinicians. The UFS-NGS Unit is actively involved in sequencing SARS-CoV-2 samples in the Free State channelled through the National Health Laboratory Services (NHLS-FS).

The sequenced data generated by the unit is continuously deposited in the Global Initiative on Sharing Avian Influenza Data (GISAID) database through the code name UFS-VIRO-NGS. The UFS-NGS Unit is currently performing whole-genome sequencing runs of approximately 100 SARS-CoV-2 samples per month.

“Through continuous processing of SARS-CoV-2 samples, the UFS-NGS Unit has optimised several techniques for COVID-19 genomics, from wet-lab to dry-lab analysis, captured in the internal protocols of the unit. The unit is continuously generating quality SARS-CoV-2 sequence data for the national consortium that is important for vaccine immunogenicity research projects geared towards regional vaccine development,” says Prof Nyaga.

Analysis of genome sequence data plays significant role in vaccine development
According to Prof Nyaga and Dr Mwangi, the sequence data generated in the UFS-NGS Unit has been key to establishing the SARS-CoV-2 variants of interest (VOI) and variants of concern (VOC). The VOI and VOC require one or more appropriate public health actions, including enhanced sequence surveillance, enhanced laboratory characterisation, or epidemiological investigations to assess how easily the virus spreads, the severity of disease, the risk of infection, and whether currently authorised vaccines offer protection.

“An example of a VOC strain is the 20H/501.V2 in lineage B.1.351 that was first discovered in South Africa after analysis of whole-genome sequence data, highlighting the importance of whole-genome SARS-CoV-2 surveillance. Consequently, analysis of the whole genome sequence data plays a significant role not only in vaccine development efforts, but also in advising policy to global and African governments on protection measures to be undertaken to curtail COVID-19 transmission,” explain the researchers.

The UFS-NGS Unit has been working collaboratively with other African scientists and actively training African students from different cultural backgrounds, not only on SARS-CoV-2 genomics, but also on different research clusters. The diversity of ideas through engagement with African researchers to share knowledge and push scientific innovation exemplifies the value of working together in the spirit of Ubuntu to develop solutions to our African problems. As we commemorate Africa Month 2021, let us be inspired by our hardworking UFS researchers, who are promoting African solidarity by working collaboratively in medical research to strive for a safe, healthy, and prosperous Africa.

• The key members of NGS-SA working on SARS-CoV-2 genomics samples from the Free State, are Prof Dominique Goedhals (Head: Division of Virology), Prof Martin Nyaga, Mr Phillip Bester (Medical Scientist: Division of Virology), Dr Peter Mwangi, Mr Milton Mogotsi (Research Assistant: UFS-NGS Unit), and Mr Ayodeji Ogunbayo (Research Assistant: UFS-NGS Unit).

News Archive

UFS hikers to Cape Town reflect on their journey
2014-05-26

 

For the four volunteers from the university who are currently on their way to the Cape on foot, every hour of every day is a victory.

It is three weeks since two employees from the University of the Free State (UFS), Adéle van Aswegen and Ntokozo Nkabinde, together with two other Bloemfontein residents, Nico Piedt and Ronel Warner, left Bloemfontein on fóót for the Cape, in order to highlight the problem of food insecurity among students.

On Sunday 18 May they crossed the halfway mark at Beaufort West and will conclude their journey on Tuesday 3 June in Cape Town.

This is what the hikers have to say after three weeks on the road:

Adéle van Aswegen
It isn’t only a physical journey, but rather an emotional journey you undertake. You learn what it means to be truly thankful for basic things like clothes, a place to sleep and food.

Nico Piedt
I know what it feels like to survive on only a glass of water in your stomach – a cup of weak tea if you’re lucky – for the whole day. If I can help (through the hike) to give someone a better chance in life, then it is worthwhile.

Ronel Warner
You think and grow simultaneously. As you plan every stride ahead of you, you also plan your life ahead.

Ntokozo Nkabinde
You don’t walk for yourself. You undertake this journey, maybe because you want to help someone, but this journey is actually in honour of something bigger and you just have to endure.”

These boots are made for walking ... to Cape Town (Article of 02 May 2014)
“Aren’t auntie and them hungry yet?” Country folk worried about NSH hikers (15 May 2014)

Daily updates:
(You can also follow us on @UFSweb for daily tweets)

Day 33: 2 June 2014
13:40
20 km
Sunset Beach, Cape Town

Day 32: 1 June 2014
16:05
26 km
Mervyn and Sanet Wessels, Belville

Day 31: 31 May 2014
16:31
39.6 km
Rhonell and Gavin Julain, Paarl

Day 30: 30 May 2014
14:00
16 km
Monte Rosa, Rawsonville

Day 29: 29 May 2014
13:16
31 km
The Habit, Worcester

Day 28: 28 May 2014
11:00
22.4 km
Monte Roza, De doorns

Day 27: 27 May 2014
17:00
21.1 km
Karoo Hotel

Day 26: 26 May 2014
18:27
43.3 km
Tows river

Day 25: 25 May 2014
12:18
Lord Milner Hotel, Matjiesfontein

Day 24: 24 May 2014
16:30
42 km
Laingsburg Country Lodge

Day 23: 23 May 2014
17:32
41.8 km
Vergenoeg

Day 22: 22 May 2014
16:42
43 km
Assendelft Lodge and Bush Camp, Prins Albert

Day 21: 21 May 2014
15:09
42 km
Leeu Gamka Hotel

Day 20: 20 May 2014
13:39
20 km
Alida, Springfontein

Day 19: 19 May 2014
12:31
27.6 km
Teri Moja Game Lodge

Day 18: 18 May 2014
First rest day
Nagenoeg Guesthouse, Beaufort West

Day 17: 17 May 2014
19:30
62.3 km
Nagenoeg Guesthouse, Beaufort West

Day 16: 16 May 2014
13:00
14 km
Taaibochfontein

Day 15: 15 May 2014
16:03
32 km
Travalia, Three Sisters

Day 14: 14 May 2014
18:33
43 km
Joalani Guest Farm

Day 13: 13 May 2014
17:30
33 km
Die Rondawels

Day 12: 12 May 2014
16:49
40 km
Aandrus B&B in Richmond

Day 11: 11 May 2014
39 km
Wortelfontein (Magdel and Christiaan)

Day 10: 10 May 2014
15:44
34 km
Hanover Lodge

Day 9: 09 May 2014
40.8 km
Camping between Colesberg and Hanover

Day 8: 08 May 2014
15:25
33.7 km
Colesberg, The Lighthouse Guesthouse

Day 7: 07 May 2014
15:08
23 km
Orange River Lodge

Day 6: 06 May 2014
15:57
51.06 km
Gariep Forever Resort

Day 5: 05 May 2014
12:18
28 km
Rondefontein

Day 4: 04 May 2014
15:27
35 km
Trompsburg: Fox Den

Day 3: 03 May 2014
17:30
46.74 km
Edenburg Country Lodge (Hotel)

Day 2: 02 May 2014
11:44 am
15.3 km
Tom's Place

Day 1: 01 May 2014
32 km
Leeuwberg

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